US20230115179A1

US20230115179A1 - Tert immunogenic compositions and methods of treatment using the same

Info

Publication number: US20230115179A1
Application number: US18/045,575
Authority: US
Inventors: David Weiner; Jian Yan
Original assignee: University of Pennsylvania Penn; Wistar Institute of Anatomy and Biology; Inovio Pharmaceuticals Inc
Current assignee: University of Pennsylvania Penn; Wistar Institute of Anatomy and Biology; Inovio Pharmaceuticals Inc
Priority date: 2016-09-30
Filing date: 2022-10-11
Publication date: 2023-04-13
Also published as: AU2017336088B2; EP3518955A4; JP2022179497A; MX2019003722A; KR20230167445A; AU2023237174A1; KR102375328B1; KR20190120743A; CA3038889A1; WO2018064588A3; EP3518955A2; US11464841B2; AU2017336088A1; KR20220024974A; JP2019534875A; CN110573173A; WO2018064588A2; US20200030426A1

Abstract

Disclosed herein are compositions comprising optimized consensus TERT antigens and methods for treating cancer and in particular immunogenic compositions that treat and provide protection against tumor.

Description

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No. 62/402,695, filed Sep. 30, 2016 and to U.S. Provisional Application No. 62/468,124, filed Mar. 7, 2017 which are hereby incorporated by reference herein in their entirety.

TECHNICAL FIELD

Disclosed herein are compositions and methods for treating cancer and in particular, immunogenic compositions that treat and provide protection against tumor growth.

BACKGROUND

Cancer is among the leading causes of death worldwide, and in the United States, is the second most common cause of death, accounting for nearly 1 of every 4 deaths. Cancer arises from a single cell that has transformed from a normal cell into a tumor cell. Such a transformation is often a multistage process, progressing from a pre-cancerous lesion to malignant tumors. Multiple factors contribute this progression, including aging, genetic contributions, and exposure to external agents such as physical carcinogens (e.g., ultraviolet and ionizing radiation), chemical carcinogens (e.g., asbestos, components of tobacco smoke, etc.), and biological carcinogens (e.g., certain viruses, bacteria, and parasites).
Prevention, diagnosis and treatment of cancer may take many different forms. Prevention may include screening for pre-disposing factors (e.g., specific genetic variants), altering behavior (e.g., smoking, diet, and amount of physical activity), and vaccination against viruses (e.g., human papilloma virus hepatitis B virus). Treatment may include chemotherapy, radiation therapy, and surgical removal of a tumor or cancerous tissue. Despite the availability of numerous prevention and treatment methods, such methods often meet with limited success in effectively preventing and/or treating the cancer at hand.
Accordingly, a need exists for the identification and development of compositions and methods for the prevention and/or treatment of cancer to facilitate clinical management of protection against and progression of disease. Furthermore, more effective treatments are required to delay disease progression and/or decrease mortality in subjects suffering from cancer.

SUMMARY OF INVENTION

In one embodiment, the invention relates to an immunogenic composition comprising a nucleic acid molecule encoding a consensus TERT antigen. In one embodiment, the consensus TERT antigen comprises an amino acid sequence selected from the group consisting of: a) an amino acid sequence selected from the group consisting of SEQ ID NO: 46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, and SEQ ID NO:56, b) an amino acid sequence that is 95% identical or greater to an amino acid sequence selected from the group consisting of SEQ ID NO: 46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, and SEQ ID NO:56, and c) a fragment of an amino acid sequence selected from the group consisting of SEQ ID NO: 46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, and SEQ ID NO:56, wherein the fragment comprises at least 95% of the full length amino acid sequence.
In one embodiment, the immunogenic composition further comprises one or more nucleotide sequences encoding one or more amino acid sequence selected from the group consisting of: a) an amino acid sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO; 58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70; b) an amino acid sequence that is 95% identical or greater to the amino acid selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO; 58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, and c) a fragment of an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO; 58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, wherein the fragment comprises at least 95% of the full length amino acid sequence.
In one embodiment, the immunogenic composition further comprises a nucleotide sequence encoding one or more antigens selected from the group consisting of: MAGE A1, gp100, a viral antigen, and combinations thereof. In one embodiment, the viral antigen is an antigen from Hepatitis B virus (HBV), Hepatitis C virus (HCV), or Human Papilloma Virus (HPV). In one embodiment, the HBV antigen is an HBV core antigen or a HBV surface antigen, or a combination thereof. In one embodiment, the HCV antigen is an HCV NS34A antigen, an HCV NS5A antigen, an HCV NS5B antigen, an HCV NS4B antigen, or a combination thereof. In one embodiment, the HPV antigen is an HPV type 6 E6 antigen, an HPV type 6 E7 antigen, an HPV type 11 E6 antigen, an HPV type 11 E7 antigen, an HPV type 16 E6 antigen, an HPV type 16 E7 antigen, an HPV type 18 E6 antigen, an HPV type 18 E7 antigen, or a combination thereof.
In one embodiment, the immunogenic composition further comprises an immune checkpoint inhibitor.
In one embodiment, the nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of a) a nucleotide sequence selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53 and SEQ ID NO: 55, b) a nucleotide sequence that is 95% identical or greater to a nucleotide sequence selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53 and SEQ ID NO: 55, and c) a fragment of a nucleotide sequence selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53 and SEQ ID NO: 55, wherein the fragment comprises at least 95% of the full length nucleotide sequence.
In one embodiment, the immunogenic composition comprises one or more nucleotide sequences selected from the group consisting of: a) a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 and SEQ ID NO:69; b) a nucleotide sequence that is 95% identical or greater to a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 and SEQ ID NO:69, and c) a fragment of a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 and SEQ ID NO:69, wherein the fragment comprises at least 95% of the full length nucleotide sequence.
In one embodiment, the nucleic acid molecule is a plasmid.
In one embodiment, the immunogenic composition comprises one or more plasmids.
In one embodiment, the immunogenic composition further comprises an adjuvant. In one embodiment, the adjuvant is IL-12, IL-15, IL-28, or RANTES.
In one embodiment, the invention relates to a method of treating or preventing cancer in a subject in need thereof, the method comprising administering an immunogenic composition of comprising a nucleic acid molecule encoding a consensus TERT antigen to the subject. In one embodiment, the method of administration includes an electroporation step. In one embodiment, the method further comprises administering an immune checkpoint inhibitor to the subject.
In one embodiment, the immunogenic composition and immune checkpoint inhibitor are administered in a single formulation to the subject. In one embodiment, the immunogenic composition and immune checkpoint inhibitor are administered separately to the subject.
In one embodiment, the cancer is selected from the group consisting of: melanoma, head and neck cancer, prostate cancer, liver cancer, cervical cancer, recurrent respiratory papillomatosis (RRP), anal cancer, a blood cancer, ovarian cancer and a combination thereof.
In one embodiment, the invention relates to a nucleic acid molecule comprising one or more nucleotide sequences selected from the group consisting of: a) a nucleotide sequence selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53 and SEQ ID NO: 55, b) a nucleotide sequence that is 95% identical or greater to a nucleotide sequence selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53 and SEQ ID NO: 55, and c) a fragment of a nucleotide sequence selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53 and SEQ ID NO: 55, wherein the fragment comprises at least 95% of the full length nucleotide sequence.
In one embodiment, the nucleic acid molecule further comprises one or more nucleotide sequences selected from the group consisting of: a) a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 and SEQ ID NO:69; b) a nucleotide sequence that is 95% identical or greater to a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 and SEQ ID NO:69, and c) a fragment of a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 and SEQ ID NO:69, wherein the fragment comprises at least 95% of the full length nucleotide sequence.
In one embodiment, the nucleic acid molecule is a plasmid.
In one embodiment, the invention relates to an amino acid molecule comprising one or more amino acid sequence selected from the group consisting of: a) an amino acid sequence selected from the group consisting of SEQ ID NO: 46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, and SEQ ID NO:56, b) an amino acid sequence that is 95% identical or greater to an amino acid sequence selected from the group consisting of SEQ ID NO: 46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, and SEQ ID NO:56, and c) a fragment of an amino acid sequence selected from the group consisting of SEQ ID NO: 46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, and SEQ ID NO:56, wherein the fragment comprises at least 95% of the full length amino acid sequence.
In one embodiment, the amino acid molecule further comprises one or more amino acid sequence selected from the group consisting of: a) an amino acid sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO; 58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70; b) an amino acid sequence that is 95% identical or greater to the amino acid selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO; 58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, and c) a fragment of an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO; 58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, wherein the fragment comprises at least 95% of the full length amino acid sequence.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 , comprising FIG. 1A through FIG. 1E, depicts the construction of pTyr.

FIG. 2 , comprising FIG. 2A through FIG. 2B, depicts the results of experiments demonstrating an immunization strategy and induction of cell mediated immune responses by Tyr DNA vaccination, respectively.

FIG. 3 depicts the results of experiments demonstrating flow fluorescence-activated cell sorting (FACS) of control and immunized mice.

FIG. 4 , comprising FIG. 4A through FIG. 4B, depicts the results of experiments demonstrating induction of tyrosinase-specific antibodies in immunized mice.

FIG. 5 , comprising FIG. 5A through FIG. 5B, depicts the results of experiments demonstrating Kaplan-Meier survival curves and tumor volume curves, respectively, after tumor challenge in control and immunized mice.

FIG. 6 , comprising FIG. 6A through FIG. 6B, depicts the results of experiments demonstrating MDSC cell populations in immunized and non-immunized mice.

FIG. 7 depicts the results of experiments demonstrating staining for MDSCs in mice immunized with pVax1 and pTyr.

FIG. 8 , comprising FIG. 8A through FIG. 8B, depicts the results of experiments demonstrating MCP-1 secretion by MDSCs.

FIG. 9 depicts the results of experiments demonstrating the phylogenetic relationship of Tyr nucleotide sequences amongst the indicated organisms.

FIG. 10 , comprising FIG. 10A through FIG. 10C, depicts the results of experiments demonstrating (A) a schematic illustrating a plasmid map of pPRAME (also known herein as pGX1411); (B) staining of RD and 293T cells for nuclei with DAPI and for the consensus PRAME antigen; and (C) western blotting for the consensus PRAME antigen in lysates from non-transfected cells (“control”), cells transfected with pVAX (“pVAX”), and cells transfected with pPRAME (“PRAME-pVAX”).

FIG. 11 , comprising FIG. 11A through FIG. 11B, depicts the results of experiments demonstrating graphs plotting mouse group vs. spot forming units (SFU)/10⁶splenocytes for interferon gamma (IFN-γ).

FIG. 12 , comprising FIG. 12A through FIG. 12C, depicts the results of experiments demonstrating (A) a schematic illustrating a plasmid map of pNY-ESO-1 (also known herein as pGX1409); (B) staining of cells for nuclei with DAPI and for the consensus NY-ESO-1 antigen; and (C) western blotting for the consensus NY-ESO-1 antigen in RD and 293T lysates from non-transfected cells (“control”), cells transfected with pVAX (“pVAX”), and cells transfected with pNY-ESO-1 (“pNY-ESO-1”).

FIG. 13 depicts a graph plotting mouse group vs. spot forming units (SFU)/10⁶splenocytes for interferon gamma (IFN-γ).

FIG. 14 depicts a graph plotting mouse group vs. spot forming units (SFU)/10⁶splenocytes for interferon gamma (IFN-γ).

FIG. 15 depicts a schematic illustrating various cancers with some of their associated cancer antigen(s).

FIG. 16 depicts a schematic design of the TERT construct. Synthetic consensus hTERT was designed for human TERT with 5 mutations to abolish its function. Native RhTERT encode Rhesus TERT with 2 mutations. Both constructs were optimized. The Table shows the protein homology between the optimized TERT and native TERT identified in human, rhesus and mice.

FIG. 17 , comprising FIG. 17A through FIG. 17B, depicts the characterization of mouse TERT-specific IFN-γ responses against rhesus native peptides. (FIG. 17A) Immunization schedule. Mice (n=8 per group) were immunized at

weeks

0, 2 and 4 with Native RhTERT and synthetic consensus hTERT via IM/electroporation. (FIG. 17B) Frequency of TERT-specific IFN-γ spot-forming units (SFU) per million splenocytes isolated from vaccinated mice, determined by IFN-γ ELISpot assay using rhesus peptides.

FIG. 18 , comprising FIG. 18A through FIG. 18C, depicts the characterization of rhesus TERT-specific IFN-γ responses. (FIG. 18A) Immunization schedule. Rhesus macaque (n=5 per group) were immunized at

weeks

0, 4, 8 and 12 with Native RhTERT or synthetic consensus hTERT as well as rhIL-12 via IM/electroporation. (FIG. 18B and FIG. 18C) Frequency of TERT-specific IFN-γ spot-forming units (SFU) per million splenocytes isolated from vaccinated mice, determined by IFN-γ ELISpot assay using native rhesus peptides and synthetic consensus hTERT peptide.

FIG. 19 depicts the results of experiments demonstrating that synthetic consensus hTERT (pGX1434) induces robust T cell responses in mice and slows TC-1 tumor growth. (left) Mice received 3 immunizations 2 weeks apart with 0, 20, 40, or 60 μg of pGX1434. T cell responses in the mice were evaluated at 5 weeks, demonstrating that pGX1434 induced a robust T cell response. (right) Mice were implanted with 25×10⁴TC-1 cells. Mice then received 4 immunizations 1 week apart with 25 μg of pGX1434. Tumor volume was measured over 32 days, demonstrating that mice treated with pGX1434 had decreased tumor volume as compared to naïve mice.

FIG. 20 depicts the results of experiments demonstrating the immunogenicity of SynCon hTERT (pGX1434) in mice.

FIG. 21 , comprising FIG. 21A through FIG. 21B, depicts the results of experiments demonstrating SynCon hTERT (pGX1434) and mut-hTERT (pGX1406) provide similar control of TC-1 tumor growth.

FIG. 22 , comprising FIG. 22A through FIG. 22B, depicts the experimental design for experiments demonstrating hTERT immunogenicity in non-human primates (NHPs). FIG. 22A depicts an exemplary immunization schedule. FIG. 22B depicts a table demonstrating the constructs that were administered to the different groups. pGX1434: hTERT; pGX1406: Mut-hTERT; pGX1447: Mut-rhTERT; pGX1404: WT-1; pGX1108: PSMA; pGX6006:rhIL-12.

FIG. 23 , comprising FIG. 23A through FIG. 23B, depicts the results of experiments demonstrating that SynCon hTERT breaks self-tolerance in NHPs. FIG. 23A depicts the results of experiments demonstrating that responses to native rhesus TERT were detected PD3 and PD4 in Group 1 animals. FIG. 23B depicts the results of experiments demonstrating that responses to native rhesus TERT were detected PD3 and PD4 in Group 2 animals.

FIG. 24 , comprising FIG. 24A through FIG. 24C, depicts the results of experiments demonstrating that the SynCon design enables breaking self-tolerance. FIG. 24A depicts a table demonstrating the percent identity of the different constructs to the native sequences. FIG. 24B depicts the results of experiments demonstrating TERT specific IFNγ response. FIG. 24C depicts the results of experiments demonstrating Rhesus TERT specific IFNγ response.

FIG. 25 , comprising FIG. 25A through FIG. 25B, depicts the results of experiments demonstrating NHP immunogenicity of the SynCon hTERT. FIG. 25A depicts the results of experiments demonstrating the TERT response generated using the combination of SynCon hTERT, PSMA, WT-1 and IL-12. FIG. 25B depicts the results of experiments demonstrating the TERT response generated using the combination of mut-hTERT, PSMA, WT-1 and IL-12.

FIG. 26 , comprising FIG. 26A through FIG. 26C, depicts the results of experiments demonstrating NHP immunogenicity of the SynCon hTERT. FIG. 26A depicts the results of experiments demonstrating the TERT response generated using the combination of TERT, PSMA, WT-1 and IL-12. FIG. 26B depicts the results of experiments demonstrating the PSMA response generated using the combination of TERT, PSMA, WT-1 and IL-12. FIG. 26C depicts the results of experiments demonstrating the WT-1 response generated using the combination of TERT, PSMA, WT-1 and IL-12.

FIG. 27 , comprising FIG. 27A through FIG. 27B, depicts the results of experiments demonstrating the breadth of the multivalent SynCon vaccines. FIG. 27A depicts the immunization schedule used. FIG. 27B depicts the percentages of antigen specific T cells that were identified following immunization.

FIG. 28 , comprising FIG. 28A through FIG. 28B, depicts the results of experiments demonstrating the multivalent SynCon vaccine reduces tumor burden and increases survival. FIG. 28A depicts the immunization schedule used. FIG. 28B depicts the average tumor volume and % survival of animals immunized with a combination of WT1, PSMA and SynCon mTERT.

DETAILED DESCRIPTION

The present invention is directed to immunogenic compositions comprising a synthetic consensus TERT antigen, alone or in combination with at least one additional cancer antigen or an inhibitor of an immune checkpoint protein, and method of use of the compositions for treating diseases or disorders. In one embodiment, the immounogenic composition comprises TERT and at least one additional cancer antigen consensus sequence. Cancer antigen consensus sequences that can be included in the immunogenic composition including, but are not limited to, tyrosinase (Tyr), preferentially expressed antigen in melanoma (PRAME), tyrosinase related protein 1 (Tyrp1), cancer testes antigen (NY-ESO-1), hepatitis B virus antigen, prostate specific antigen (PSA), prostate-specific membrane antigen (PSMA), six-transmembrane epithelial antigen of the prostate (STEAP), prostate stem cell antigen (PSCA), Fibroblast Activation Protein (FAP), follicle stimulating hormone receptor (FSHR) and Wilms tumor 1 antigen (WT-1). In one embodiment, the immunogenic composition of the invention can provide a combination of cancer antigens for the prevention or treatment of the cancer of a subject that is in need thereof.
One manner for designing the nucleic acid and corresponding encoded amino acid sequence of the recombinant cancer antigen is to introduce mutations that change particular amino acids in the overall amino acid sequence of the native cancer antigen. The introduction of mutations does not alter the cancer antigen so much that it cannot be universally applied across a mammalian subject, for example a human or dog subject, but changes the antigen enough that the resulting amino acid sequence breaks tolerance or is considered a foreign antigen in order to generate an immune response. Another manner may be creating a consensus recombinant cancer antigen that has at least 85% and up to 99% amino acid sequence identity, at least 90% and up to 98% sequence identity, at least 93% and up to 98% sequence identity, or at least 95% and up to 98% sequence identity to a corresponding native cancer antigen. In some instances the recombinant cancer antigen is 95%, 96%, 97%, 98%, or 99% amino acid sequence identity to a corresponding native cancer antigen. The native cancer antigen is the antigen normally associated with the particular cancer or cancer tumor. Depending upon the cancer antigen, the consensus sequence of the cancer antigen can be across mammalian species or within subtypes of a species or across viral strains or serotypes. Some cancer antigens do not vary greatly from the wild type amino acid sequence of the cancer antigen. Some cancer antigens have nucleic acid/amino acid sequences that are so divergent across species, that a consensus sequence cannot be generated. In these instances, a recombinant cancer antigen that will break tolerance and generate an immune response is generated that has at least 85% and up to 99% amino acid sequence identity; at least 90% and up to 98% sequence identity; at least 93% and up to 98% sequence identity; or at least 95% and up to 98% sequence identity to a corresponding native cancer antigen. In some instances the recombinant cancer antigen is 95%, 96%, 97%, 98%, or 99% amino acid sequence identity to a corresponding native cancer antigen. The aforementioned approaches can be combined so that the final recombinant cancer antigen has a percent similarity to a native cancer antigen amino acid sequence as discussed, above.
The recombinant cancer antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule.
The immunogenic composition may be combined further with antibodies to checkpoint inhibitors such as PD-1 and PDL-1 to increase the stimulation of both the cellular and humoral immune responses. Using anti-PD-1 or anti-PDL-1 antibodies prevents PD-1 or PDL-1 from suppressing T-cell and/or B-cell responses. Overall, by designing the cancer antigens to be recognized by the immune system helps to overcome other forms of immune suppression by tumor cells, and these immunogenic compositions can be used in combination with suppression or inhibition therapies (such as anti-PD-1 and anti-PDL-1 antibody therapies) to further increase T-cell and/or B-cell responses.

1. DEFINITIONS

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. In case of conflict, the present document, including definitions, will control. Exemplary methods and materials are described below, although methods and materials similar or equivalent to those described herein can be used in practice or testing of the present invention. All publications, patent applications, patents and other references mentioned herein are incorporated by reference in their entirety. The materials, methods, and examples disclosed herein are illustrative only and not intended to be limiting. The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting.
The terms “comprise(s),” “include(s),” “having,” “has,” “can,” “contain(s),” and variants thereof, as used herein, are intended to be open-ended transitional phrases, terms, or words that do not preclude the possibility of additional acts or structures. The singular forms “a,” “and” and “the” include plural references unless the context clearly dictates otherwise. The present disclosure also contemplates other embodiments “comprising,” “consisting of” and “consisting essentially of” the embodiments or elements presented herein, whether explicitly set forth or not.
For recitation of numeric ranges herein, each intervening number there between with the same degree of precision is explicitly contemplated. For example, for the range of 6-9, the numbers 7 and 8 are contemplated in addition to 6 and 9, and for the range 6.0-7.0, the numbers 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, and 7.0 are explicitly contemplated.
“Adjuvant” as used herein means any molecule added to the immunogenic compositions described herein to enhance the immunogenicity of the antigens encoded by the Nucleic acid molecules and the encoding nucleic acid sequences described hereinafter.
“Antibody” as used herein means an antibody of classes IgG, IgM, IgA, IgD or IgE, or fragments, or derivatives thereof, including Fab, F(ab′)2, Fd, and single chain antibodies, diabodies, bispecific antibodies, bifunctional antibodies and derivatives thereof. The antibody can be an antibody isolated from the serum sample of mammal, a polyclonal antibody, affinity purified antibody, or mixtures thereof which exhibits sufficient binding specificity to a desired epitope or a sequence derived therefrom.
“Coding sequence” or “encoding nucleic acid” as used herein means the nucleic acids (RNA or DNA molecule) that comprise a nucleotide sequence which encodes a protein. The coding sequence can further include initiation and termination signals operably linked to regulatory elements including a promoter and polyadenylation signal capable of directing expression in the cells of an individual or mammal to which the nucleic acid is administered.
“Complement” or “complementary” as used herein means a nucleic acid can mean Watson-Crick (e.g., A-T/U and C-G) or Hoogsteen base pairing between nucleotides or nucleotide analogs of nucleic acid molecules.
“Consensus” or “consensus sequence” as used herein means a polypeptide sequence based on analysis of an alignment of multiple sequences for the same gene from different organisms. Nucleic acid sequences that encode a consensus polypeptide sequence can be prepared. Immunogenic compositions comprising proteins that comprise consensus sequences and/or nucleic acid molecules that encode such proteins can be used to induce broad immunity against an antigen.
“Electroporation,” “electro-permeabilization,” or “electro-kinetic enhancement” (“EP”) as used interchangeably herein means the use of a transmembrane electric field pulse to induce microscopic pathways (pores) in a bio-membrane; their presence allows biomolecules such as plasmids, oligonucleotides, siRNA, drugs, ions, and water to pass from one side of the cellular membrane to the other.
“Fragment” as used herein with respect to nucleic acid sequences means a nucleic acid sequence or a portion thereof, that encodes a polypeptide capable of eliciting an immune response in a mammal that cross reacts with an antigen disclosed herein. The fragments can be DNA fragments selected from at least one of the various nucleotide sequences that encode protein fragments set forth below. Fragments can comprise at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95% of one or more of the nucleic acid sequences set forth below. In some embodiments, fragments can comprise at least 20 nucleotides or more, at least 30 nucleotides or more, at least 40 nucleotides or more, at least 50 nucleotides or more, at least 60 nucleotides or more, at least 70 nucleotides or more, at least 80 nucleotides or more, at least 90 nucleotides or more, at least 100 nucleotides or more, at least 150 nucleotides or more, at least 200 nucleotides or more, at least 250 nucleotides or more, at least 300 nucleotides or more, at least 350 nucleotides or more, at least 400 nucleotides or more, at least 450 nucleotides or more, at least 500 nucleotides or more, at least 550 nucleotides or more, at least 600 nucleotides or more, at least 650 nucleotides or more, at least 700 nucleotides or more, at least 750 nucleotides or more, at least 800 nucleotides or more, at least 850 nucleotides or more, at least 900 nucleotides or more, at least 950 nucleotides or more, or at least 1000 nucleotides or more of at least one of the nucleic acid sequences set forth below.
“Fragment” or “immunogenic fragment” with respect to polypeptide sequences means a polypeptide capable of eliciting an immune response in a mammal that cross reacts with an antigen disclosed herein. The fragments can be polypeptide fragments selected from at least one of the various amino acids sequences below. Fragments of consensus proteins can comprise at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 95% of a consensus protein. In some embodiments, fragments of consensus proteins can comprise at least 20 amino acids or more, at least 30 amino acids or more, at least 40 amino acids or more, at least 50 amino acids or more, at least 60 amino acids or more, at least 70 amino acids or more, at least 80 amino acids or more, at least 90 amino acids or more, at least 100 amino acids or more, at least 110 amino acids or more, at least 120 amino acids or more, at least 130 amino acids or more, at least 140 amino acids or more, at least 150 amino acids or more, at least 160 amino acids or more, at least 170 amino acids or more, at least 180 amino acids or more of a protein sequence disclosed herein.
As used herein, the term “genetic construct” refers to the DNA or RNA molecules that comprise a nucleotide sequence which encodes a protein. The coding sequence includes initiation and termination signals operably linked to regulatory elements including a promoter and polyadenylation signal capable of directing expression in the cells of the individual to whom the nucleic acid molecule is administered. As used herein, the term “expressible form” refers to gene constructs that contain the necessary regulatory elements operable linked to a coding sequence that encodes a protein such that when present in the cell of the individual, the coding sequence will be expressed.
The term “homology,” as used herein, refers to a degree of complementarity. There can be partial homology or complete homology (i.e., identity). A partially complementary sequence that at least partially inhibits a completely complementary sequence from hybridizing to a target nucleic acid is referred to using the functional term “substantially homologous.” When used in reference to a double-stranded nucleic acid sequence such as a cDNA or genomic clone, the term “substantially homologous,” as used herein, refers to a probe that can hybridize to a strand of the double-stranded nucleic acid sequence under conditions of low stringency. When used in reference to a single-stranded nucleic acid sequence, the term “substantially homologous,” as used herein, refers to a probe that can hybridize to (i.e., is the complement of) the single-stranded nucleic acid template sequence under conditions of low stringency.
“Identical” or “identity” as used herein in the context of two or more nucleic acids or polypeptide sequences means that the sequences have a specified percentage of residues that are the same over a specified region. The percentage can be calculated by optimally aligning the two sequences, comparing the two sequences over the specified region, determining the number of positions at which the identical residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the specified region, and multiplying the result by 100 to yield the percentage of sequence identity. In cases where the two sequences are of different lengths or the alignment produces one or more staggered ends and the specified region of comparison includes only a single sequence, the residues of single sequence are included in the denominator but not the numerator of the calculation. When comparing DNA and RNA, thymine (T) and uracil (U) can be considered equivalent. Identity can be performed manually or by using a computer sequence algorithm such as BLAST or BLAST 2.0.
“Immune response” as used herein means the activation of a host's immune system, e.g., that of a mammal, in response to the introduction of antigen. The immune response can be in the form of a cellular or humoral response, or both.
“Nucleic acid” or “oligonucleotide” or “polynucleotide” as used herein means at least two nucleotides covalently linked together. The depiction of a single strand also defines the sequence of the complementary strand. Thus, a nucleic acid also encompasses the complementary strand of a depicted single strand. Many variants of a nucleic acid can be used for the same purpose as a given nucleic acid. Thus, a nucleic acid also encompasses substantially identical nucleic acids and complements thereof. A single strand provides a probe that can hybridize to a target sequence under stringent hybridization conditions. Thus, a nucleic acid also encompasses a probe that hybridizes under stringent hybridization conditions.
Nucleic acids can be single stranded or double stranded, or can contain portions of both double stranded and single stranded sequence. The nucleic acid can be DNA, both genomic and cDNA, RNA, or a hybrid, where the nucleic acid can contain combinations of deoxyribo- and ribo-nucleotides, and combinations of bases including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine hypoxanthine, isocytosine and isoguanine. Nucleic acids can be obtained by chemical synthesis methods or by recombinant methods.
“Operably linked” as used herein means that expression of a gene is under the control of a promoter with which it is spatially connected. A promoter can be positioned 5′ (upstream) or 3′ (downstream) of a gene under its control. The distance between the promoter and a gene can be approximately the same as the distance between that promoter and the gene it controls in the gene from which the promoter is derived. As is known in the art, variation in this distance can be accommodated without loss of promoter function.
A “peptide,” “protein,” or “polypeptide” as used herein can mean a linked sequence of amino acids and can be natural, synthetic, or a modification or combination of natural and synthetic.
“Promoter” as used herein means a synthetic or naturally-derived molecule which is capable of conferring, activating or enhancing expression of a nucleic acid in a cell. A promoter can comprise one or more specific transcriptional regulatory sequences to further enhance expression and/or to alter the spatial expression and/or temporal expression of same. A promoter can also comprise distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription. A promoter can be derived from sources including viral, bacterial, fungal, plants, insects, and animals. A promoter can regulate the expression of a gene component constitutively, or differentially with respect to cell, the tissue or organ in which expression occurs or, with respect to the developmental stage at which expression occurs, or in response to external stimuli such as physiological stresses, pathogens, metal ions, or inducing agents. Representative examples of promoters include the bacteriophage T7 promoter, bacteriophage T3 promoter, SP6 promoter, lac operator-promoter, tac promoter, SV40 late promoter, SV40 early promoter, RSV-LTR promoter, CMV IE promoter, SV40 early promoter or SV40 late promoter and the CMV IE promoter.
“Signal peptide” and “leader sequence” are used interchangeably herein and refer to an amino acid sequence that can be linked at the amino terminus of a protein set forth herein. Signal peptides/leader sequences typically direct localization of a protein. Signal peptides/leader sequences used herein can facilitate secretion of the protein from the cell in which it is produced. Signal peptides/leader sequences are often cleaved from the remainder of the protein, often referred to as the mature protein, upon secretion from the cell. Signal peptides/leader sequences are linked at the amino terminus (i.e., N terminus) of the protein.
“Stringent hybridization conditions” as used herein means conditions under which a first nucleic acid sequence (e.g., probe) will hybridize to a second nucleic acid sequence (e.g., target), such as in a complex mixture of nucleic acids. Stringent conditions are sequence-dependent and will be different in different circumstances. Stringent conditions can be selected to be about 5-10° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength pH. The Tm can be the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions can be those in which the salt concentration is less than about 1.0 M sodium ion, such as about 0.01-1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., about 10-50 nucleotides) and at least about 60° C. for long probes (e.g., greater than about 50 nucleotides). Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal can be at least 2 to 10 times background hybridization. Exemplary stringent hybridization conditions include the following: 50% formamide, 5×SSC, and 1% SDS, incubating at 42° C., or, 5×SSC, 1% SDS, incubating at 65° C., with wash in 0.2×SSC, and 0.1% SDS at 65° C.
“Subject” as used herein can mean a mammal that wants to or is in need of being immunized with the herein described immunogenic compositions. The mammal can be a human, chimpanzee, dog, cat, horse, cow, mouse, or rat.
“Substantially complementary” as used herein means that a first sequence is at least 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the complement of a second sequence over a region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 180, 270, 360, 450, 540, or more nucleotides or amino acids, or that the two sequences hybridize under stringent hybridization conditions.
“Substantially identical” as used herein means that a first and second sequence are at least 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical over a region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 180, 270, 360, 450, 540 or more nucleotides or amino acids, or with respect to nucleic acids, if the first sequence is substantially complementary to the complement of the second sequence.
“Treatment” or “treating” as used herein can mean protecting an animal from a disease through means of preventing, suppressing, repressing, or completely eliminating the disease. Preventing the disease involves administering an immunogenic composition of the present invention to an animal prior to onset of the disease. Suppressing the disease involves administering an immunogenic composition of the present invention to an animal after induction of the disease but before its clinical appearance. Repressing the disease involves administering an immunogenic composition of the present invention to an animal after clinical appearance of the disease.
“Variant” used herein with respect to a nucleic acid means (i) a portion or fragment of a referenced nucleotide sequence; (ii) the complement of a referenced nucleotide sequence or portion thereof; (iii) a nucleic acid that is substantially identical to a referenced nucleic acid or the complement thereof; or (iv) a nucleic acid that hybridizes under stringent conditions to the referenced nucleic acid, complement thereof, or a sequences substantially identical thereto.
“Variant” with respect to a peptide or polypeptide that differs in amino acid sequence by the insertion, deletion, or conservative substitution of amino acids, but retain at least one biological activity. Variant can also mean a protein with an amino acid sequence that is substantially identical to a referenced protein with an amino acid sequence that retains at least one biological activity. A conservative substitution of an amino acid, i.e., replacing an amino acid with a different amino acid of similar properties (e.g., hydrophilicity, degree and distribution of charged regions) is recognized in the art as typically involving a minor change. These minor changes can be identified, in part, by considering the hydropathic index of amino acids, as understood in the art. Kyte et al., J. Mol. Biol. 157:105-132 (1982). The hydropathic index of an amino acid is based on a consideration of its hydrophobicity and charge. It is known in the art that amino acids of similar hydropathic indexes can be substituted and still retain protein function. In one aspect, amino acids having hydropathic indexes of ±2 are substituted. The hydrophilicity of amino acids can also be used to reveal substitutions that would result in proteins retaining biological function. A consideration of the hydrophilicity of amino acids in the context of a peptide permits calculation of the greatest local average hydrophilicity of that peptide, a useful measure that has been reported to correlate well with antigenicity and immunogenicity. U.S. Pat. No. 4,554,101, incorporated fully herein by reference. Substitution of amino acids having similar hydrophilicity values can result in peptides retaining biological activity, for example immunogenicity, as is understood in the art. Substitutions can be performed with amino acids having hydrophilicity values within ±2 of each other. Both the hyrophobicity index and the hydrophilicity value of amino acids are influenced by the particular side chain of that amino acid. Consistent with that observation, amino acid substitutions that are compatible with biological function are understood to depend on the relative similarity of the amino acids, and particularly the side chains of those amino acids, as revealed by the hydrophobicity, hydrophilicity, charge, size, and other properties.
A variant may be a nucleic acid sequence that is substantially identical over the full length of the full gene sequence or a fragment thereof. The nucleic acid sequence may be 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the full length of the gene sequence or a fragment thereof. A variant may be an amino acid sequence that is substantially identical over the full length of the amino acid sequence or fragment thereof. The amino acid sequence may be 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the full length of the amino acid sequence or a fragment thereof.
“Vector” as used herein means a nucleic acid sequence containing an origin of replication. A vector can be a viral vector, bacteriophage, bacterial artificial chromosome or yeast artificial chromosome. A vector can be a DNA or RNA vector. A vector can be a self-replicating extrachromosomal vector, and in one embodiment, is an expression plasmid. The vector can contain or include one or more heterologous nucleic acid sequences.

2. SYNTHETIC CONSENSUS TERT

The invention provides an optimized consensus sequence of a TERT antigen. In one embodiment, the antigen encoded by the optimized consensus sequence is capable of eliciting an immune response in a mammal. In one embodiment, the antigen encoded by the optimized consensus sequence can comprise an epitope(s) that makes it particularly effective as an immunogen against which an immune response can be induced.
The optimized consensus sequence can be a consensus sequence derived from two or more native TERT antigens. The optimized consensus sequence can comprise a consensus sequence and/or modification(s) for improved expression. Modification can include codon optimization, RNA optimization, addition of a kozak sequence for increased translation initiation, and/or the addition of an immunoglobulin leader sequence to increase immunogenicity. The TERT antigen encoded by the optimized consensus sequence can comprise a signal peptide such as an immunoglobulin signal peptide, for example, but not limited to, an immunoglobulin E (IgE) or immunoglobulin (IgG) signal peptide. In some embodiments, the antigen encoded by the optimized consensus sequence can comprise a hemagglutinin (HA) tag. The TERT antigen encoded by the optimized consensus sequence can be designed to elicit stronger cellular and/or humoral immune responses than a corresponding native antigen. The TERT antigen encoded by the optimized consensus sequence can be designed to break tolerance and synergize with anti-cancer immune therapy.
In one embodiment, an optimized consensus TERT is designed to break tolerance to native human TERT. In one embodiment, a human optimized consensus TERT encoding sequence is as set forth in SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55. In one embodiment, a human optimized consensus TERT encoded antigen has an amino acid sequence as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56.
In one embodiment, an optimized consensus TERT is designed to break tolerance to native mouse TERT. In one embodiment, a mouse optimized consensus TERT encoding sequence is as set forth in SEQ ID NO:49 or SEQ ID NO:51. In one embodiment, a mouse optimized consensus TERT encoded antigen has an amino acid sequence as set forth in SEQ ID NO:50 or SEQ ID NO:52.
In one embodiment, an optimized consensus TERT is designed to break tolerance to native rhesus macaque TERT. In one embodiment, a rhesus macaque optimized consensus TERT encoding sequence is as set forth in SEQ ID NO:53 or SEQ ID NO:55. In one embodiment, a mouse optimized consensus TERT encoded antigen has an amino acid sequence as set forth in SEQ ID NO:54 or SEQ ID NO:56.
In one embodiment, an optimized consensus encoded TERT antigen is operably linked to one or more regulatory elements. In one embodiment, a regulatory element is a leader sequence. In one embodiment, the optimized consensus DNA sequence operably linked to an IgE leader encoding sequence is set forth in SEQ ID NO:45, SEQ ID NO:49 and SEQ ID NO:53. In one embodiment, the optimized consensus-encoded TERT antigen operably linked to an IgE leader sequence is as set forth in SEQ ID NO:46, SEQ ID NO:50 and SEQ ID NO:54.
In one embodiment, a regulatory element is a start codon. Therefore, in one embodiment, the invention relates to a nucleic acid sequence as set forth in SEQ ID NO:47, SEQ ID NO:51, SEQ ID NO:55, or a fragment or homolog thereof, operably linked to a nucleotide sequence comprising a start codon at the 5′ terminus. In one embodiment, the invention relates to an amino acid sequence as set forth in SEQ ID NO:48, SEQ ID NO:52 or SEQ ID NO:56, or a fragment or homolog thereof, operably linked to an amino acid encoded by a start codon (e.g., a Methionine) at the N-terminus.
In one embodiment, a regulatory element is at least one stop codon. Therefore, in one embodiment, the invention relates to a nucleic acid sequence as set forth in SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 or a fragment or homolog thereof, operably linked to a nucleotide sequence comprising at least one stop codon at the 3′ terminus. In one embodiment, the nucleotide sequence is operably linked to two stop codons to increase the efficiency of translational termination.
In one embodiment, the optimized consensus sequence encoding a TERT antigen can encode a peptide having the amino acid sequence set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. In one embodiment, the optimized consensus sequence can have the nucleotide sequence set forth in SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55. In some embodiments, the sequence can be the nucleotide sequence having at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identity over an entire length of the nucleotide sequence set forth in SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55. In other embodiments, sequence can be the nucleotide sequence that encodes the amino acid sequence having at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56.
In some embodiments, the optimized consensus TERT antigen can be encoded by an RNA that is a transcript from a DNA sequence having at least about 96%, 97%, 98%, 99% or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55. In some embodiments, the optimized consensus TERT antigen can be encoded by an RNA that encodes an amino acid sequence having at least about 96%, 97%, 98%, 99% or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56.
The optimized consensus-encoded TERT antigen can be a peptide having the amino acid sequence set forth in SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6 or SEQ ID NO:8. In some embodiments, the antigen can have an amino acid sequence having at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56, can be provided. Such immunogenic fragments can comprise at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% homologous to SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, immunogenic fragments include a leader sequence, such as for example an immunoglobulin leader, such as the IgE leader. In some embodiments, immunogenic fragments are free of a leader sequence.
In one embodiment, an immunogenic fragment of an optimized consensus TERT antigen encodes at least one immunodominant or sub-immunodominant epitope of a full length optimized consensus TERT antigen.
Some embodiments relate to immunogenic fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 comprising at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of the full length of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55. Immunogenic fragments can be at least 96%, at least 97% at least 98% or at least 99% homologous to fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55. In some embodiments, immunogenic fragments include sequences that encode a leader sequence, such as for example an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence.

3. IMMUNOGENIC COMPOSITION

In one embodiment, the immunogenic composition of the present invention can comprise the synthetic consensus TERT antigen, a fragment thereof, or a variant thereof. In one embodiment, the TERT antigen is a human TERT antigen (hTERT). hTERT is a human telomerase reverse transcriptase that synthesizes a TTAGGG tag on the end of telomeres to prevent cell death due to chromosomal shortening. Hyperproliferative cells can have abnormally high expression of hTERT. Abnormal expression of hTERT can also occur in hyperproliferative cells infected with HCV and HPV. Thus, immunotherapy for both HPV and HCV may be enhanced by targeting cells that express hTERT at abnormal levels. HPV and HCV antigens are discussed below in more detail. In one aspect, the hTERT cancer antigen can further be defined by U.S. patent application Ser. No. 14/139,660, filed Dec. 23, 2013, which is incorporated by reference in its' entirety.
In one embodiment, the TERT antigen is a non-human TERT antigen. Non-human TERT antigens include, but are not limited to, mouse TERT (mTERT) and rhesus macaque TERT (rhTERT).
TERT expression in dendritic cells transfected with TERT genes can induce CD8⁺ cytotoxic T cells and elicit CD4⁺ T cells in an antigen-specific fashion. Therefore, use of hTERT expression within antigen presenting cells (APCs) to delay senescence and sustain their capacity to present the antigen of choice can be used in immunotherapeutic methods such as in the methods described herein.
The TERT antigen can be associated with or expressed by any number of cancers including, but not limited to, melanoma, prostate cancer, liver cancer, cervical cancer, recurrent respiratory papillomatosis (RRP), anal cancer, head and neck cancer, and blood cancers. Accordingly, the vaccine, when including the TERT antigen described herein, can be used for treating subjects suffering from any number of cancers including, but not limited to, melanoma, prostate cancer, liver cancer, cervical cancer, recurrent respiratory papillomatosis (RRP), anal cancer, head and neck cancer, and blood cancers.
The TERT antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The TERT antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-TERT immune responses can be induced. The TERT antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The TERT antigen can comprise a consensus protein.
The nucleic acid sequence encoding the TERT antigen or consensus TERT antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the TERT antigen or consensus TERT antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the TERT antigen or consensus TERT antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the TERT antigen or consensus TERT antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the TERT antigen or consensus TERT antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the TERT antigen or consensus TERT antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the TERT antigen or consensus TERT antigen by a peptide bond, respectively. The nucleic encoding the TERT antigen or consensus TERT antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the TERT antigen or consensus TERT antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
In some embodiments, the nucleic acid encoding the TERT antigen or consensus TERT antigen can be a heterologous nucleic acid sequence and/or contain one or more heterologous nucleic acid sequences. The nucleic acid encoding the TERT antigen or consensus TERT antigen can be mutated relative to the wild-type TERT antigen such that one or more amino acids or residues in the amino acid sequence of the TERT antigen or consensus TERT antigen, respectively, is replaced or substituted with another amino acid or residue. The nucleic acid encoding the TERT antigen or consensus TERT antigen can be mutated relative to the wild-type TERT antigen such that one or more residues in the amino acid sequence of the TERT antigen or consensus TERT antigen, respectively, are replaced or substituted with another residue, thereby causing the immune system to no longer be tolerant of TERT in the mammal administered the nucleic acid encoding the TERT antigen or consensus TERT antigen, the TERT antigen or consensus TERT antigen, or combinations thereof. The nucleic acid encoding TERT antigen or consensus TERT antigen can be mutated relative to the wild-type TERT antigen such that arginine 589, aspartate 1005, or both arginine 589 and aspartate 1005 in the amino acid sequence of the TERT antigen or consensus TERT antigen is replaced or substituted by a tyrosine residue.
In one aspect, the TERT antigen can be the nucleic acid sequence SEQ ID NO:23 or SEQ ID NO:57, which encode for the amino acid sequence SEQ ID NO:24 and SEQ ID NO:58 respectively. SEQ ID NO:23 and SEQ ID NO:57 encode a TERT antigen linked to an IgE leader sequence. In one embodiment, the TERT antigen can be linked to the IgE leader sequence and an HA tag. In other embodiments, the TERT antigen can be free of or not linked to an IgE leader sequence and/or an HA tag.
In some embodiments, the TERT antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in SEQ ID NO:23 or SEQ ID NO:57. In other embodiments, the TERT antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:24 or SEQ ID NO:58. The TERT antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:24 or SEQ ID NO:58.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the TERT antigen, immunogenic fragment of the TERT antigen, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a sequence, up to 96% homology to a sequence, up to 97% homology to a sequence, up to 98% homology to a sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length TERT antigen, immunogenic fragment of the TERT antigen, and immunogenic fragments of proteins having identity to the TERT antigen. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length TERT sequence, up to 85% identity to a full length sequence, up to 90% identity to a full length TERT sequence, up to 91% identity to a full length TERT sequence, up to 92% identity to a full length TERT sequence, up to 93% identity to a full length TERT sequence, up to 94% identity to a full length TERT sequence, up to 95% identity to a full length TERT sequence, up to 96% identity to a full length TERT sequence, up to 97% identity to a full length TERT sequence, up to 98% identity to a full length TERT sequence, and up to 99% identity to a full length TERT sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the TERT antigens set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:23 or SEQ ID NO:57. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:23 or SEQ ID NO:57. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:23 or SEQ ID NO:57. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:23 or SEQ ID NO:57. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the TERT antigen is SEQ ID NO:24 or SEQ ID NO:58. The amino acid sequence of the TERT antigen linked to an IgE leader is SEQ ID NO:24 or SEQ ID NO:58. The amino acid sequence of the TERT antigen linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have 95% homology to the protein sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have 96% homology to the protein sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have 97% homology to the protein sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have 98% homology to the protein sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have 99% homology to the protein sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58.
Some embodiments relate to proteins that are identical to SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length amino acid sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length amino acid sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length amino acid sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length amino acid sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length amino acid sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length amino acid sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length amino acid sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length amino acid sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length amino acid sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length amino acid sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length amino acid sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length amino acid sequences as set forth in SEQ ID NO:24 or SEQ ID NO:58.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a protein. Immunogenic fragments of SEQ ID NO:24 or SEQ ID NO:58 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:24 or SEQ ID NO:58. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:24 or SEQ ID NO:58 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:18. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:24 or SEQ ID NO:58 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:24 or SEQ ID NO:58. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
Fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 30 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 45 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 60 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 75 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 90 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 120 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 150 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 180 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 210 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 240 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 270 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 300 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 360 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 420 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 480 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 540 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 600 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 300 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 660 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 720 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 780 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 840 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 900 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 960 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1020 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1080 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1140 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1200 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1260 or more embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1320 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1380 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1440 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1500 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1560 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1620 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1680 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1740 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1800 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1860 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1920 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 1980 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2040 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2100 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2160 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2220 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2280 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2340 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2400 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2460 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2520 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2580 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2640 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2700 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2760 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2820 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2880 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 2940 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 3000 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 3060 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 3120 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 3180 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 3240 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 3300 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 3360 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 3420 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise 3480 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 may comprise coding sequences for the IgE leader sequences. In some embodiments, fragments of SEQ ID NO:23 or SEQ ID NO:57 do not comprise coding sequences for the IgE leader sequences.
Fragments may comprise fewer than 60 nucleotides, in some embodiments fewer than 75 nucleotides, in some embodiments fewer than 90 nucleotides, in some embodiments fewer than 120 nucleotides, in some embodiments fewer than 150 nucleotides, in some embodiments fewer than 180 nucleotides, in some embodiments fewer than 210 nucleotides, in some embodiments fewer than 240 nucleotides, in some embodiments fewer than 270 nucleotides, in some embodiments fewer than 300 nucleotides, in some embodiments fewer than 360 nucleotides, in some embodiments fewer than 420 nucleotides, in some embodiments fewer than 480 nucleotides, in some embodiments fewer than 540 nucleotides, in some embodiments fewer than 600 nucleotides, in some embodiments fewer than 660 nucleotides, in some embodiments fewer than 720 nucleotides, in some embodiments fewer than 780 nucleotides, in some embodiments fewer than 840 nucleotides, in some embodiments fewer than 900 nucleotides, in some embodiments fewer than 960 nucleotides, in some embodiments fewer than 1020 nucleotides, in some embodiments fewer than 1080 nucleotides, in some embodiments fewer than 1140 nucleotides, in some embodiments fewer than 1200 nucleotides, in some embodiments fewer than 1260 nucleotides, in some embodiments fewer than 1320 nucleotides, in some embodiments fewer than 1380 nucleotides, in some embodiments fewer than 1440 nucleotides, in some embodiments fewer than 1500 nucleotides, in some embodiments fewer than 1560 nucleotides, in some embodiments fewer than 1620 nucleotides, in some embodiments fewer than 1680 nucleotides, in some embodiments fewer than 1740 nucleotides, in some embodiments fewer than 1800 nucleotides, in some embodiments fewer than 1860 nucleotides, in some embodiments fewer than 1920 nucleotides, in some embodiments fewer than 1980 nucleotides, in some embodiments fewer than 2040 nucleotides, in some embodiments fewer than 2100 nucleotides, in some embodiments fewer than 2160 nucleotides, in some embodiments fewer than 2220 nucleotides, in some embodiments fewer than 2280 nucleotides, in some embodiments fewer than 2340 nucleotides, in some embodiments fewer than 2400 nucleotides, in some embodiments fewer than 2460 nucleotides, in some embodiments fewer than 2520 nucleotides, in some embodiments fewer than 2580 nucleotides, in some embodiments fewer than 2640 nucleotides, in some embodiments fewer than 2700 nucleotides, in some embodiments fewer than 2760 nucleotides, in some embodiments fewer than 2820 nucleotides, in some embodiments fewer than 2860 nucleotides, in some embodiments fewer than 2940 nucleotides, in some embodiments fewer than 3000 nucleotides, in some embodiments fewer than 3060 nucleotides, in some embodiments fewer than 3120 nucleotides, in some embodiments fewer than 3180 nucleotides, in some embodiments fewer than 3240 nucleotides, in some embodiments fewer than 3300 nucleotides, in some embodiments fewer than 3360 nucleotides, in some embodiments fewer than 3420 nucleotides, in some embodiments fewer than 3480 nucleotides, and in some embodiments fewer than 3510 nucleotides.
Fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 15 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 18 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 21 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 24 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 30 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 36 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 42 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 48 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 54 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 60 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 66 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 72 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 90 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 120 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 150 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 180 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 210 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 240 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 270 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 300 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 330 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 360 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 390 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 420 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 450 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 480 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 510 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 540 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 570 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 600 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 630 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 660 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 690 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 720 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 750 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 780 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 810 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 840 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 870 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 900 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 930 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 960 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 990 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1020 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1050 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1080 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1110 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1140 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1170 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1200 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1230 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1260 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1290 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1320 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1350 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1380 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1410 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1440 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1470 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise 1500 or more amino acids, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 may comprise coding sequences for the IgE leader sequences. In some embodiments, fragments of SEQ ID NO:24 or SEQ ID NO:58 do not comprise coding sequences for the IgE leader sequences.
Fragments may comprise fewer than 24 amino acids, in some embodiments fewer than 30 amino acids, in some embodiments fewer than 36 amino acids, in some embodiments fewer than 42 amino acids, in some embodiments fewer than 48 amino acids, in some embodiments fewer than 54 amino acids, in some embodiments fewer than 60 amino acids, in some embodiments fewer than 72 amino acids, in some embodiments fewer than 90 amino acids, in some embodiments fewer than 120 amino acids, in some embodiments fewer than 150 amino acids, in some embodiments fewer than 180 amino acids, in some embodiments fewer than 210 amino acids in some embodiments fewer than 240 amino acids, in some embodiments fewer than 260 amino acids, in some embodiments fewer than 290 amino acids, in some embodiments fewer than 320 amino acids, in some embodiments fewer than 350 amino acids, in some embodiments fewer than 380 amino acids, in some embodiments fewer than 410 amino acids in some embodiments fewer than 440 amino acids, in some embodiments fewer than 470 amino acids in some embodiments fewer than 500 amino acids, in some embodiments fewer than 530 amino acids in some embodiments fewer than 560 amino acids, in some embodiments fewer than 590 amino acids, in some embodiments fewer than 620 amino acids, in some embodiments fewer than 650 amino acids, in some embodiments fewer than 680 amino acids, in some embodiments fewer than 710 amino acids, in some embodiments fewer than 740 amino acids, in some embodiments fewer than 770 amino acids, in some embodiments fewer than 800 amino acids, in some embodiments fewer than 830 amino acids, in some embodiments fewer than 860 amino acids, in some embodiments fewer than 890 amino acids, in some embodiments fewer than 920 amino acids, in some embodiments fewer than 950 amino acids, in some embodiments fewer than 980 amino acids, in some embodiments fewer than 1010 amino acids, in some embodiments fewer than 1040 amino acids, in some embodiments fewer than 1070 amino acids, in some embodiments fewer than 1200 amino acids, in some embodiments fewer than 1230 amino acids, in some embodiments fewer than 1260 amino acids, in some embodiments fewer than 1290 amino acids, in some embodiments fewer than 1320 amino acids, in some embodiments fewer than 1350 amino acids, in some embodiments fewer than 1380 amino acids, in some embodiments fewer than 1410 amino acids, in some embodiments fewer than 1440 amino acids, in some embodiments fewer than 1470 amino acids, and in some embodiments fewer than 1500 amino acids.
In one embodiment, the TERT antigen is a synthetic consensus TERT antigen. In certain embodiments, the synthetic consensus TERT comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more 9 or more, 10 or more, 15 or more, 20 or more, 30 or more, or 50 or more amino acid mutations relative to a native TERT antigen.
In one embodiment, the consensus hTERT antigen can be the nucleic acid sequence SEQ ID NO:45, which encodes for the amino acid sequence SEQ ID NO:46. SEQ ID NO:45 encodes the consensus hTERT antigen linked to an IgE leader sequence. The consensus hTERT antigen can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus hTERT antigen can be free of or not linked to an IgE leader sequence and/or an HA tag. In one embodiment, the consensus hTERT antigen can be the nucleic acid sequence SEQ ID NO:47, which encodes for the amino acid sequence SEQ ID NO:48. SEQ ID NO:47 encodes the consensus hTERT antigen free of or not linked to an IgE leader sequence and/or an HA tag.
In one embodiment, the consensus mTERT antigen can be the nucleic acid sequence SEQ ID NO:49, which encodes for the amino acid sequence SEQ ID NO:50. SEQ ID NO:49 encodes the consensus mTERT antigen linked to an IgE leader sequence. The consensus mTERT antigen can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus mTERT antigen can be free of or not linked to an IgE leader sequence and/or an HA tag. In one embodiment, the consensus mTERT antigen can be the nucleic acid sequence SEQ ID NO:51, which encodes for the amino acid sequence SEQ ID NO:52. SEQ ID NO:51 encodes the consensus mTERT antigen free of or not linked to an IgE leader sequence and/or an HA tag.
In one embodiment, the consensus rhTERT antigen can be the nucleic acid sequence SEQ ID NO:53, which encodes for the amino acid sequence SEQ ID NO:54. SEQ ID NO:53 encodes the consensus rhTERT antigen linked to an IgE leader sequence. The consensus rhTERT antigen can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus rhTERT antigen can be free of or not linked to an IgE leader sequence and/or an HA tag. In one embodiment, the consensus rhTERT antigen can be the nucleic acid sequence SEQ ID NO:55, which encodes for the amino acid sequence SEQ ID NO:56. SEQ ID NO:55 encodes the consensus rhTERT antigen free of or not linked to an IgE leader sequence and/or an HA tag.
In some embodiments, the consensus TERT antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55. In other embodiments, the consensus TERT antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. The consensus TERT antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the consensus TERT antigen, immunogenic fragment of the consensus TERT antigen, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a sequence, up to 96% homology to a sequence, up to 97% homology to a sequence, up to 98% homology to a sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length consensus TERT antigen, immunogenic fragment of the consensus TERT antigen, and immunogenic fragments of proteins having identity to the consensus TERT antigen. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length consensus TERT sequence, up to 85% identity to a full length sequence, up to 90% identity to a full length consensus TERT sequence, up to 91% identity to a full length consensus TERT sequence, up to 92% identity to a full length consensus TERT sequence, up to 93% identity to a full length consensus TERT sequence, up to 94% identity to a full length consensus TERT sequence, up to 95% identity to a full length consensus TERT sequence, up to 96% identity to a full length consensus TERT sequence, up to 97% identity to a full length consensus TERT sequence, up to 98% identity to a full length consensus TERT sequence, and up to 99% identity to a full length consensus TERT sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the consensus TERT antigens set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, in one embodiment, the amino acid sequence of the consensus TERT antigen is SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. The amino acid sequence of the consensus TERT antigen linked to an IgE leader is SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. The amino acid sequence of the consensus TERT antigen linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have 95% homology to the protein sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have 96% homology to the protein sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have 97% homology to the protein sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have 98% homology to the protein sequences as set forth in SEQ ID NO:46. Some embodiments relate to immunogenic proteins that have 99% homology to the protein sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56.
Some embodiments relate to proteins that are identical to SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length amino acid sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length amino acid sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length amino acid sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length amino acid sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length amino acid sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length amino acid sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length amino acid sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length amino acid sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length amino acid sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length amino acid sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length amino acid sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length amino acid sequences as set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a protein. Immunogenic fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
Fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 30 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 45 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 60 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 75 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 90 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 120 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 150 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 180 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 210 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 240 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 270 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 300 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 360 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 420 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 480 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 540 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 600 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 300 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 660 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 720 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 780 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 840 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 900 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 960 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1020 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1080 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1140 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1200 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1260 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1320 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1380 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1440 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1500 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1560 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1620 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1680 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1740 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1800 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1860 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1920 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 1980 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2040 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2100 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2160 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2220 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2280 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2340 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2400 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2460 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2520 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2580 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2640 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2700 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2760 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2820 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2880 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 2940 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 3000 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 3060 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 3120 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 3180 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 3240 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 3300 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 3360 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 3420 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise 3480 or more nucleotides, including sequences that encode an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 may comprise coding sequences for the IgE leader sequences. In some embodiments, fragments of SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53 or SEQ ID NO:55 do not comprise coding sequences for the IgE leader sequences.
Fragments may comprise fewer than 60 nucleotides, in some embodiments fewer than 75 nucleotides, in some embodiments fewer than 90 nucleotides, in some embodiments fewer than 120 nucleotides, in some embodiments fewer than 150 nucleotides, in some embodiments fewer than 180 nucleotides, in some embodiments fewer than 210 nucleotides, in some embodiments fewer than 240 nucleotides, in some embodiments fewer than 270 nucleotides, in some embodiments fewer than 300 nucleotides, in some embodiments fewer than 360 nucleotides, in some embodiments fewer than 420 nucleotides, in some embodiments fewer than 480 nucleotides, in some embodiments fewer than 540 nucleotides, in some embodiments fewer than 600 nucleotides, in some embodiments fewer than 660 nucleotides, in some embodiments fewer than 720 nucleotides, in some embodiments fewer than 780 nucleotides, in some embodiments fewer than 840 nucleotides, in some embodiments fewer than 900 nucleotides, in some embodiments fewer than 960 nucleotides, in some embodiments fewer than 1020 nucleotides, in some embodiments fewer than 1080 nucleotides, in some embodiments fewer than 1140 nucleotides, in some embodiments fewer than 1200 nucleotides, in some embodiments fewer than 1260 nucleotides, in some embodiments fewer than 1320 nucleotides, in some embodiments fewer than 1380 nucleotides, in some embodiments fewer than 1440 nucleotides, in some embodiments fewer than 1500 nucleotides, in some embodiments fewer than 1560 nucleotides, in some embodiments fewer than 1620 nucleotides, in some embodiments fewer than 1680 nucleotides, in some embodiments fewer than 1740 nucleotides, in some embodiments fewer than 1800 nucleotides, in some embodiments fewer than 1860 nucleotides, in some embodiments fewer than 1920 nucleotides, in some embodiments fewer than 1980 nucleotides, in some embodiments fewer than 2040 nucleotides, in some embodiments fewer than 2100 nucleotides, in some embodiments fewer than 2160 nucleotides, in some embodiments fewer than 2220 nucleotides, in some embodiments fewer than 2280 nucleotides, in some embodiments fewer than 2340 nucleotides, in some embodiments fewer than 2400 nucleotides, in some embodiments fewer than 2460 nucleotides, in some embodiments fewer than 2520 nucleotides, in some embodiments fewer than 2580 nucleotides, in some embodiments fewer than 2640 nucleotides, in some embodiments fewer than 2700 nucleotides, in some embodiments fewer than 2760 nucleotides, in some embodiments fewer than 2820 nucleotides, in some embodiments fewer than 2860 nucleotides, in some embodiments fewer than 2940 nucleotides, in some embodiments fewer than 3000 nucleotides, in some embodiments fewer than 3060 nucleotides, in some embodiments fewer than 3120 nucleotides, in some embodiments fewer than 3180 nucleotides, in some embodiments fewer than 3240 nucleotides, in some embodiments fewer than 3300 nucleotides, in some embodiments fewer than 3360 nucleotides, in some embodiments fewer than 3420 nucleotides, in some embodiments fewer than 3480 nucleotides, and in some embodiments fewer than 3510 nucleotides.
Fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 15 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 18 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 21 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 24 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 30 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 36 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 42 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 48 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 54 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 60 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 66 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 72 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 90 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 120 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 150 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 180 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 210 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 240 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 270 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 300 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 330 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 360 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 390 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 420 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 450 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 480 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 510 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 540 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 570 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 600 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 630 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 660 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 690 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 720 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 750 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 780 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 810 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 840 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 870 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 900 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 930 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 960 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 990 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1020 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1050 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1080 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1110 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1140 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1170 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1200 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1230 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1260 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1290 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1320 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1350 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1380 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1410 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1440 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1470 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise 1500 or more amino acids, including sequences that comprise an immunodominant epitope. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 may comprise coding sequences for the IgE leader sequences. In some embodiments, fragments of SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54 or SEQ ID NO:56 do not comprise coding sequences for the IgE leader sequences.
Fragments may comprise fewer than 24 amino acids, in some embodiments fewer than 30 amino acids, in some embodiments fewer than 36 amino acids, in some embodiments fewer than 42 amino acids, in some embodiments fewer than 48 amino acids, in some embodiments fewer than 54 amino acids, in some embodiments fewer than 60 amino acids, in some embodiments fewer than 72 amino acids, in some embodiments fewer than 90 amino acids, in some embodiments fewer than 120 amino acids, in some embodiments fewer than 150 amino acids, in some embodiments fewer than 180 amino acids, in some embodiments fewer than 210 amino acids in some embodiments fewer than 240 amino acids, in some embodiments fewer than 260 amino acids, in some embodiments fewer than 290 amino acids, in some embodiments fewer than 320 amino acids, in some embodiments fewer than 350 amino acids, in some embodiments fewer than 380 amino acids, in some embodiments fewer than 410 amino acids in some embodiments fewer than 440 amino acids, in some embodiments fewer than 470 amino acids in some embodiments fewer than 500 amino acids, in some embodiments fewer than 530 amino acids in some embodiments fewer than 560 amino acids, in some embodiments fewer than 590 amino acids, in some embodiments fewer than 620 amino acids, in some embodiments fewer than 650 amino acids, in some embodiments fewer than 680 amino acids, in some embodiments fewer than 710 amino acids, in some embodiments fewer than 740 amino acids, in some embodiments fewer than 770 amino acids, in some embodiments fewer than 800 amino acids, in some embodiments fewer than 830 amino acids, in some embodiments fewer than 860 amino acids, in some embodiments fewer than 890 amino acids, in some embodiments fewer than 920 amino acids, in some embodiments fewer than 950 amino acids, in some embodiments fewer than 980 amino acids, in some embodiments fewer than 1010 amino acids, in some embodiments fewer than 1040 amino acids, in some embodiments fewer than 1070 amino acids, in some embodiments fewer than 1200 amino acids, in some embodiments fewer than 1230 amino acids, in some embodiments fewer than 1260 amino acids, in some embodiments fewer than 1290 amino acids, in some embodiments fewer than 1320 amino acids, in some embodiments fewer than 1350 amino acids, in some embodiments fewer than 1380 amino acids, in some embodiments fewer than 1410 amino acids, in some embodiments fewer than 1440 amino acids, in some embodiments fewer than 1470 amino acids, and in some embodiments fewer than 1500 amino acids.
The present invention is directed to an anti-cancer immunogenic composition. The immunogenic composition can comprise one or more cancer antigens. The immunogenic composition can prevent tumor growth. The immunogenic composition can reduce tumor growth. The immunogenic composition can prevent metastasis of tumor cells. Depending upon the cancer antigen, the immunogenic composition can be targeted to treat cancers, including but not limited to, liver cancer, prostate cancer, melanomas, blood cancers, head and neck cancer, glioblastoma, recurrent respiratory papillomatosis, anal cancer, cervical cancer, and brain cancer.
The first step in development of the immunogenic composition is to identify a cancer antigen that is not recognized by the immune system and is a self-antigen. The cancer antigen identified is changed from a self-antigen to a foreign antigen in order to be recognized by the immune system. The redesign of the nucleic acid and amino acid sequence of the recombinant cancer antigen from a self to a foreign antigen breaks tolerance of antigen by the immune system. In order to break tolerance, several redesign measures can be applied to the cancer antigen as described below.
The recombinant cancer antigen of the immunogenic composition is not recognized as self, therefore breaking tolerance. The breaking of tolerance can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule.
In a particular embodiment, the immunogenic composition can mediate clearance or prevent growth of tumor cells by inducing (1) humoral immunity via B cell responses to generate antibodies that block monocyte chemoattractant protein-1 (MCP-1) production, thereby retarding myeloid derived suppressor cells (MDSCs) and suppressing tumor growth; (2) increase cytotoxic T lymphocyte such as CD8⁺(CTL) to attack and kill tumor cells; (3) increase T helper cell responses; (4) and increase inflammatory responses via IFN-γ and TFN-α or a combination of the aforementioned. The immunogenic composition can increase tumor free survival by 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, and 45%. The immunogenic composition can reduce tumor mass by 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, and 60% after immunization. The immunogenic composition can prevent and block increases in monocyte chemoattractant protein 1 (MCP-1), a cytokine secreted by myeloid derived suppressor cells. The immunogenic composition can increase tumor survival by 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, and 60%.
The immunogenic composition can increase a cellular immune response in a subject administered the immunogenic composition by about 50-fold to about 6000-fold, about 50-fold to about 5500-fold, about 50-fold to about 5000-fold, about 50-fold to about 4500-fold, about 100-fold to about 6000-fold, about 150-fold to about 6000-fold, about 200-fold to about 6000-fold, about 250-fold to about 6000-fold, or about 300-fold to about 6000-fold as compared to a cellular immune response in a subject not administered the immunogenic composition. In some embodiments the immunogenic composition can increase the cellular immune response in the subject administered the immunogenic composition by about 50-fold, 100-fold, 150-fold, 200-fold, 250-fold, 300-fold, 350-fold, 400-fold, 450-fold, 500-fold, 550-fold, 600-fold, 650-fold, 700-fold, 750-fold, 800-fold, 850-fold, 900-fold, 950-fold, 1000-fold, 1100-fold, 1200-fold, 1300-fold, 1400-fold, 1500-fold, 1600-fold, 1700-fold, 1800-fold, 1900-fold, 2000-fold, 2100-fold, 2200-fold, 2300-fold, 2400-fold, 2500-fold, 2600-fold, 2700-fold, 2800-fold, 2900-fold, 3000-fold, 3100-fold, 3200-fold, 3300-fold, 3400-fold, 3500-fold, 3600-fold, 3700-fold, 3800-fold, 3900-fold, 4000-fold, 4100-fold, 4200-fold, 4300-fold, 4400-fold, 4500-fold, 4600-fold, 4700-fold, 4800-fold, 4900-fold, 5000-fold, 5100-fold, 5200-fold, 5300-fold, 5400-fold, 5500-fold, 5600-fold, 5700-fold, 5800-fold, 5900-fold, or 6000-fold as compared to the cellular immune response in the subject not administered the immunogenic composition.
The immunogenic composition can increase interferon gamma (IFN-γ) levels in a subject administered the immunogenic composition by about 50-fold to about 6000-fold, about 50-fold to about 5500-fold, about 50-fold to about 5000-fold, about 50-fold to about 4500-fold, about 100-fold to about 6000-fold, about 150-fold to about 6000-fold, about 200-fold to about 6000-fold, about 250-fold to about 6000-fold, or about 300-fold to about 6000-fold as compared to IFN-γ levels in a subject not administered the immunogenic composition. In some embodiments the immunogenic composition can increase IFN-γ levels in the subject administered the immunogenic composition by about 50-fold, 100-fold, 150-fold, 200-fold, 250-fold, 300-fold, 350-fold, 400-fold, 450-fold, 500-fold, 550-fold, 600-fold, 650-fold, 700-fold, 750-fold, 800-fold, 850-fold, 900-fold, 950-fold, 1000-fold, 1100-fold, 1200-fold, 1300-fold, 1400-fold, 1500-fold, 1600-fold, 1700-fold, 1800-fold, 1900-fold, 2000-fold, 2100-fold, 2200-fold, 2300-fold, 2400-fold, 2500-fold, 2600-fold, 2700-fold, 2800-fold, 2900-fold, 3000-fold, 3100-fold, 3200-fold, 3300-fold, 3400-fold, 3500-fold, 3600-fold, 3700-fold, 3800-fold, 3900-fold, 4000-fold, 4100-fold, 4200-fold, 4300-fold, 4400-fold, 4500-fold, 4600-fold, 4700-fold, 4800-fold, 4900-fold, 5000-fold, 5100-fold, 5200-fold, 5300-fold, 5400-fold, 5500-fold, 5600-fold, 5700-fold, 5800-fold, 5900-fold, or 6000-fold as compared to IFN-γ levels in the subject not administered the immunogenic composition.
The immunogenic composition can be a nucleic acid vaccine. In one embodiment, the nucleic acid vaccine is a DNA vaccine. DNA vaccines are disclosed in U.S. Pat. Nos. 5,593,972, 5,739,118, 5,817,637, 5,830,876, 5,962,428, 5,981,505, 5,580,859, 5,703,055, and 5,676,594, which are incorporated herein fully by reference. The DNA vaccine can further comprise elements or reagents that inhibit it from integrating into the chromosome.
The immunogenic composition can be an RNA vaccine. The RNA vaccine can be introduced into the cell. The RNA vaccine can further comprise elements or reagents that inhibit it from integrating into the chromosome.
The immunogenic composition can be an attenuated live vaccine, a vaccine using recombinant vectors to deliver antigen, subunit vaccines, and glycoprotein vaccines, for example, but not limited, the vaccines described in U.S. Pat. Nos. 4,510,245; 4,797,368; 4,722,848; 4,790,987; 4,920,209; 5,017,487; 5,077,044; 5,110,587; 5,112,749; 5,174,993; 5,223,424; 5,225,336; 5,240,703; 5,242,829; 5,294,441; 5,294,548; 5,310,668; 5,387,744; 5,389,368; 5,424,065; 5,451,499; 5,453,364; 5,462,734; 5,470,734; 5,474,935; 5,482,713; 5,591,439; 5,643,579; 5,650,309; 5,698,202; 5,955,088; 6,034,298; 6,042,836; 6,156,319 and 6,589,529, which are each incorporated herein by reference.
The immunogenic composition of the present invention can have features required of effective vaccines such as being safe so that the vaccine itself does not cause illness or death; being protective against illness; inducing neutralizing antibody; inducing protective T cell responses; and providing ease of administration, few side effects, biological stability, and low cost per dose. The immunogenic composition can accomplish some or all of these features by containing the cancer antigen as discussed below.
As described in more detail below, the immunogenic composition can further comprise one or more inhibitors of one or more immune checkpoint molecules (i.e., an immune checkpoint inhibitor). Immune check point molecules are described below in more detail. The immune checkpoint inhibitor is any nucleic acid or protein that prevents the suppression of any component in the immune system such as MHC class presentation, T cell presentation and/or differentiation, B cell presentation and/or differentiation, any cytokine, chemokine or signaling for immune cell proliferation and/or differentiation. As also described below in more detail, the immunogenic composition may be combined further with antibodies to checkpoint inhibitors such as PD-1, PDL-1, CTLA4, TIM3 and LAG3 to increase the stimulation of both the cellular and humoral immune responses. Using antibodies directed to immune checkpoint proteins prevents the immune checkpoint protein from suppressing T-cell and/or B-cell responses.
The immunogenic composition can also comprise an antigen, or fragment or variant thereof. The antigen can be anything that induces an immune response in a subject. The antigen can be a nucleic acid sequence, an amino acid sequence, or a combination thereof. The nucleic acid sequence can be DNA, RNA, cDNA, a variant thereof, a fragment thereof, or a combination thereof. The nucleic acid sequence can also include additional sequences that encode linker or tag sequences that are linked to the antigen by a peptide bond. The amino acid sequence can be a protein, a peptide, a variant thereof, a fragment thereof, or a combination thereof.
The antigen can be contained in a protein, a nucleic acid, or a fragment thereof, or a variant thereof, or a combination thereof from any number of organisms, for example, a virus, a parasite, a bacterium, a fungus, or a mammal. The antigen can be associated with an autoimmune disease, allergy, or asthma. In other embodiments, the antigen can be associated with cancer, herpes, influenza, hepatitis B, hepatitis C, human papilloma virus (HPV), or human immunodeficiency virus (HIV).
Some antigens can induce a strong immune response. Other antigens can induce a weak immune response. The antigen can elicit a greater immune response when combined with the TERT antigen.
a. Cancer Antigen
The immunogenic composition can comprise one or more cancer antigens. The cancer antigen can be a nucleic acid sequence, an amino acid sequence, or a combination thereof. The nucleic acid sequence can be DNA, RNA, cDNA, a variant thereof, a fragment thereof, or a combination thereof. The nucleic acid sequence can also include additional sequences that encode linker or tag sequences that are linked to the cancer antigen by a peptide bond. The amino acid sequence can be a protein, a peptide, a variant thereof, a fragment thereof, or a combination thereof. The cancer antigen can be a recombinant cancer antigen.
In the context of the present invention, “tumor antigen” or “hyperproliferative disorder antigen” or “antigen associated with a hyperproliferative disorder,” refers to antigens that are common to specific hyperproliferative disorders such as cancer. The antigens discussed herein are merely included by way of example. The list is not intended to be exclusive and further examples will be readily apparent to those of skill in the art.
Cancer antigens, or tumor antigens, are proteins that are produced by tumor cells that elicit an immune response, particularly T-cell mediated immune responses. The selection of the antigen binding moiety of the invention will depend on the particular type of cancer to be treated. Tumor antigens are well known in the art and include, for example, a glioma-associated antigen, carcinoembryonic antigen (CEA), β-human chorionic gonadotropin, alphafetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut hsp70-2, M-CSF, prostase, prostate-specific antigen (PSA), PAP, NY-ESO-1, LAGE-la, p53, prostein, PSMA, Her2/neu, survivin and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrinB2, CD22, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor and mesothelin.
In one embodiment, the tumor antigen comprises one or more antigenic cancer epitopes associated with a malignant tumor. Malignant tumors express a number of proteins that can serve as target antigens for an immune attack. These molecules include but are not limited to tissue-specific antigens such as MART-1, tyrosinase and GP 100 in melanoma and prostatic acid phosphatase (PAP) and prostate-specific antigen (PSA) in prostate cancer. Other target molecules belong to the group of transformation-related molecules such as the oncogene HER-2/Neu/ErbB-2. Yet another group of target antigens are onco-fetal antigens such as carcinoembryonic antigen (CEA). In B-cell lymphoma the tumor-specific idiotype immunoglobulin constitutes a truly tumor-specific immunoglobulin antigen that is unique to the individual tumor. B-cell differentiation antigens such as CD19, CD20 and CD37 are other candidates for target antigens in B-cell lymphoma. Some of these antigens (CEA, HER-2, CD19, CD20, idiotype) have been used as targets for passive immunotherapy with monoclonal antibodies with limited success.
The type of tumor antigen referred to in the invention may also be a tumor-specific antigen (TSA) or a tumor-associated antigen (TAA). A TSA is unique to tumor cells and does not occur on other cells in the body. A TAA associated antigen is not unique to a tumor cell and instead is also expressed on a normal cell under conditions that fail to induce a state of immunologic tolerance to the antigen. The expression of the antigen on the tumor may occur under conditions that enable the immune system to respond to the antigen. TAAs may be antigens that are expressed on normal cells during fetal development when the immune system is immature and unable to respond or they may be antigens that are normally present at extremely low levels on normal cells but which are expressed at much higher levels on tumor cells.
Non-limiting examples of TSA or TAA antigens include the following: Differentiation antigens such as MART-1/MelanA (MART-I), gp100 (Pmel 17), tyrosinase, TRP-1, TRP-2 and tumor-specific multilineage antigens such as MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, p15; overexpressed embryonic antigens such as CEA; overexpressed oncogenes and mutated tumor-suppressor genes such as p53, Ras, HER-2/neu; unique tumor antigens resulting from chromosomal translocations; such as BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR; and viral antigens, such as the Epstein Barr virus antigens EBVA and the human papillomavirus (HPV) antigens E6 and E7. Other large, protein-based antigens include TSP-180, MAGE-4, MAGE-5, MAGE-6, RAGE, NY-ESO, p185erbB2, p180erbB-3, c-met, nm-23H1, PSA, TAG-72, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, beta-Catenin, CDK4, Mum-1, p 15, p 16, 43-9F, 5T4, 791Tgp72, alpha-fetoprotein, beta-HCG, BCA225, BTAA, CA 125, CA 15-3\CA 27.29\BCAA, CA 195, CA 242, CA-50, CAM43, CD68\P1, CO-029, FGF-5, G250, Ga733\EpCAM, HTgp-175, M344, MA-50, MG7-Ag, MOV18, NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90\Mac-2 binding protein\cyclophilin C-associated protein, TAAL6, TAG72, TLP, and TPS.
The TERT antigen and optionally one or more antibody targeting one or more immune checkpoint proteins can be associated or combined with a tumor antigen or fragment or variant thereof. Cancer markers are known proteins that are present or upregulated vis-à-vis certain cancer cells. By methodology of generating antigens that represent such markers in a way to break tolerance to self, a cancer vaccine can be generated. Such cancer vaccines can include the TERT antigen and optionally one or more antibody targeting one or more immune checkpoint proteins to enhance the immune response and optionally one or more additional tumor antigens. The following are some exemplary tumor antigens:
(1) Tyrosinase (Tyr)
The immunogenic composition of the present invention can comprise the cancer antigen tyrosinase (Tyr), a fragment thereof, or a variant thereof. Tyrosinase is a copper-containing enzyme having tyrosine hydroxylase and dopa oxidase catalytic activities that can be found in microorganisms and plant and animal tissues. Specifically, tyrosinase catalyzes the production of melanin and other pigments by the oxidation of phenols such as tyrosine. Mutations in the TYR gene result in oculocutaneous albinism in mammals and non-pathological polymorphisms in the TYR gene contribute to variation in skin pigmentation.
Additionally, in cancer or tumors such as melanoma, tyrosinase can become unregulated, resulting in increased melanin synthesis. Accordingly, tyrosinase can be a cancer antigen associated with melanoma. In subjects suffering from melanoma, tyrosinase can be a target of cytotoxic T cell recognition. In some instances, however, the immune response to the cancer or tumor (including melanoma) can be suppressed, leading to a microenvironment that supports tumor formation and/or growth and thus, disease progression.
Immune suppression can be facilitated by myeloid derived suppressor cells (MDSCs), which are a mixed population of immature macrophages, granulocytes, dendritic cells, and myeloid cells. The myeloid cells can be a heterogenous population of myeloid progenitor cells and immature myeloid cells (IMCs). Markers of MDSCs can include expression of Gr-1 and CD11b (i.e., Gr-1⁺ and CD11b⁺ cells).
Circulation of MDSCs can increase due to chronic infection and expansion of MDSC populations can be associated with autoimmunity and inflammation. Particularly, MDSC expansion (or presence in the tumor or cancerous tissue) can facilitate tumor growth and escape from immune detection and/or regulation, and thus, MDSCs can affect immune responses to anticancer vaccines.
MDSCs can be regulated by Regulator of G-protein signaling 2 (Rgs2) and Rgs2 can be highly expressed in MDSCs derived from tumors. Rgs2 can also be widely expressed in a variety of cells, for example, myeloid cells. MDSCs derived from tumor bearing mice can function differently from MDSCs derived from non-tumor bearing mice. One such difference can be the up-regulation of the production of the chemokine MCP-1, which is secreted by MDSCs. MCP-1 can promote cell migration by signaling through CCR2, a G-protein coupled receptor (GPCR) found on monocytes, endothelial cells, and T cells. Accordingly, MCP-1 can cause migration of endothelial cells, thereby promoting vascularization. Blocking MCP-1 via neutralizing antibodies can inhibit angiogenesis, and thus, can lead to decreased tumor metastases and increased survival. As such, MCP-1 can be considered an angiogenic factor. Besides secreting MCP-1, MDSCs can secrete growth factors, thereby further contributing to tumor growth.
The Tyr antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
As demonstrated herein, the Tyr antigen induces antigen-specific T-cell and high titer antibody responses against cancerous or tumor cells (e.g., melanoma cells). Specifically, the Tyr antigen is an important target for immune mediated clearance by inducing (1) humoral immunity via B cell responses to generate antibodies that block monocyte chemoattractant protein-1 (MCP-1) production, thereby retarding myeloid derived suppressor cells (MDSCs) and suppressing tumor growth; (2) increase cytotoxic T lymphocyte such as CD8⁺ (CTL) to attack and kill tumor cells; (3) increase T helper cell responses; and (4) increase inflammatory responses via IFN-γ and TFN-α or a combination of the aforementioned. As such, a protective immune response is provided against tumor formation and tumor growth by immunogenic compositions comprising the Tyr antigen (e.g., the consensus Tyr antigen, which is described below in more detail) because these immunogenic compositions prevent immune suppression by decreasing the population of MDSCs found within the cancerous or tumor tissue and block vascularization of the cancerous or tumor tissue by reducing production or secretion of MCP-1. Accordingly, any user can design an immunogenic composition of the present invention to include a Tyr antigen to provide broad immunity against tumor formation, metastasis of tumors, and tumor growth.
The Tyr antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-Tyr immune responses can be induced. The Tyr antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The Tyr antigen can comprise a consensus protein.
The nucleic acid sequence encoding the consensus Tyr antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus Tyr antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus Tyr antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus Tyr antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus Tyr antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus Tyr antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus Tyr antigen by a peptide bond. The nucleic encoding the consensus Tyr antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus Tyr antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
The consensus Tyr antigen can be the nucleic acid sequence SEQ ID NO:1, which encodes for the amino acid sequence SEQ ID NO:2. SEQ ID NO:1 encodes the consensus Tyr protein linked to an IgE leader sequence. The consensus Tyr protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus Tyr protein can be free of or not linked to an IgE leader sequence and/or an HA tag.
In some embodiments, the consensus Tyr antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:1. In other embodiments, the consensus Tyr antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:2. The consensus Tyr antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:2.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the Tyr consensus protein, immunogenic fragment of the Tyr consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length Tyr consensus protein, immunogenic fragment of the Tyr consensus protein, and immunogenic fragments of proteins having identity to the Tyr consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length Tyr consensus sequence, up to 85% identity to a full length consensus sequence, up to 90% identity to a full length Tyr consensus sequence, up to 91% identity to a full length Tyr consensus sequence, up to 92% identity to a full length Tyr consensus sequence, up to 93% identity to a full length Tyr consensus sequence, up to 94% identity to a full length Tyr consensus sequence, up to 95% identity to a full length Tyr consensus sequence, up to 96% identity to a full length Tyr consensus sequence, up to 97% identity to a full length Tyr consensus sequence, up to 98% identity to a full length Tyr consensus sequence, and up to 99% identity to a full length Tyr consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the Tyr proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:1. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:1. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:1. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:1. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus Tyr protein is SEQ ID NO:2. The amino acid sequence of the consensus Tyr protein linked to an IgE leader is SEQ ID NO:2. The amino acid sequence of the consensus Tyr protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:2.
Some embodiments relate to proteins that are identical to SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:2. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:2.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:2 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:2. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:2 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:2. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:2 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:2. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
(2) Tyrosinase-Related Protein 1 (TYRP1)
The immunogenic composition of the present invention can comprise the cancer antigen tyrosinase-related Protein 1 (TYRP1), a fragment thereof, or a variant thereof. TYRP1, encoded by the TYRP1 gene, is a 75 kDa transmembrane glycoprotein and is expressed in both normal and malignant melanocytes and melanoma cells. Like tyrosinase, TYRP1 contains a modified termed M-box that can bind to the microphtalmia transcription factor (MITF), which plays a central role within the melanocyte in activating pigmentation, cell proliferation and differentiation. TYRP1 may help to stabilize tyrosinase and can form a heterodimer, which may prevent the premature death of melanocytes by attenuating tyrosinase-mediated cytotoxicity.
As described above for tyrosinase, tyrosinase-related protein 1 (TYRP-1) can also be involved in the synthesis of melanin and pigmentary machinery of the melanocyte, and can be recognized by the immune system in subjects suffering from melanoma. Accordingly, TYRP-1 can be antigen associated with melanoma.
The TRYP-1 antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The TYRP-1 antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-TYRP-1 immune responses can be induced. The TYRP-1 antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The TYRP-1 antigen can comprise a consensus protein.
The nucleic acid sequence encoding the consensus TYRP-1 antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus TYRP-1 antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus TYRP-1 antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus TYRP-1 antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus TYRP-1 antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus TYRP-1 antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus TYRP-1 antigen by a peptide bond. The nucleic encoding the consensus TYRP-1 antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus TYRP-1 antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
The consensus TYRP-1 antigen can be the nucleic acid sequence SEQ ID NO:3, which encodes for the amino acid sequence SEQ ID NO:4. SEQ ID NO:3 encodes the consensus TYRP-1 protein linked to an IgE leader sequence. The consensus TYRP-1 protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus TYRP-1 protein can be free of or not linked to an IgE leader sequence and/or an HA tag.
In some embodiments, the consensus TYRP-1 antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:3. In other embodiments, the consensus TYRP-1 antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:4. The consensus TYRP-1 antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:4.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the TYRP-1 consensus protein, immunogenic fragment of the TYRP-1 consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length TYRP-1 consensus protein, immunogenic fragment of the TYRP-1 consensus protein, and immunogenic fragments of proteins having identity to the TYRP-1 consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length TYRP-1 consensus sequence, up to 85% identity to a full length TYRP-1 consensus sequence, up to 90% identity to a full length TYRP-1 consensus sequence, up to 91% identity to a full length TYRP-1 consensus sequence, up to 92% identity to a full length TYRP-1 consensus sequence, up to 93% identity to a full length TYRP-1 consensus sequence, up to 94% identity to a full length TYRP-1 consensus sequence, up to 95% identity to a full length TYRP-1 consensus sequence, up to 96% identity to a full length TYRP-1 consensus sequence, up to 97% identity to a full length TYRP-1 consensus sequence, up to 98% identity to a full length TYRP-1 consensus sequence, and up to 99% identity to a full length TYRP-1 consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the TYRP-1 proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:3. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:3. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:3. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:3. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus TYRP-1 protein is SEQ ID NO:4. The amino acid sequence of the consensus TYRP-1 protein linked to an IgE leader is SEQ ID NO:4. The amino acid sequence of the consensus TYRP-1 protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:4.
Some embodiments relate to proteins that are identical to SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:4. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:4.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus TYRP-1 protein. Immunogenic fragments of SEQ ID NO:4 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:4. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:4 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:4. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:4 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:4. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
(3) Tyrosinase-Related Protein 2 (TYRP2)
The immunogenic composition of the present invention can comprise the cancer antigen tyrosinase-related Protein 2 (TYRP2; also known as dopachrome tautomerase (DCT)), a fragment thereof, or a variant thereof. TYRP2/DCT, encoded by the TYRP2/DCT gene, is a protein comprised of 519 amino acids and is expressed in both normal and malignant melanocytes and melanoma cells. TYRP2/DCT is a well-characterized melanocyte-specific enzyme that, in conjunction with tyrosinase and TYRP1, functions in the conversion of L-tyrosine to melanin in melanocytes. DCT specifically catalyses the tautomerization of the melanin precursors L-DOPAchrome to 5,6-dihydroindole-2-carboxylic acid (DHICA), which is subsequently oxidized by TYRP1 (as discussed above) to form eumelanin. Studies have shown that TYRP2/DCT may be a mediator of drug resistance in melanoma cells, with specificity for DNA-damaging agents. Since TYRP2/DCT has frequently been reported to be highly expressed in melanomas, this melanocyte-specific enzyme plays an important role contributing to intrinsic resistance phenotype of melanomas to various anticancer DNA-damaging drugs.
As described above for tyrosinase, tyrosinase-related protein 2 (TYRP-2) can also be involved in the synthesis of melanin and recognized by the immune system in subjects suffering from melanoma. Additionally, TYRP-2 can mediate drug resistance in melanoma cells. Accordingly, TYRP-2 can be an antigen associated with melanoma.
The TRYP-2 antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The TYRP2 antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-TYRP2 immune responses can be induced. The TYRP2 antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The TYRP2 antigen can comprise a consensus protein.
The nucleic acid sequence encoding the consensus TYRP2 antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus TYRP2 antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus TYRP2 antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus TYRP2 antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus TYRP2 antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus TYRP2 antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus TYRP2 antigen by a peptide bond. The nucleic encoding the consensus TYRP2 antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus TYRP2 antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
The consensus TYRP2 antigen can be the nucleic acid sequence SEQ ID NO:5, which encodes for the amino acid sequence SEQ ID NO:6. SEQ ID NO:5 encodes the consensus TYRP2 protein linked to an IgE leader sequence. The consensus TYRP2 protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus TYRP2 protein can be free of or not linked to an IgE leader sequence and/or an HA tag.
In some embodiments, the consensus TYRP2 antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:5. In other embodiments, the consensus TYRP2 antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:6. The consensus TYRP2 antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:6.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the TYRP2 consensus protein, immunogenic fragment of the TYRP2 consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length TYRP2 consensus protein, immunogenic fragment of the TYRP2 consensus protein, and immunogenic fragments of proteins having identity to the TYRP2 consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length TYRP2 consensus sequence, up to 85% identity to a full length consensus sequence, up to 90% identity to a full length TYRP2 consensus sequence, up to 91% identity to a full length TYRP2 consensus sequence, up to 92% identity to a full length TYRP2 consensus sequence, up to 93% identity to a full length TYRP2 consensus sequence, up to 94% identity to a full length TYRP2 consensus sequence, up to 95% identity to a full length TYRP2 consensus sequence, up to 96% identity to a full length TYRP2 consensus sequence, up to 97% identity to a full length TYRP2 consensus sequence, up to 98% identity to a full length TYRP2 consensus sequence, and up to 99% identity to a full length TYRP2 consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the TYRP2 proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:5. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:5. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:5. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:5. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus TYRP2 protein is SEQ ID NO:6. The amino acid sequence of the consensus TYRP2 protein linked to an IgE leader is SEQ ID NO:6. The amino acid sequence of the consensus TYRP2 protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:6.
Some embodiments relate to proteins that are identical to SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:6. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:6.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:6 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:6. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:6 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:6. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:6 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:6. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
(4) Melanoma-Associated Antigen 4 (MAGEA4)
The immunogenic composition of the present invention can comprise the cancer antigen Melanoma-associated Antigen 4 (MAGEA4), a fragment thereof, or a variant thereof. MAGE-A4, encoded by the MAGE-A4 gene, is a protein comprised of 317 amino acids and is expressed in male germ cells and tumor cells of various histological types such as gastrointestinal, esophageal and pulmonary carcinomas. MAGE-A4 binds the oncoprotein, Gankyrin. This MAGE-A4 specific binding is mediated by its C-terminus. Studies have shown that exogenous MAGE-A4 can partly inhibit the adhesion-independent growth of Gankyrin-overexpressing cells in vitro and suppress the formation of migrated tumors from these cells in nude mice. This inhibition is dependent upon binding between MAGE-A4 and Gankyrin, suggesting that interactions between Gankyrin and MAGE-A4 inhibit Gankyrin-mediated carcinogenesis. It is likely that MAGE expression in tumor tissue is not a cause, but a result of tumor genesis, and MAGE genes take part in the immune process by targeting early tumor cells for destruction.
Melanoma-associated antigen 4 protein (MAGEA4) can be involved in embryonic development and tumor transformation and/or progression. MAGEA4 is normally expressed in testes and placenta. MAGEA4, however, can be expressed in many different types of tumors, for example, melanoma, head and neck squamous cell carcinoma, lung carcinoma, and breast carcinoma. Accordingly, MAGEA4 can be antigen associated with a variety of tumors.
The MAGEA4 antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The MAGEA4 antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-MAGEA4 immune responses can be induced. The MAGEA4 antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The MAGEA4 antigen can comprise a consensus protein.
The nucleic acid sequence encoding the consensus MAGEA4 antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus MAGEA4 antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus MAGEA4 antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus MAGEA4 antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus MAGEA4 antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus Tyr antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus MAGEA4 antigen by a peptide bond. The nucleic encoding the consensus MAGEA4 antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus MAGEA4 antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
The consensus MAGEA4 antigen can be the nucleic acid sequence SEQ ID NO:7, which encodes for the amino acid sequence SEQ ID NO:8. SEQ ID NO:7 encodes the consensus MAGEA4 protein linked to an IgE leader sequence. The consensus MAGEA4 protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus MAGEA4 protein can be free of or not linked to an IgE leader sequence and/or an HA tag.
In some embodiments, the consensus MAGEA4 antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:7. In other embodiments, the consensus MAGEA4 antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:8. The consensus MAGEA4 antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:8.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the MAGEA4 consensus protein, immunogenic fragment of the MAGEA4 consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length MAGEA4 consensus protein, immunogenic fragment of the MAGEA4 consensus protein, and immunogenic fragments of proteins having identity to the MAGEA4 consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length MAGEA4 consensus sequence, up to 85% identity to a full length consensus sequence, up to 90% identity to a full length MAGEA4 consensus sequence, up to 91% identity to a full length MAGEA4 consensus sequence, up to 92% identity to a full length MAGEA4 consensus sequence, up to 93% identity to a full length MAGEA4 consensus sequence, up to 94% identity to a full length MAGEA4 consensus sequence, up to 95% identity to a full length MAGEA4 consensus sequence, up to 96% identity to a full length MAGEA4 consensus sequence, up to 97% identity to a full length MAGEA4 consensus sequence, up to 98% identity to a full length MAGEA4 consensus sequence, and up to 99% identity to a full length MAGEA4 consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the MAGEA4 proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:7. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:7. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:7. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:7. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus MAGEA4 protein is SEQ ID NO:8. The amino acid sequence of the consensus MAGEA4 protein linked to an IgE leader is SEQ ID NO:8. The amino acid sequence of the consensus MAGEA4 protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:8.
Some embodiments relate to proteins that are identical to SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:8. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:8.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:8 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:8. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:8 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:8. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:8 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:8. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
(5) Growth Hormone Releasing Hormone (GHRH)
The immunogenic composition of the present invention can comprise the cancer antigen growth hormone releasing hormone (GHRH; also known as growth-hormone-releasing factor (GRF or GHRF) or somatocrinin), a fragment thereof, or a variant thereof GHRH is a 44 amino acid peptide hormone produced in the arcuate nucleus of the hypothalamus. GHRH is secreted by the hypothalamus and stimulates the release of growth hormone, a regulator of growth, metabolism, and body structure, from the pituitary gland. GHRH also stimulates the product of growth hormone. Antagonists of GHRH can inhibit the growth of a variety of cancers, for example, osteosarcomas, glioblastomas, prostate cancer, renal cancer, pancreatic cancer, colorectal cancer, and breast cancer. Accordingly, GHRH can be an antigen associated with a variety of tumors.
The GHRH antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The GHRH antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-GHRH immune responses can be induced. The GHRH antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The GHRH antigen can comprise a consensus protein.
The nucleic acid sequence encoding the consensus GHRH antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus GHRH antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus GHRH antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus GHRH antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus GHRH antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus GHRH antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus GHRH antigen by a peptide bond. The nucleic encoding the consensus GHRH antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus GHRH antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
The consensus GHRH antigen can be the nucleic acid sequence SEQ ID NO:9, which encodes for the amino acid sequence SEQ ID NO:10. SEQ ID NO:9 encodes the consensus GHRH protein linked to an IgE leader sequence. The consensus GHRH protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus GHRH protein can be free of or not linked to an IgE leader sequence and/or an HA tag.
In some embodiments, the consensus GHRH antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:9. In other embodiments, the consensus GHRH antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:10. The consensus GHRH antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:10.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the GHRH consensus protein, immunogenic fragment of the GHRH consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length GHRH consensus protein, immunogenic fragment of the GHRH consensus protein, and immunogenic fragments of proteins having identity to the GHRH consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length GHRH consensus sequence, up to 85% identity to a full length consensus sequence, up to 90% identity to a full length GHRH consensus sequence, up to 91% identity to a full length GHRH consensus sequence, up to 92% identity to a full length GHRH consensus sequence, up to 93% identity to a full length GHRH consensus sequence, up to 94% identity to a full length GHRH consensus sequence, up to 95% identity to a full length GHRH consensus sequence, up to 96% identity to a full length GHRH consensus sequence, up to 97% identity to a full length GHRH consensus sequence, up to 98% identity to a full length GHRH consensus sequence, and up to 99% identity to a full length GHRH consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the GHRH proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:9. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:9. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:9. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:9. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus GHRH protein is SEQ ID NO:10. The amino acid sequence of the consensus GHRH protein linked to an IgE leader is SEQ ID NO:10. The amino acid sequence of the consensus GHRH protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:10.
Some embodiments relate to proteins that are identical to SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:10. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:10.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:10 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:10. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:10 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:10. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:10 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:10. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
(6) MART-1/Melan-A
The immunogenic composition of the present invention can comprise the cancer antigen MART-1 (also known as Melan-A), a fragment thereof, or a variant thereof. MART-1, encoded by MLANA gene, is a 118-amino acid protein containing a single transmembrane domain and is expressed in most melanoma cells. MART-1 forms a complex with a structural protein and affects its expression, stability, trafficking and processing which is required for melanosome structure and maturation. Accordingly, MART-1 is indispensable for regulating mammalian pigmentation. Defects in melanosome maturation have been linked to susceptibility to cancer. MART-1 may be expressed in numerous cancers, including, but not limited to, melanomas.
Melan-A, also known as melanoma antigen recognized by T cells (MART-1,) is a melanocyte differentiation antigen and can be found in normal skin, retina, and melanocytes. Melan-a can be associated with the endoplasmic reticulum and melanosomes. Melan-A can be recognized by cytotoxic T cells as an antigen on melanoma cells, but can also be associated with other tumors having melanocytic origin or differentiation (i.e., cells have melansomes), for example, clear cell sarcoma and melanotic neurofibroma. Accordingly, Melan-A can be antigen associated with a variety of tumors derived from cells having melanosomes.
The Melan-A antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The Melan-A antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-Melan-A immune responses can be induced. The Melan-A antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The Melan-A antigen can comprise a consensus protein.
The nucleic acid sequence encoding the consensus Melan-A antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus Melan-A antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus Melan-A antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus Melan-A antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus Melan-A antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus Melan-A antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus Melan-A antigen by a peptide bond. The nucleic encoding the consensus Melan-A antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus Melan-A antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
The consensus Melan-A antigen can be the nucleic acid sequence SEQ ID NO:11, which encodes for the amino acid sequence SEQ ID NO:12. SEQ ID NO:11 encodes the consensus MELAN-A protein linked to an IgE leader sequence. The consensus Melan-A protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus Melan-A protein can be free of or not linked to an IgE leader sequence and/or an HA tag.
In some embodiments, the consensus Melan-A antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:11. In other embodiments, the consensus Melan-A antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:12. The consensus Melan-A antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:12.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the Melan-A consensus protein, immunogenic fragment of the Melan-A consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length Melan-A consensus protein, immunogenic fragment of the Melan-A consensus protein, and immunogenic fragments of proteins having identity to the Melan-A consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length Melan-A consensus sequence, up to 85% identity to a full length Melan-A consensus sequence, up to 90% identity to a full length Melan-A consensus sequence, up to 91% identity to a full length Melan-A consensus sequence, up to 92% identity to a full length Melan-A consensus sequence, up to 93% identity to a full length Melan-A consensus sequence, up to 94% identity to a full length Melan-A consensus sequence, up to 95% identity to a full length Melan-A consensus sequence, up to 96% identity to a full length Melan-A consensus sequence, up to 97% identity to a full length Melan-A consensus sequence, up to 98% identity to a full length Melan-A consensus sequence, and up to 99% identity to a full length Melan-A consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the Melan-A proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:11. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:11. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:11. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:11. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus Melan-A protein is SEQ ID NO:12. The amino acid sequence of the consensus Melan-A protein linked to an IgE leader is SEQ ID NO:12. The amino acid sequence of the consensus Melan-A protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:12.
Some embodiments relate to proteins that are identical to SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:12. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:12.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:12 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:12. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:12 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:12. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:12 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:12. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
(7) NY-ESO-1
The immunogenic composition of the present invention can comprise the cancer antigen New York-esophageal cancer-1 (NY-ESO-1; also called CTAG1), a fragment thereof, or a variant thereof. NY-ESO-1, encoded by the CTAG1B gene, is a 180 amino-acid long protein, with a glycine-rich N-terminal region and an extremely hydrophobic C-terminal region. NY-ESO-1 has restricted expression in normal tissues but frequent occurrence in cancer. NY-ESO-1 may be expressed in numerous cancers including, but not limited to, bladder, colorectal, esophagus, gastric, hepatocarcinoma, head and neck, melanoma, non-small cell lung, ovarian, pancreatic, synovial carcinoma and prostate cancers.
Cancer-testis antigen (NY-ESO-1) can be expressed in the testis and ovary. NY-ESO-1 can be associated with a variety of cancers and can induce humoral immune responses. Subjects suffering from cancer or tumors can develop immunogenicity to NY-ESO-1. Accordingly, NY-ESO-1 can be an antigen associated with a variety of tumors.
The NY-ESO-1 antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The NY-ESO-1 antigen can increase a cellular immune response in a subject administered the NY-ESO-1 antigen by about 50-fold to about 6000-fold, about 50-fold to about 5500-fold, about 50-fold to about 5000-fold, about 50-fold to about 4500-fold, about 100-fold to about 6000-fold, about 150-fold to about 6000-fold, about 200-fold to about 6000-fold, about 250-fold to about 6000-fold, or about 300-fold to about 6000-fold as compared to a cellular immune response in a subject not administered the NY-ESO-1 antigen. In some embodiments the NY-ESO-1 antigen can increase the cellular immune response in the subject administered the NY-ESO-1 antigen by about 50-fold, 100-fold, 150-fold, 200-fold, 250-fold, 300-fold, 350-fold, 400-fold, 450-fold, 500-fold, 550-fold, 600-fold, 650-fold, 700-fold, 750-fold, 800-fold, 850-fold, 900-fold, 950-fold, 1000-fold, 1100-fold, 1200-fold, 1300-fold, 1400-fold, 1500-fold, 1600-fold, 1700-fold, 1800-fold, 1900-fold, 2000-fold, 2100-fold, 2200-fold, 2300-fold, 2400-fold, 2500-fold, 2600-fold, 2700-fold, 2800-fold, 2900-fold, 3000-fold, 3100-fold, 3200-fold, 3300-fold, 3400-fold, 3500-fold, 3600-fold, 3700-fold, 3800-fold, 3900-fold, 4000-fold, 4100-fold, 4200-fold, 4300-fold, 4400-fold, 4500-fold, 4600-fold, 4700-fold, 4800-fold, 4900-fold, 5000-fold, 5100-fold, 5200-fold, 5300-fold, 5400-fold, 5500-fold, 5600-fold, 5700-fold, 5800-fold, 5900-fold, or 6000-fold as compared to the cellular immune response in the subject not administered the NY-ESO-1 antigen.
The NY-ESO-1 antigen can increase interferon gamma (IFN-γ) levels in a subject administered the NY-ESO-1 antigen by about 50-fold to about 6000-fold, about 50-fold to about 5500-fold, about 50-fold to about 5000-fold, about 50-fold to about 4500-fold, about 100-fold to about 6000-fold, about 150-fold to about 6000-fold, about 200-fold to about 6000-fold, about 250-fold to about 6000-fold, or about 300-fold to about 6000-fold as compared to IFN-γ levels in a subject not administered the NY-ESO-1 antigen. In some embodiments, the NY-ESO-1 antigen can increase IFN-γ levels in the subject administered the NY-ESO-1 antigen by about 50-fold, 100-fold, 150-fold, 200-fold, 250-fold, 300-fold, 350-fold, 400-fold, 450-fold, 500-fold, 550-fold, 600-fold, 650-fold, 700-fold, 750-fold, 800-fold, 850-fold, 900-fold, 950-fold, 1000-fold, 1100-fold, 1200-fold, 1300-fold, 1400-fold, 1500-fold, 1600-fold, 1700-fold, 1800-fold, 1900-fold, 2000-fold, 2100-fold, 2200-fold, 2300-fold, 2400-fold, 2500-fold, 2600-fold, 2700-fold, 2800-fold, 2900-fold, 3000-fold, 3100-fold, 3200-fold, 3300-fold, 3400-fold, 3500-fold, 3600-fold, 3700-fold, 3800-fold, 3900-fold, 4000-fold, 4100-fold, 4200-fold, 4300-fold, 4400-fold, 4500-fold, 4600-fold, 4700-fold, 4800-fold, 4900-fold, 5000-fold, 5100-fold, 5200-fold, 5300-fold, 5400-fold, 5500-fold, 5600-fold, 5700-fold, 5800-fold, 5900-fold, or 6000-fold as compared to IFN-γ levels in the subject not administered the NY-ESO-1 antigen.
The NY-ESO-1 antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-NY-ESO-1 immune responses can be induced. The NY-ESO-1 antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The NY-ESO-1 antigen can comprise a consensus protein.
The nucleic acid sequence encoding the consensus NY-ESO-1 antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus NY-ESO-1 antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus NY-ESO-1 antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus NY-ESO-1 antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus NY-ESO-1 antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus NY-ESO-1 antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus NY-ESO-1 antigen by a peptide bond. The nucleic encoding the consensus NY-ESO-1 antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus NY-ESO-1 antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
The consensus NY-ESO-1 antigen can be the nucleic acid sequence SEQ ID NO:13, which encodes for the amino acid sequence SEQ ID NO:14. SEQ ID NO:13 encodes the consensus NY-ESO-1 protein linked to an IgE leader sequence. The consensus NY-ESO-1 protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus NY-ESO-1 protein can be free of or not linked to an IgE leader sequence and/or an HA tag.
In some embodiments, the consensus NY-ESO-1 antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:13. In other embodiments, the consensus NY-ESO-1 antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:14. The consensus NY-ESO-1 antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:14.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the NY-ESO-1 consensus protein, immunogenic fragment of the NY-ESO-1 consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length NY-ESO-1 consensus protein, immunogenic fragment of the NY-ESO-1 consensus protein, and immunogenic fragments of proteins having identity to the NY-ESO-1 consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length NY-ESO-1 consensus sequence, up to 85% identity to a full length consensus sequence, up to 90% identity to a full length NY-ESO-1 consensus sequence, up to 91% identity to a full length NY-ESO-1 consensus sequence, up to 92% identity to a full length NY-ESO-1 consensus sequence, up to 93% identity to a full length NY-ESO-1 consensus sequence, up to 94% identity to a full length NY-ESO-1 consensus sequence, up to 95% identity to a full length NY-ESO-1 consensus sequence, up to 96% identity to a full length NY-ESO-1 consensus sequence, up to 97% identity to a full length NY-ESO-1 consensus sequence, up to 98% identity to a full length NY-ESO-1 consensus sequence, and up to 99% identity to a full length NY-ESO-1 consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the NY-ESO-1 proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:13. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:13. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:13. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:13. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus NY-ESO-1 protein is SEQ ID NO:14. The amino acid sequence of the consensus NY-ESO-1 protein linked to an IgE leader is SEQ ID NO:14. The amino acid sequence of the consensus NY-ESO-1 protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:14.
Some embodiments relate to proteins that are identical to SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:14. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:14.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:14 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:14. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:14 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:14. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:14 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:14. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
(8) NY-ESO-2
The immunogenic composition of the present invention can comprise the cancer antigen New York-esophageal cancer-2 (NY-ESO-2; also known as cancer/testis antigen 2, ESO2, and LAGE1), a fragment thereof, or a variant thereof. NY-ESO-2 is an autoimmunogenic tumor antigen that belongs to the ESO/LAGE family of cancer-testis antigens. NY-ESO-2 can be expressed in a variety of cancers including melanoma, breast cancer, bladder cancer and prostate cancer and is normally expressed in testis tissue. Additionally, NY-ESO-2 can be observed in 25-50% of tumor samples of melanomas, non-small-cell lung carcinomas, bladder, prostate and head and neck cancers. The gene encoding NY-ESO-2 also contains an alternative open reading frame that encodes the protein named CAMEL, a tumor antigen that is recognized by melanoma-specific cytotoxic T-lymphocytes.
Similar to NY-ESO-1, NY-ESO-2 can be expressed in the testis and ovary. NY-ESO-2 can also be associated with a variety of cancers and immunogenic in subjects suffering from cancer or tumors. Accordingly, NY-ESO-2 can be an antigen associated with numerous tumors.
The NY-ESO-2 antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The NY-ESO-2 antigen can increase a cellular immune response in a subject administered the NY-ESO-2 antigen by about 50-fold to about 6000-fold, about 50-fold to about 5500-fold, about 50-fold to about 5000-fold, about 50-fold to about 4500-fold, about 100-fold to about 6000-fold, about 150-fold to about 6000-fold, about 200-fold to about 6000-fold, about 250-fold to about 6000-fold, or about 300-fold to about 6000-fold as compared to a cellular immune response in a subject not administered the NY-ESO-2 antigen. In some embodiments the NY-ESO-2 antigen can increase the cellular immune response in the subject administered the NY-ESO-2 antigen by about 50-fold, 100-fold, 150-fold, 200-fold, 250-fold, 300-fold, 350-fold, 400-fold, 450-fold, 500-fold, 550-fold, 600-fold, 650-fold, 700-fold, 750-fold, 800-fold, 850-fold, 900-fold, 950-fold, 1000-fold, 1100-fold, 1200-fold, 1300-fold, 1400-fold, 1500-fold, 1600-fold, 1700-fold, 1800-fold, 1900-fold, 2000-fold, 2100-fold, 2200-fold, 2300-fold, 2400-fold, 2500-fold, 2600-fold, 2700-fold, 2800-fold, 2900-fold, 3000-fold, 3100-fold, 3200-fold, 3300-fold, 3400-fold, 3500-fold, 3600-fold, 3700-fold, 3800-fold, 3900-fold, 4000-fold, 4100-fold, 4200-fold, 4300-fold, 4400-fold, 4500-fold, 4600-fold, 4700-fold, 4800-fold, 4900-fold, 5000-fold, 5100-fold, 5200-fold, 5300-fold, 5400-fold, 5500-fold, 5600-fold, 5700-fold, 5800-fold, 5900-fold, or 6000-fold as compared to the cellular immune response in the subject not administered the NY-ESO-2 antigen.
The NY-ESO-2 antigen can increase interferon gamma (IFN-γ) levels in a subject administered the NY-ESO-2 antigen by about 50-fold to about 6000-fold, about 50-fold to about 5500-fold, about 50-fold to about 5000-fold, about 50-fold to about 4500-fold, about 100-fold to about 6000-fold, about 150-fold to about 6000-fold, about 200-fold to about 6000-fold, about 250-fold to about 6000-fold, or about 300-fold to about 6000-fold as compared to IFN-γ levels in a subject not administered the NY-ESO-2 antigen. In some embodiments, the NY-ESO-2 antigen can increase IFN-γ levels in the subject administered the NY-ESO-2 antigen by about 50-fold, 100-fold, 150-fold, 200-fold, 250-fold, 300-fold, 350-fold, 400-fold, 450-fold, 500-fold, 550-fold, 600-fold, 650-fold, 700-fold, 750-fold, 800-fold, 850-fold, 900-fold, 950-fold, 1000-fold, 1100-fold, 1200-fold, 1300-fold, 1400-fold, 1500-fold, 1600-fold, 1700-fold, 1800-fold, 1900-fold, 2000-fold, 2100-fold, 2200-fold, 2300-fold, 2400-fold, 2500-fold, 2600-fold, 2700-fold, 2800-fold, 2900-fold, 3000-fold, 3100-fold, 3200-fold, 3300-fold, 3400-fold, 3500-fold, 3600-fold, 3700-fold, 3800-fold, 3900-fold, 4000-fold, 4100-fold, 4200-fold, 4300-fold, 4400-fold, 4500-fold, 4600-fold, 4700-fold, 4800-fold, 4900-fold, 5000-fold, 5100-fold, 5200-fold, 5300-fold, 5400-fold, 5500-fold, 5600-fold, 5700-fold, 5800-fold, 5900-fold, or 6000-fold as compared to IFN-γ levels in the subject not administered the NY-ESO-2 antigen.
The NY-ESO-2 antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-NY-ESO-2 immune responses can be induced. The NY-ESO-2 antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The NY-ESO-2 antigen can comprise a consensus protein.
The nucleic acid sequence encoding the consensus NY-ESO-2 antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus NY-ESO-2 antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus NY-ESO-2 antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus NY-ESO-2 antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus NY-ESO-2 antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus NY-ESO-2 antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus NY-ESO-2 antigen by a peptide bond. The nucleic encoding the consensus NY-ESO-2 antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus NY-ESO-2 antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
The consensus NY-ESO-2 antigen can be the nucleic acid sequence SEQ ID NO:15, which encodes for the amino acid sequence SEQ ID NO:16. SEQ ID NO:1 encodes the consensus NY-ESO-2 protein linked to an IgE leader sequence. The consensus NY-ESO-2 protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus NY-ESO-2 protein can be free of or not linked to an IgE leader sequence and/or an HA tag.
In some embodiments, the consensus NY-ESO-2 antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:15. In other embodiments, the consensus NY-ESO-2 antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:16. The consensus NY-ESO-2 antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:16.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the NY-ESO-2 consensus protein, immunogenic fragment of the NY-ESO-2 consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length NY-ESO-2 consensus protein, immunogenic fragment of the NY-ESO-2 consensus protein, and immunogenic fragments of proteins having identity to the NY-ESO-2 consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length NY-ESO-2 consensus sequence, up to 85% identity to a full length consensus sequence, up to 90% identity to a full length NY-ESO-2 consensus sequence, up to 91% identity to a full length NY-ESO-2 consensus sequence, up to 92% identity to a full length NY-ESO-2 consensus sequence, up to 93% identity to a full length NY-ESO-2 consensus sequence, up to 94% identity to a full length NY-ESO-2 consensus sequence, up to 95% identity to a full length NY-ESO-2 consensus sequence, up to 96% identity to a full length NY-ESO-2 consensus sequence, up to 97% identity to a full length NY-ESO-2 consensus sequence, up to 98% identity to a full length NY-ESO-2 consensus sequence, and up to 99% identity to a full length NY-ESO-2 consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the NY-ESO-2 proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:15. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:15. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:15. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:15. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus NY-ESO-2 protein is SEQ ID NO:16. The amino acid sequence of the consensus NY-ESO-2 protein linked to an IgE leader is SEQ ID NO:16. The amino acid sequence of the consensus NY-ESO-2 protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:16.
Some embodiments relate to proteins that are identical to SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:16. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:16.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:16 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:16. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:16 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:16. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:16 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:16. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
(9) PRAME
The immunogenic composition of the present invention can comprise the cancer antigen PRAME, a fragment thereof, or a variant thereof. PRAME, encoded by the PRAME gene, is a protein comprised of 509 amino acids and is expressed in testis, placenta, endometrium, ovary, adrenals, and in tissues derived from melanoma, lung, kidney, and head and neck carcinomas. PRAME is also expressed in adult and pediatric acute leukemias, and multiple myeloma. PRAME contains an immunogenic nonapeptide able to elicit a cytotoxic response when presented by HLA-A24. Studies show that overexpression of PRAME in cultured cells induces a caspace-independent cell death responsible for a slower proliferation rate. Other studies demonstrate that overexpression of PRAME also confers growth or survival advantages by antagonizing retinoic acid receptor (RAR) signaling, and is causally involved in the tumorigenic process. Interference of RAR signaling leads to a loss in regulating cellular proliferation, development and differentiation.
PRAME can have an expression pattern similar to the cancer-testis antigens MAGE, BAGE, and GAGE, namely expression in the testis. PRAME, however, can be expressed in human melanomas and acute leukemias. PRAME can be recognized by cytolytic T lymphocytes. Accordingly, PRAME can be an antigen associated with melanoma and leukemias.
The PRAME antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The PRAME antigen can increase a cellular immune response in a subject administered the PRAME antigen by about 50-fold to about 6000-fold, about 50-fold to about 5500-fold, about 50-fold to about 5000-fold, about 50-fold to about 4500-fold, about 100-fold to about 6000-fold, about 150-fold to about 6000-fold, about 200-fold to about 6000-fold, about 250-fold to about 6000-fold, or about 300-fold to about 6000-fold as compared to a cellular immune response in a subject not administered the PRAME antigen. In some embodiments the PRAME antigen can increase the cellular immune response in the subject administered the PRAME antigen by about 50-fold, 100-fold, 150-fold, 200-fold, 250-fold, 300-fold, 350-fold, 400-fold, 450-fold, 500-fold, 550-fold, 600-fold, 650-fold, 700-fold, 750-fold, 800-fold, 850-fold, 900-fold, 950-fold, 1000-fold, 1100-fold, 1200-fold, 1300-fold, 1400-fold, 1500-fold, 1600-fold, 1700-fold, 1800-fold, 1900-fold, 2000-fold, 2100-fold, 2200-fold, 2300-fold, 2400-fold, 2500-fold, 2600-fold, 2700-fold, 2800-fold, 2900-fold, 3000-fold, 3100-fold, 3200-fold, 3300-fold, 3400-fold, 3500-fold, 3600-fold, 3700-fold, 3800-fold, 3900-fold, 4000-fold, 4100-fold, 4200-fold, 4300-fold, 4400-fold, 4500-fold, 4600-fold, 4700-fold, 4800-fold, 4900-fold, 5000-fold, 5100-fold, 5200-fold, 5300-fold, 5400-fold, 5500-fold, 5600-fold, 5700-fold, 5800-fold, 5900-fold, or 6000-fold as compared to the cellular immune response in the subject not administered the PRAME antigen.
The PRAME antigen can increase interferon gamma (IFN-γ) levels in a subject administered the PRAME antigen by about 50-fold to about 6000-fold, about 50-fold to about 5500-fold, about 50-fold to about 5000-fold, about 50-fold to about 4500-fold, about 100-fold to about 6000-fold, about 150-fold to about 6000-fold, about 200-fold to about 6000-fold, about 250-fold to about 6000-fold, or about 300-fold to about 6000-fold as compared to IFN-γ levels in a subject not administered the PRAME antigen. In some embodiments, the PRAME antigen can increase IFN-γ levels in the subject administered the PRAME antigen by about 50-fold, 100-fold, 150-fold, 200-fold, 250-fold, 300-fold, 350-fold, 400-fold, 450-fold, 500-fold, 550-fold, 600-fold, 650-fold, 700-fold, 750-fold, 800-fold, 850-fold, 900-fold, 950-fold, 1000-fold, 1100-fold, 1200-fold, 1300-fold, 1400-fold, 1500-fold, 1600-fold, 1700-fold, 1800-fold, 1900-fold, 2000-fold, 2100-fold, 2200-fold, 2300-fold, 2400-fold, 2500-fold, 2600-fold, 2700-fold, 2800-fold, 2900-fold, 3000-fold, 3100-fold, 3200-fold, 3300-fold, 3400-fold, 3500-fold, 3600-fold, 3700-fold, 3800-fold, 3900-fold, 4000-fold, 4100-fold, 4200-fold, 4300-fold, 4400-fold, 4500-fold, 4600-fold, 4700-fold, 4800-fold, 4900-fold, 5000-fold, 5100-fold, 5200-fold, 5300-fold, 5400-fold, 5500-fold, 5600-fold, 5700-fold, 5800-fold, 5900-fold, or 6000-fold as compared to IFN-γ levels in the subject not administered the PRAME antigen.
The PRAME antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-PRAME immune responses can be induced. The PRAME antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The PRAME antigen can comprise a consensus protein.
The nucleic acid sequence encoding the consensus PRAME antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus PRAME antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus PRAME antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus PRAME antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus PRAME antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus PRAME antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus PRAME antigen by a peptide bond. The nucleic encoding the consensus PRAME antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus PRAME antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
The consensus PRAME antigen can be the nucleic acid sequence SEQ ID NO:17, which encodes for the amino acid sequence SEQ ID NO:18. SEQ ID NO:17 encodes the consensus PRAME protein linked to an IgE leader sequence. The consensus PRAME protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus PRAME protein can be free of or not linked to an IgE leader sequence and/or an HA tag.
In some embodiments, the consensus PRAME antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:17. In other embodiments, the consensus PRAME antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:18. The consensus PRAME antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:18.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the PRAME consensus protein, immunogenic fragment of the PRAME consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length PRAME consensus protein, immunogenic fragment of the PRAME consensus protein, and immunogenic fragments of proteins having identity to the PRAME consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length PRAME consensus sequence, up to 85% identity to a full length consensus sequence, up to 90% identity to a full length PRAME consensus sequence, up to 91% identity to a full length PRAME consensus sequence, up to 92% identity to a full length PRAME consensus sequence, up to 93% identity to a full length PRAME consensus sequence, up to 94% identity to a full length PRAME consensus sequence, up to 95% identity to a full length PRAME consensus sequence, up to 96% identity to a full length PRAME consensus sequence, up to 97% identity to a full length PRAME consensus sequence, up to 98% identity to a full length PRAME consensus sequence, and up to 99% identity to a full length PRAME consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the PRAME proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:17. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:17. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:17. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:17. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus PRAME protein is SEQ ID NO:18. The amino acid sequence of the consensus PRAME protein linked to an IgE leader is SEQ ID NO:18. The amino acid sequence of the consensus PRAME protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:18.
Some embodiments relate to proteins that are identical to SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:18. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:18.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:18 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:18. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:18 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:18. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:18 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:18. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
(10) PSA
The immunogenic composition of the present invention can comprise the cancer antigen prostate specific antigen (PSA; also known as gamma-seminoprotein or kallikrein-3 (KLK3)), a fragment thereof, or a variant thereof. PSA is an androgen-regulated serine protease produced by prostate epithelial cells and prostate cancer cells and encoded by the KLK3 gene. PSA is often used as a serum marker for prostate cancer. PSA is a member of the tissue kallikrein family and cleaves semenogelins in seminal coagulum after cleavage of the proenzyme to release the active enzyme, thereby liquefying semen to allow sperm to swim freely. Additionally, PSA enzymatic activity is regulated by zinc concentration, namely high zinc concentrations inhibit enzymatic activity of PSA.
The PSA antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The PSA antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-PSA immune responses can be induced. The PSMA antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The PSA antigen can comprise a consensus protein.
The consensus PSA antigen can be the nucleic acid sequence SEQ ID NO:63, which encodes for the amino acid sequence SEQ ID NO:64. The consensus PSA protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus PSA protein can be free of or not linked to an IgE leader sequence and/or an HA tag. The consensus PSA sequence can be operably linked to a regulatory sequence including, but not limited to, a start codon and at least one stop codon.
In some embodiments, the consensus PSA antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:63. In other embodiments, the consensus PSA antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:64. The consensus PSA antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:64.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the PSA consensus protein, immunogenic fragment of the PSA consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length PSA consensus protein, immunogenic fragment of the PSA consensus protein, and immunogenic fragments of proteins having identity to the PSA consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length PSA consensus sequence, up to 85% identity to a full length consensus sequence, up to 90% identity to a full length PSA consensus sequence, up to 91% identity to a full length PSA consensus sequence, up to 92% identity to a full length PSA consensus sequence, up to 93% identity to a full length PSA consensus sequence, up to 94% identity to a full length PSA consensus sequence, up to 95% identity to a full length PSA consensus sequence, up to 96% identity to a full length PSA consensus sequence, up to 97% identity to a full length PSA consensus sequence, up to 98% identity to a full length PSA consensus sequence, and up to 99% identity to a full length PSA consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the PSA proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:63. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:63. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:63. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:63. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus PSA protein is SEQ ID NO:64. The amino acid sequence of the consensus PSA protein linked to an IgE leader is SEQ ID NO:64. The amino acid sequence of the consensus PSA protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:64.
Some embodiments relate to proteins that are identical to SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:64. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:64.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:64 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:64. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:64 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:64. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:64 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:64. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
The nucleic acid sequence encoding the consensus PSA antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus PSA antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus PSA antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus PSA antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus PSA antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus PSA antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus PSA P antigen by a peptide bond. The nucleic encoding the consensus PSA antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus PSA antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
In some embodiments, the nucleic acid encoding the consensus PSA antigen can be a heterologous nucleic acid sequence and/or contain one or more heterologous nucleic acid sequences.
(11) PSMA
The immunogenic composition of the present invention can comprise the cancer antigen prostate specific membrane antigen (PSMA; also known as Glutamate carboxypeptidase II (GCPII), N-acetyl-L-aspartyl-L-glutamate peptidase I (NAALADase I), and NAAG peptidase), a fragment thereof, or a variant thereof. PSMA is encoded by the folate hydrolase 1 (FOLH1) gene. PSMA is a zinc metalloenzyme found residing in membranes and the extracellular space. PSMA is highly expressed in the human prostate and is upregulated in prostate cancer. PSMA is also found to be overexpressed in other cancers such as solid tumors of the kidney, breast, and colon.
The PSMA antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The PSMA antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-PSMA immune responses can be induced. The PSMA antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The PSMA antigen can comprise a consensus protein.
The consensus PSMA antigen can be the nucleic acid sequence SEQ ID NO:65, which encodes for the amino acid sequence SEQ ID NO:66. The consensus PSMA protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus PSMA protein can be free of or not linked to an IgE leader sequence and/or an HA tag. The consensus PSMA sequence can be operably linked to a regulatory sequence including, but not limited to, a start codon and at least one stop codon.
In some embodiments, the consensus PSMA antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:65. In other embodiments, the consensus PSMA antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:66. The consensus PSMA antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:66.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the PSMA consensus protein, immunogenic fragment of the PSMA consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length PSMA consensus protein, immunogenic fragment of the PSMA consensus protein, and immunogenic fragments of proteins having identity to the PSMA consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length PSMA consensus sequence, up to 85% identity to a full length consensus sequence, up to 90% identity to a full length PSMA consensus sequence, up to 91% identity to a full length PSMA consensus sequence, up to 92% identity to a full length PSMA consensus sequence, up to 93% identity to a full length PSMA consensus sequence, up to 94% identity to a full length PSMA consensus sequence, up to 95% identity to a full length PSMA consensus sequence, up to 96% identity to a full length PSMA consensus sequence, up to 97% identity to a full length PSMA consensus sequence, up to 98% identity to a full length PSMA consensus sequence, and up to 99% identity to a full length PSMA consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the PSMA proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:65. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:65. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:65. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:65. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus PSMA protein is SEQ ID NO:66. The amino acid sequence of the consensus PSMA protein linked to an IgE leader is SEQ ID NO:66. The amino acid sequence of the consensus PSMA protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:66.
Some embodiments relate to proteins that are identical to SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:66. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:66.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:66 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:66. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:66 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:66. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:66 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:66. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
The nucleic acid sequence encoding the consensus PSMA antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus PSMA antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus PSMA antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus PSMA antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus PSMA antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus PSMA antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus PSMA P antigen by a peptide bond. The nucleic encoding the consensus PSMA antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus PSMA antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
In some embodiments, the nucleic acid encoding the consensus PSMA antigen can be a heterologous nucleic acid sequence and/or contain one or more heterologous nucleic acid sequences.
(12) STEAP
The immunogenic composition of the present invention can comprise the cancer antigen six-transmembrane epithelial antigen of the prostate antigen (STEAP), a fragment thereof, or a variant thereof. STEAP is a metalloreductase encoded by the STEAP1 gene. STEAP is largely expressed in prostate tissues and is upregulated in cancer cells. STEAP is predicted to be a six-transmembrane protein and is a cell surface antigen found at cell-cell junctions.
The STEAP antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The STEAP antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-STEAP immune responses can be induced. The STEAP antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The STEAP antigen can comprise a consensus protein.
The consensus STEAP antigen can be the nucleic acid sequence SEQ ID NO:67, which encodes for the amino acid sequence SEQ ID NO:68. The consensus STEAP protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus STEAP protein can be free of or not linked to an IgE leader sequence and/or an HA tag. The consensus STEAP sequence can be operably linked to a regulatory sequence including, but not limited to, a start codon and at least one stop codon.
In some embodiments, the consensus STEAP antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:67. In other embodiments, the consensus STEAP antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:68. The consensus STEAP antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:68.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the STEAP consensus protein, immunogenic fragment of the STEAP consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length STEAP consensus protein, immunogenic fragment of the STEAP consensus protein, and immunogenic fragments of proteins having identity to the STEAP consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length STEAP consensus sequence, up to 85% identity to a full length consensus sequence, up to 90% identity to a full length STEAP consensus sequence, up to 91% identity to a full length STEAP consensus sequence, up to 92% identity to a full length STEAP consensus sequence, up to 93% identity to a full length STEAP consensus sequence, up to 94% identity to a full length STEAP consensus sequence, up to 95% identity to a full length STEAP consensus sequence, up to 96% identity to a full length STEAP consensus sequence, up to 97% identity to a full length STEAP consensus sequence, up to 98% identity to a full length STEAP consensus sequence, and up to 99% identity to a full length STEAP consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the STEAP proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:67. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:67. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:67. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:67. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus STEAP protein is SEQ ID NO:68. The amino acid sequence of the consensus STEAP protein linked to an IgE leader is SEQ ID NO:68. The amino acid sequence of the consensus STEAP protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:68.
Some embodiments relate to proteins that are identical to SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:68. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:68.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:68 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:68. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:68 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:68. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:68 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:68. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
The nucleic acid sequence encoding the consensus STEAP antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus STEAP antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus STEAP antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus STEAP antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus STEAP antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus STEAP antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus STEAP antigen by a peptide bond. The nucleic encoding the consensus STEAP antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus STEAP antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
In some embodiments, the nucleic acid encoding the consensus STEAP antigen can be a heterologous nucleic acid sequence and/or contain one or more heterologous nucleic acid sequences.
(13) PSCA
The immunogenic composition of the present invention can comprise the cancer antigen prostate specific stem cell antigen (PSCA), a fragment thereof, or a variant thereof. PSCA is a glycosylphosphatidylinositol (GPI)-anchored cell surface protein and is encoded by an androgen-responsive gene. PSCA is a member of the Thy-1/Ly-6 family of GPI-anchored cell surface antigens. PSCA is upregulated in many cancers including prostate, bladder, and pancreatic cancers.
The PSCA antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The PSCA antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-PSCA immune responses can be induced. The PSCA antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The PSCA antigen can comprise a consensus protein.
The consensus PSCA antigen can be the nucleic acid sequence SEQ ID NO:69, which encodes for the amino acid sequence SEQ ID NO:70. The consensus PSCA protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus PSCA protein can be free of or not linked to an IgE leader sequence and/or an HA tag. The consensus PSCA sequence can be operably linked to a regulatory sequence including, but not limited to, a start codon and at least one stop codon.
In some embodiments, the consensus PSCA antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:69. In other embodiments, the consensus PSCA antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:70. The consensus PSCA antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:70.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the PSCA consensus protein, immunogenic fragment of the PSCA consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length PSCA consensus protein, immunogenic fragment of the PSCA consensus protein, and immunogenic fragments of proteins having identity to the PSCA consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length PSCA consensus sequence, up to 85% identity to a full length consensus sequence, up to 90% identity to a full length PSCA consensus sequence, up to 91% identity to a full length PSCA consensus sequence, up to 92% identity to a full length PSCA consensus sequence, up to 93% identity to a full length PSCA consensus sequence, up to 94% identity to a full length PSCA consensus sequence, up to 95% identity to a full length PSCA consensus sequence, up to 96% identity to a full length PSCA consensus sequence, up to 97% identity to a full length PSCA consensus sequence, up to 98% identity to a full length PSCA consensus sequence, and up to 99% identity to a full length PSCA consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the PSCA proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:69. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:69. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:69. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:69. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus PSCA protein is SEQ ID NO:70. The amino acid sequence of the consensus PSCA protein linked to an IgE leader is SEQ ID NO:70. The amino acid sequence of the consensus PSCA protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:70.
Some embodiments relate to proteins that are identical to SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:70. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:70.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:70 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:70. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:70 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:70. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:70 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:70. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
The nucleic acid sequence encoding the consensus PSCA antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus PSCA antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus PSCA antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus PSCA antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus PSCA antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus PSCA antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus PSCA antigen by a peptide bond. The nucleic encoding the consensus PSCA antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus PSCA antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
In some embodiments, the nucleic acid encoding the consensus PSCA antigen can be a heterologous nucleic acid sequence and/or contain one or more heterologous nucleic acid sequences.
(14) MAGE A1
The immunogenic composition of the present invention can comprise the cancer antigen melanoma-associated antigen 1 (MAGE A1), a fragment thereof, or a variant thereof. MAGE A1, encoded by the MAGEA1 gene, is a 280-amino acid protein, and has been found only to be expressed by tumor cells and germ cells. MAGE A1 relies on DNA methylation for its repression in normal somatic tissues. These genes become activated in many types of tumors in the course of the genome-wide demethylation process, which often accompanies tumorgenesis. Specifically, during neoplastic transformation, these genes are activated, expressed, and may become antigenic targets that are recognized and attacked by the immune system. Therefore, MAGE genes take part in the immune process by targeting some early tumor cells for immune destruction. MAGE A1 may be expressed in numerous cancers, including, but not limited to, melanomas, lung carcenomas and esophageal squamous-cell carcinomas.
The MAGE A1 antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
(15) WT1
The immunogenic composition of the present invention can comprise the cancer antigen Wilm's tumor 1 (WT1), a fragment thereof, or a variant thereof. WT1 is a transcription factor containing at the N-terminus, a proline/glutamine-rich DNA-binding domain and at the C-terminus, four zinc finger motifs. WT1 plays a role in the normal development of the urogenital system and interacts with numerous factors, for example, p53, a known tumor suppressor and the serine protease HtrA2, which cleaves WT1 at multiple sites after treatment with a cytotoxic drug.
Mutation of WT1 can lead to tumor or cancer formation, for example, Wilm's tumor or tumors expressing WT1. Wilm's tumor often forms in one or both kidneys before metastasizing to other tissues, for example, but not limited to, liver tissue, urinary tract system tissue, lymph tissue, and lung tissue. Accordingly, Wilm's tumor can be considered a metastatic tumor. Wilm's tumor usually occurs in younger children (e.g., less than 5 years old) and in both sporadic and hereditary forms. The WT1 cancer antigen can further be defined by PCT/US13/75141, filed Dec. 23, 2013, which are hereby incorporated by reference in its' entirety.
The WT-1 antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
Accordingly, the immunogenic composition can be used for treating subjects suffering from Wilm's tumor. The immunogenic composition can be used for treating subjects suffering from any number of cancers including, but not limited to, melanoma, prostate cancer, liver cancer, cervical cancer, recurrent respiratory papillomatosis (RRP), anal cancer, head and neck cancer, and blood cancers. The immunogenic composition can also be used for treating subjects with cancers or tumors that express WT1 for preventing development of such tumors in subjects. The WT1 antigen can differ from the native, “normal” WT1 gene, and thus, provide therapy or prophylaxis against an WT1 antigen-expressing tumor. Accordingly, WT1 antigen sequences that differ from the native WT1 gene (i.e., mutated WT1 genes or sequences) are provided herein.
Transcripts of the native WT1 gene are processed into a variety of mRNAs, and the resulting proteins are not all of equal value for inducing an immune response. The mutated WT1 genes described herein avoid alternative processing, producing one full-length transcript and resulting in stronger induction of effector T and B cell responses. The first mutated WTI sequence is referred to as CON WT1 with modified Zinc Fingers or ConWT1-L. SEQ ID NO: 19 is a nucleic acid sequence encoding the WT1 antigen CON WT1 with modified Zinc Fingers. SEQ ID NO:20 is the amino acid sequence of WT1 antigen CON WT1 with modified Zinc Fingers. The second mutated WT1 sequence is referred to as CON WT1 without Zinc Fingers or ConWT1-S. SEQ ID NO:21 is a nucleic acid sequence encoding the WTI antigen CON WT1 without Zinc Fingers. SEQ ID NO:22 is the amino acid sequence of WT1 antigen CON WT1 without modified Zinc Fingers.
The WT1 antigen can be a consensus antigen (or immunogen) sequence derived from two or more species. The WT1 antigen can comprise a consensus sequence and/or modification(s) for improved expression. Modification can include codon optimization, RNA optimization, additional of a kozak sequence (e.g., GCC ACC) for increased translation initiation and/or the addition of an immunoglobulin leader sequence to increase the immunogenicity of the WT1 antigen. The WT1 antigen can comprise a signal peptide such as an immunoglobulin signal peptide, for example, but not limited to, an immunoglobulin E (IgE) or immunoglobulin G (IgG) signal peptide. In some embodiments, the WT1 consensus antigen can comprise a hemagglutinin (HA) tag. The WT1 consensus antigen can be designed to elicit stronger and broader cellular and/or humoral immune responses than a corresponding codon optimized WT1 antigen.
The WT1 consensus antigen can comprise one or more mutations in one or more zinc fingers, thereby eliciting stronger and broader cellular and/or humoral immune responses than a corresponding codon optimized WT1 antigen. The one or more mutations can be a substitution of one or more of the amino acids that coordinate the zinc ion in the one or more zinc fingers. The one or more amino acids that coordinate the zinc ion can be a CCHH motif. Accordingly, in some embodiments, the one or more mutations can replace 1, 2, 3, or all 4 amino acids of CCHH motif.
In other embodiments, the one or more mutations are such that residues 312, 317, 342, and 347 of SEQ ID NO:20 are any residue other than cysteine (C) and residues 330, 334, 360, and 364 of SEQ ID NO:20 are any residue other than histidine (H). In particular, the one or more mutations are such that residues 312, 317, 330, 334, 342, 347, 360, and 364 of SEQ ID NO:20 are glycine (G).
In other embodiments, one or more of the zinc fingers can be removed from the WT1 consensus antigen. One, two, three, or all four of the zinc fingers can be removed from the WT1 consensus antigen.
The WT1 consensus antigen can be the nucleic acid SEQ ID NO:19, which encodes SEQ ID NO:20. In some embodiments, the WT1 consensus antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity over an entire length of the nucleic acid sequence set forth in SEQ ID NO:19. In other embodiments, the WT1 consensus antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:20.
In still other embodiments, the WT1 consensus antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:20, provided that residues 312, 317, 342, and 347 of SEQ ID NO:20 are any residue other than cysteine (C) and residues 330, 334, 360, and 364 of SEQ ID NO:20 are any residue other than histidine (H). In other embodiments, the WT1 consensus antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:20, provided that residues 312, 317, 330, 334, 342, 347, 360, and 364 of SEQ ID NO:20 are glycine (G).
The WT1 consensus antigen can be the amino acid sequence SEQ ID NO:20. In some embodiments, the WT1 consensus antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:20. The WT1 consensus antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:20, provided that residues 312, 317, 342, and 347 of SEQ ID NO:20 are any residue other than cysteine (C) and residues 330, 334, 360, and 364 of SEQ ID NO:20 are any residue other than histidine (H). In some embodiments, the WT1 consensus antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:20, provided that residues 312, 317, 330, 334, 342, 347, 360, and 364 of SEQ ID NO:20 are glycine (G).
The WT1 consensus antigen can be the nucleic acid SEQ ID NO:21, which encodes SEQ ID NO:22. In some embodiments, the WT1 consensus antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity over an entire length of the nucleic acid sequence set forth in SEQ ID NO:21. In other embodiments, the WT1 consensus antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:22.
The WT1 consensus antigen can be the amino acid sequence SEQ ID NO:22. In some embodiments, the WT1 consensus antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:22.
Immunogenic fragments of SEQ ID NO:20 and SEQ ID NO:22 can be provided. Immunogenic fragments can comprise at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of SEQ ID NO:20 and/or SEQ ID NO:22. In some embodiments, immunogenic fragments can comprise at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of SEQ ID NO:20, provided that if residues 312, 317, 342, and 347 of SEQ ID NO:20 are present in the immunogenic fragment, then these residues are any residue other than cysteine (C), and provided that if residues 330, 334, 360, and 364 of SEQ ID NO:20 are present in the immunogenic fragment, then these residues are any residue other than histidine (H). In other embodiments, immunogenic fragments can comprise at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of SEQ ID NO:20, provided that if residues 312, 317, 330, 334, 342, 347, 360, and 364 of SEQ ID NO:20 are present in the immunogenic fragment, then these residues are glycine (G).
In some embodiments, immunogenic fragments include a leader sequence, for example, an immunoglobulin leader sequence, such as the immunoglobulin E (IgE) leader sequence. In some embodiments, immunogenic fragments are free of a leader sequence.
Immunogenic fragments of proteins with amino acid sequences having identity to immunogenic fragments of SEQ ID NO:20 and 22 can be provided. Such fragments can comprise at least 60%, at least 65%, at least 70%, at least 75%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of proteins having 95% or greater identity to SEQ ID NO:20 and/or SEQ ID NO:22. Some embodiments relate to immunogenic fragments that have 96% or greater identity to the immunogenic fragments of WT1 protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% or greater identity to the immunogenic fragments of WT1 protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% or greater identity to the immunogenic fragments of WT1 protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% or greater identity to the immunogenic fragments of WT1 protein sequences herein. In some embodiments, immunogenic fragments include a leader sequence, for example, an immunoglobulin leader sequence such as the IgE leader sequence. In some embodiments, the immunogenic fragments are free of a leader sequence.
Some embodiments relate to immunogenic fragments of SEQ ID NO:19 and SEQ ID NO:21. Immunogenic fragments can comprise at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of SEQ ID NO:19 and/or SEQ ID NO:21. In some embodiments, immunogenic fragments include sequences that encode a leader sequence, for example, an immunoglobulin leader sequence such as the IgE leader sequence. In some embodiments, immunogenic fragments are free of coding sequences that encode a leader sequence.
Immunogenic fragments of nucleic acids with nucleotide sequences having identity to immunogenic fragments of SEQ ID NO:19 and SEQ ID NO:21 can be provided. Such fragments can comprise at least 60%, at least 65%, at least 70%, at least 75%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% of nucleic acids having 95% or greater identity to SEQ ID NO:19 and/or SEQ ID NO:21. Some embodiments relate to immunogenic fragments that have 96% or greater identity to the immunogenic fragments of WT1 nucleic acid sequences herein. Some embodiments relate to immunogenic fragments that have 97% or greater identity to the immunogenic fragments of WT1 nucleic acid sequences herein. Some embodiments relate to immunogenic fragments that have 98% or greater identity to the immunogenic fragments of WT1 nucleic acid sequences herein. Some embodiments relate to immunogenic fragments that have 99% or greater identity to the immunogenic fragments of WT1 nucleic sequences herein. In some embodiments, immunogenic fragments include sequences that encode a leader sequence, for example, an immunoglobulin leader sequence such as the IgE leader sequence. In some embodiments, immunogenic fragments are free of coding sequences that encode a leader sequence.
(16) FAP
The immunogenic composition of the present invention can comprise the cancer antigen fibroblast activating protein (FAP), a fragment thereof, or a variant thereof. The FAP antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The FAP antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-FAP immune responses can be induced. The PSMA antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The FAP antigen can comprise a consensus protein.
The consensus FAP antigen can be the nucleic acid sequence SEQ ID NO:59, which encodes for the amino acid sequence SEQ ID NO:60. The consensus FAP protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus FAP protein can be free of or not linked to an IgE leader sequence and/or an HA tag. The consensus FAP sequence can be operably linked to a regulatory sequence including, but not limited to, a start codon and at least one stop codon.
In some embodiments, the consensus FAP antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:59. In other embodiments, the consensus FAP antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:60. The consensus FAP antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:60.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the FAP consensus protein, immunogenic fragment of the FAP consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length FAP consensus protein, immunogenic fragment of the FAP consensus protein, and immunogenic fragments of proteins having identity to the FAP consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length FAP consensus sequence, up to 85% identity to a full length consensus sequence, up to 90% identity to a full length FAP consensus sequence, up to 91% identity to a full length FAP consensus sequence, up to 92% identity to a full length FAP consensus sequence, up to 93% identity to a full length FAP consensus sequence, up to 94% identity to a full length FAP consensus sequence, up to 95% identity to a full length FAP consensus sequence, up to 96% identity to a full length FAP consensus sequence, up to 97% identity to a full length FAP consensus sequence, up to 98% identity to a full length FAP consensus sequence, and up to 99% identity to a full length FAP consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the FAP proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:59. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:59. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:59. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:59. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus FAP protein is SEQ ID NO:60. The amino acid sequence of the consensus FAP protein linked to an IgE leader is SEQ ID NO:60. The amino acid sequence of the consensus FAP protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:60.
Some embodiments relate to proteins that are identical to SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:60. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:60.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:60 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:60. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:60 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:60. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:60 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:60. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
The nucleic acid sequence encoding the consensus FAP antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus FAP antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus FAP antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus FAP antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus FAP antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus FAP antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus FAP P antigen by a peptide bond. The nucleic encoding the consensus FAP antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus FAP antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
In some embodiments, the nucleic acid encoding the consensus FAP antigen can be a heterologous nucleic acid sequence and/or contain one or more heterologous nucleic acid sequences.
(17) FSHR
The immunogenic composition of the present invention can comprise the cancer antigen follicle stimulating hormone receptor (FSHR) a fragment thereof, or a variant thereof. The FSHR antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
The FSHR antigen can comprise protein epitopes that make them particularly effective as immunogens against which anti-FSHR immune responses can be induced. The PSMA antigen can comprise the full length translation product, a variant thereof, a fragment thereof or a combination thereof. The FSHR antigen can comprise a consensus protein.
The consensus FSHR antigen can be the nucleic acid sequence SEQ ID NO:61, which encodes for the amino acid sequence SEQ ID NO:62. The consensus FSHR protein can be linked to the IgE leader sequence and an HA tag. In other embodiments, the consensus FSHR protein can be free of or not linked to an IgE leader sequence and/or an HA tag. The consensus FSHR sequence can be operably linked to a regulatory sequence including, but not limited to, a start codon and at least one stop codon.
In some embodiments, the consensus FSHR antigen can be the nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the nucleic acid sequence set forth in the SEQ ID NO:61. In other embodiments, the consensus FSHR antigen can be the nucleic acid sequence that encodes the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:62. The consensus FSHR antigen can be the amino acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity over an entire length of the amino acid sequence set forth in SEQ ID NO:62.
Some embodiments relate to nucleic acid sequences encoding proteins homologous to the FSHR consensus protein, immunogenic fragment of the FSHR consensus protein, and immunogenic fragments of homologous proteins. Such nucleic acid molecules that encode immunogenic proteins that have up to 95% homology to a consensus sequence, up to 96% homology to a consensus sequence, up to 97% homology to a consensus sequence, up to 98% homology to a consensus sequence and up to 99% can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins homologous to the proteins set forth herein are also provided.
Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 95% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 96% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 97% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 98% homology to the nucleic acid coding sequences herein. Some embodiments relate to nucleic acid molecules that encode immunogenic proteins that have 99% homology to the nucleic acid coding sequences herein. In some embodiments, the nucleic acid molecules with coding sequences disclosed herein that are homologous to a coding sequence of a consensus protein disclosed herein include sequences encoding an IgE leader sequence linked to the 5′ end of the coding sequence encoding the homologous protein sequences disclosed herein.
Some embodiments relate to nucleic acid sequences encoding proteins with a particular percent identity to the full length FSHR consensus protein, immunogenic fragment of the FSHR consensus protein, and immunogenic fragments of proteins having identity to the FSHR consensus protein. Such nucleic acid molecules that encode immunogenic proteins that have up to 80% identity to a full length FSHR consensus sequence, up to 85% identity to a full length consensus sequence, up to 90% identity to a full length FSHR consensus sequence, up to 91% identity to a full length FSHR consensus sequence, up to 92% identity to a full length FSHR consensus sequence, up to 93% identity to a full length FSHR consensus sequence, up to 94% identity to a full length FSHR consensus sequence, up to 95% identity to a full length FSHR consensus sequence, up to 96% identity to a full length FSHR consensus sequence, up to 97% identity to a full length FSHR consensus sequence, up to 98% identity to a full length FSHR consensus sequence, and up to 99% identity to a full length FSHR consensus sequence can be provided. Likewise, nucleic acid sequences encoding the immunogenic fragments set forth herein and the immunogenic fragments of proteins with similar percent identities as indicated above to the FSHR proteins set forth herein are also provided.
In some embodiments, the nucleic acid sequence is free of coding sequence that encodes a leader sequence. In some embodiments, the nucleic acid sequence is free of coding sequence that encodes the IgE leader.
Some embodiments relate to fragments of SEQ ID NO:61. Fragments can be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:61. Fragments can be at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to fragments of SEQ ID NO:61. Fragments can be at least 80%, at least 85%, at least 90% at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to fragments of SEQ ID NO:61. In some embodiments, fragments include sequences that encode a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of coding sequences that encode a leader sequence. In some embodiments, fragments are free of coding sequences that encode a leader sequence, such as for example, the IgE leader.
Furthermore, the amino acid sequence of the consensus FSHR protein is SEQ ID NO:62. The amino acid sequence of the consensus FSHR protein linked to an IgE leader is SEQ ID NO:62. The amino acid sequence of the consensus FSHR protein linked to the IgE leader may be linked to HA tag.
Some embodiments relate to proteins that are homologous to SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have 95% homology to the consensus protein sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have 96% homology to the consensus protein sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have 97% homology to the consensus protein sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have 98% homology to the consensus protein sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have 99% homology to the consensus protein sequences as set forth in SEQ ID NO:62.
Some embodiments relate to proteins that are identical to SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 80% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 85% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 90% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 91% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 92% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 93% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 94% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 95% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 96% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 97% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 98% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:62. Some embodiments relate to immunogenic proteins that have an amino acid sequence that is 99% identical to the full length consensus amino acid sequences as set forth in SEQ ID NO:62.
In some embodiments, the protein is free of a leader sequence. In some embodiments, the protein is free of the IgE leader. Fragments of consensus proteins can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of a consensus protein. Immunogenic fragments of SEQ ID NO:62 can be provided. Immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of SEQ ID NO:62. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences homologous to immunogenic fragments of SEQ ID NO:62 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 95% or greater homologous to SEQ ID NO:62. Some embodiments relate to immunogenic fragments that have 96% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 97% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 98% homology to the immunogenic fragments of consensus protein sequences herein. Some embodiments relate to immunogenic fragments that have 99% homology to the immunogenic fragments of consensus protein sequences herein. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
Immunogenic fragments of proteins with amino acid sequences identical to immunogenic fragments of SEQ ID NO:62 can be provided. Such immunogenic fragments can comprise at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55% at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of proteins that are 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequences set forth in SEQ ID NO:62. In some embodiments, fragments include a leader sequence, such as for example, an immunoglobulin leader, such as the IgE leader. In some embodiments, fragments are free of a leader sequence. In some embodiments, fragments are free of a leader sequence, such as for example, the IgE leader.
As referred to herein with regard to linking a signal peptide or leader sequence to the N terminus of a protein, the signal peptide/leader sequence replaces the N terminal methionine of a protein which is encoded by the start codon of the nucleic acid sequence than encodes the protein without a signal peptide coding sequences.
The nucleic acid sequence encoding the consensus FSHR antigen can be optimized with regards to codon usage and corresponding RNA transcripts. The nucleic acid encoding the consensus FSHR antigen can be codon and RNA optimized for expression. In some embodiments, the nucleic acid sequence encoding the consensus FSHR antigen can include a Kozak sequence (e.g., GCC ACC) to increase the efficiency of translation. The nucleic acid encoding the consensus FSHR antigen can include multiple stop codons (e.g., TGA TGA) to increase the efficiency of translation termination.
The nucleic acid encoding the consensus FSHR antigen can also encode an immunoglobulin E (IgE) leader sequence. The nucleic acid encoding the consensus FSHR antigen can further encode the IgE leader sequence such that the amino acid sequence of the IgE leader sequence is linked to the amino acid sequence of the consensus FSHR P antigen by a peptide bond. The nucleic encoding the consensus FSHR antigen can also include a nucleotide sequence encoding the IgE leader sequence. In some embodiments, the nucleic acid encoding the consensus FSHR antigen is free of or does not contain a nucleotide sequence encoding the IgE leader sequence.
In some embodiments, the nucleic acid encoding the consensus FSHR antigen can be a heterologous nucleic acid sequence and/or contain one or more heterologous nucleic acid sequences.
(18) gp100
The immunogenic composition of the present invention can comprise the cancer antigen glycoprotein 100 (gp100; also known as Trp2 and premelanosome protein (PMEL)), a fragment thereof, or a variant thereof gp100 is encoded by the PMEL gene. It is a 70 kDa type 1 transmembrane glycoprotein, comprised of 661 amino acids that plays a central role in the biogenesis of melanosomes as it is involved in the maturation of melanosomes from stage I to II. gp100 drives the formation of striations from within multivesicular bodies and is directly involved in the biogenesis of premelanosomes. gp100 is enriched in premelanosomes relative to mature melanosomes, but overexpressed by proliferating neonatal melanocytes and during tumor growth. The gp100 protein includes a variety of immunogenic epitopes that are recognized by cytotoxic T lymphocytes from peripheral blood of melanoma patients and from tumor infiltrating lymphocytes.
The gp100 antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
(19) Viral Antigens
The cancer antigen can be a viral antigen, a fragment thereof, or a variant thereof. The viral antigen can be antigen from a hepatitis B virus, a hepatitis C virus, or a human papilloma virus (HPV). The HPV can be HPV 6, HPV 11, HPV 16, or HPV 18 as discussed below.
The viral antigen can induce antigen-specific T cell and/or high titer antibody responses, thereby inducing or eliciting an immune response that is directed to or reactive against the cancer or tumor expressing the antigen. In some embodiments, the induced or elicited immune response can be a cellular, humoral, or both cellular and humoral immune responses. In some embodiments, the induced or elicited cellular immune response can include induction or secretion of interferon-gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α). In other embodiments, the induced or elicited immune response can reduce or inhibit one or more immune suppression factors that promote growth of the tumor or cancer expressing the antigen, for example, but not limited to, factors that down regulate MHC presentation, factors that up regulate antigen-specific regulatory T cells (Tregs), PD-L1, FasL, cytokines such as IL-10 and TFG-β, tumor associated macrophages, tumor associated fibroblasts, soluble factors produced by immune suppressor cells, CTLA-4, PD-1, MDSCs, MCP-1, and an immune checkpoint molecule, which is described below in more detail.
(a) Hepatitis B Virus Antigen
The viral antigen can be an antigen from Hepatitis B virus (HBV), a fragment thereof, or a variant thereof. The HBV antigen can be associated with or cause liver cancer. In some embodiments, the HBV antigen can be a heterologous nucleic acid molecule(s), such as a plasmid(s), which encodes one or more of the antigens from HBV. The HBV antigen can be full-length or immunogenic fragments of full-length proteins.
The HBV antigen can comprise consensus sequences and/or one or more modifications for improved expression. Genetic modifications, including codon optimization, RNA optimization, and the addition of a highly efficient immunoglobulin leader sequence to increase the immunogenicity of the constructs, can be included in the modified consensus sequences. The consensus HBV antigen may comprise a signal peptide such as an immunoglobulin signal peptide such as an IgE or IgG signal peptide, and in some embodiments, may comprise an HA tag. The immunogens can be designed to elicit stronger and broader cellular immune responses than corresponding codon optimized immunogens.
The HBV antigen can be a HBV core protein, a HBV surface protein, a HBV DNA polymerase, a HBV protein encoded by gene X, fragment thereof, variant thereof, or combination thereof. The HBV antigen can be a HBV genotype A core protein, a HBV genotype B core protein, a HBV genotype C core protein, a HBV genotype D core protein, a HBV genotype E core protein, a HBV genotype F core protein, a HBV genotype G core protein, a HBV genotype H core protein, a HBV genotype A surface protein, a HBV genotype B surface protein, a HBV genotype C surface protein, a HBV genotype D surface protein, a HBV genotype E surface protein, a HBV genotype F surface protein, a HBV genotype G surface protein, a HBV genotype H surface protein, fragment thereof, variant thereof, or combination thereof. The HBV antigen can be a consensus HBV core protein, or a consensus HBV surface protein.
In some embodiments, the HBV antigen can be a HBV genotype A consensus core nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype A core protein, or a HBV genotype A consensus core protein sequence.
In other embodiments, the HBV antigen can be a HBV genotype B consensus core nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype B core protein, or a HBV genotype B consensus core protein sequence.
In still other embodiments, the HBV antigen can be a HBV genotype C consensus core nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype C core protein, or a HBV genotype C consensus core protein sequence.
In some embodiments, the HBV antigen can be a HBV genotype D consensus core nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype D core protein, or a HBV genotype D consensus core protein sequence.
In other embodiments, the HBV antigen can be a HBV genotype E consensus core nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype E core protein, or a HBV genotype E consensus core protein sequence.
In some embodiments, the HBV antigen can be a HBV genotype F consensus core nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype F core protein, or a HBV genotype F consensus core protein sequence.
In other embodiments, the HBV antigen can be a HBV genotype G consensus core nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype G core protein, or a HBV genotype G consensus core protein sequence.
In some embodiments, the HBV antigen can be a HBV genotype H consensus core nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype H core protein, or a HBV genotype H consensus core protein sequence.
In still other embodiments, the HBV antigen can be a HBV genotype A consensus surface nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype A surface protein, or a HBV genotype A consensus surface protein sequence.
In some embodiments, the HBV antigen can be a HBV genotype B consensus surface nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype B surface protein, or a HBV genotype B consensus surface protein sequence.
In other embodiments, the HBV antigen can be a HBV genotype C consensus surface nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype C surface protein, or a HBV genotype C consensus surface protein sequence.
In still other embodiments, the HBV antigen can be a HBV genotype D consensus surface nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype D surface protein, or a HBV genotype D consensus surface protein sequence.
In some embodiments, the HBV antigen can be a HBV genotype E consensus surface nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype E surface protein, or a HBV genotype E consensus surface protein sequence.
In other embodiments, the HBV antigen can be a HBV genotype F consensus surface nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype F surface protein, or a HBV genotype F consensus surface protein sequence.
In still other embodiments, the HBV antigen can be a HBV genotype G consensus surface nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype G surface protein, or a HBV genotype G consensus surface protein sequence.
In other embodiments, the HBV antigen can be a HBV genotype H consensus surface nucleic acid sequence construct, an IgE leader sequence linked to a consensus sequence for HBV genotype H surface protein, or a HBV genotype H consensus surface protein sequence.
(b) Hepatitis C Virus Antigen
The viral antigen can be an antigen from Hepatitis C virus (HCV), a fragment thereof, or a variant thereof. The HCV antigen can be associated with or cause liver cancer. In some embodiments, the HCV antigen can be a heterologous nucleic acid molecule(s), such as a plasmid(s), which encodes one or more of the antigens from HCV. The HCV antigen can be full-length or immunogenic fragments of full-length proteins.
The HCV antigen can comprise consensus sequences and/or one or more modifications for improved expression. Genetic modifications, including codon optimization, RNA optimization, and the addition of a highly efficient immunoglobulin leader sequence to increase the immunogenicity of the constructs, can be included in the modified consensus sequences. The consensus HCV antigen may comprise a signal peptide such as an immunoglobulin signal peptide such as an IgE or IgG signal peptide, and in some embodiments, may comprise an HA tag. The immunogens can be designed to elicit stronger and broader cellular immune responses than corresponding codon optimized immunogens.
The HCV antigen can be a HCV nucleocapsid protein (i.e., core protein), a HCV envelope protein (e.g., E1 and E2), a HCV non-structural protein (e.g., NS1, NS2, NS3, NS4a, NS4b, NS5a, and NS5b), a fragment thereof, a variant thereof, or a combination thereof.
(c) Human Papilloma Virus
The viral antigen can be an antigen from HPV, a fragment thereof, or a variant thereof. The HPV antigen can be from HPV types 16, 18, 31, 33, 35, 45, 52, and 58, which cause cervical cancer, rectal cancer, and/or other cancers. The HPV antigen can be from HPV types 6 and/or 11, which cause genital warts, and are known to be causes of head and neck cancer. The HPV antigen can be from HPV types 16 and/or 18, which cause cervical cancer. The HPV antigen can be from HPV types 6, 11, and/or 16, which cause RRP and anal cancer. The HPV cancer antigen can further be defined by U.S. Pat. No. 8,168,769 filed Jul. 30, 2007, U.S. Pat. No. 8,389,706 filed Jan. 21, 2010, U.S. patent application Ser. No. 13/271,576 filed Oct. 21, 2011 and U.S. Patent Appl. No. 61/777,198, filed Mar. 12, 2013, each of which are incorporated by reference in their entirety.
The HPV antigens can be the HPV E6 or E7 domains from each HPV type. For example, for HPV type 16 (HPV16), the HPV16 antigen can include the HPV16 E6 antigen, the HPV16 E7 antigen, fragments, variants, or combinations thereof. Similarly, the HPV antigen can be HPV 6 E6 and/or E7, HPV 11 E6 and/or E7, HPV 16 E6 and/or E7, HPV 18 E6 and/or E7, HPV 31 E6 and/or E7, HPV 33 E6 and/or E7, HPV 52 E6 and/or E7, or HPV 58 E6 and/or E7, fragments, variants, or combinations thereof.
(d) Herpes Viruses
The viral antigen may be a herpes viral antigen. The herpes viral antigen can be an antigen selected from the group consisting of CMV, HSV1, HSV2, VZV, CeHV1, EBV, roseolovirus, Kaposi's sarcoma-associated herpesvirus, and MuHV.
A consensus protein HCMV-gB (SEQ ID NO:26), a consensus protein HCMV-gM (SEQ ID NO:28), a consensus protein HCMV-gN (SEQ ID NO:30), a consensus protein HCMV-gH (SEQ ID NO:32), a consensus protein HCMV-gL (SEQ ID NO:34), a consensus protein HCMV-gO (SEQ ID NO:36), a consensus protein HCMV-UL128 (SEQ ID NO:38), a consensus protein HCMV-UL130 (SEQ ID NO:40), a consensus protein HCMV-UL-131A (SEQ ID NO:42), a consensus protein HCMV-UL-83 (pp65) (SEQ ID NO:44).
Nucleic acid sequences including sequences encoding SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42 or SEQ ID NO: 44. Nucleic acid molecules encoding the consensus amino acid sequences were generated. Immunogenic compositions may comprise one or more nucleic acid sequences that encode one or more of the consensus versions of the immunogenic proteins selected from this group of sequences generated to optimize stability and expression in humans. Nucleic acid sequence encoding consensus protein HCMV-gB (SEQ ID NO:25), nucleic acid sequence encoding consensus protein HCMV-gM (SEQ ID NO:27), nucleic acid sequence encoding consensus protein HCMV-gN (SEQ ID NO:29), nucleic acid sequence encoding consensus protein HCMV-gH (SEQ ID NO:31), nucleic acid sequence encoding consensus protein HCMV-gL (SEQ ID NO:33), nucleic acid sequence encoding consensus protein HCMV-gO (SEQ ID NO:35), nucleic acid sequence encoding consensus protein HCMV-UL128 (SEQ ID NO:37), nucleic acid sequence encoding consensus protein HCMV-UL130 (SEQ ID NO:39), nucleic acid sequence encoding consensus protein HCMV-UL-131A (SEQ ID NO:41), nucleic acid sequence encoding consensus protein HCMV-UL-83 (pp65) (SEQ ID NO:43). The nucleic acid sequence can additionally have an encoding IgE leader linked to the 5′ end.
In view of evolutionary divergence from clinical isolates and extensive genetic differences among prevalent circulating human strains consensus amino acid sequences for each of immunogenic proteins have been generated. Consensus amino acid sequences for gB, gM, gH, gL, gE, gI, gK, gC, gD, UL128, UL130, UL-131A and UL-83 (pp65) were based upon sequences from human clinical isolates. Due to the great evolutionary divergence of the gN protein, the consensus sequence was generated from only one (gN-4c) of seven serotypes that represents the most sero-prevalent (gN-4). Similarly, in the case gO, a consensus amino acid sequences was generated from one (gO-5) of eight sero-types due to that particular serotypes reported linkage with the gN-4c sero-type.
As described above, the herpes viral antigen may be a consensus herpes virus. The consensus herpes viral antigen may be provided with a signal peptide. In some embodiments, the IgE leader is linked to the N terminus. As described herein, when referring to a signal peptide linked to the N terminus of a consensus sequence, it is intended to specifically include embodiments in which the N terminal Xaa residue of the consensus sequences is replaced with a signal peptide. That is, as used herein Xaa is intended to refer to any amino acid or no amino acid. The proteins which comprise a consensus sequence set forth herein SEQ ID NOs: 26, 28, 30, 32, 34, 36, 38, 40, 42, 44 may comprise those sequences free of the N terminal Xaa.
Amino acid sequences were generated which comprised in each particular instance, the IgE leader sequence at the N terminus of the herpes virus immunogenic protein consensus sequences. In some embodiments, nucleic acid constructs are provided in which two or more herpes virus antigens are expressed as fusion proteins linked to each other by proteolytic cleavage sites. A furin proteolytic cleavage site is an example of a proteolytic cleavage site which may link herpes virus antigens in a fusion protein expressed by a construct. The viral cancer antigen of the herpes family may further be any antigen disclosed in U.S. patent application Ser. No. 13/982,457, the contents of which is incorporated by reference in its' entirety.

4. IMMUNOGENIC COMPOSITION IN COMBINATION WITH IMMUNE CHECKPOINT INHIBITOR

The immunogenic composition can further comprise one or more inhibitors of one or more immune checkpoint molecules (i.e., an immune checkpoint inhibitor). Immune check point molecules are described below in more detail. The immune checkpoint inhibitor is any nucleic acid or protein that prevents the suppression of any component in the immune system such as MHC class presentation, T cell presentation and/or differentiation, B cell presentation and/or differentiation, any cytokine, chemokine or signaling for immune cell proliferation and/or differentiation.
Such an inhibitor can be a nucleic acid sequence, an amino acid sequence, a small molecule, or a combination thereof. The nucleic acid sequence can be DNA, RNA, cDNA, a variant thereof, a fragment thereof, or a combination thereof. The nucleic acid can also include additional sequences that encode linker or tag sequences that are linked to the immune checkpoint inhibitor by a peptide bond. The small molecule may be a low molecular weight, for example, less than 800 Daltons, organic or inorganic compound that can serve as an enzyme substrate, ligand (or analog thereof) bound by a protein or nucleic acid, or regulator of a biological process. The amino acid sequence can be protein, a peptide, a variant thereof, a fragment thereof, or a combination thereof.
In some embodiments, the immune checkpoint inhibitor can be one or more nucleic acid sequences encoding an antibody, a variant thereof, a fragment thereof, or a combination thereof. In other embodiments, the immune check point inhibitor can be an antibody, a variant thereof, a fragment thereof, or a combination thereof.
a. Immune Checkpoint Molecule
The immune check point molecule can be a nucleic acid sequence, an amino acid sequence, a small molecule, or a combination thereof. The nucleic acid sequence can be DNA, RNA, cDNA, a variant thereof, a fragment thereof, or a combination thereof. The nucleic acid can also include additional sequences that encode linker or tag sequences that are linked to the immune checkpoint inhibitor by a peptide bond. The small molecule may be a low molecular weight, for example, less than 800 Daltons, organic or inorganic compound that can serve as an enzyme substrate, ligand (or analog thereof) bound by a protein or nucleic acid, or regulator of a biological process. The amino acid sequence can be protein, a peptide, a variant thereof, a fragment thereof, or a combination thereof. The immune checkpoint molecule may be an inhibitor of at least one immune checkpoint protein. Immune checkpoint proteins include, but are not limited to, PD-1, PD-L1, CTLA4, TIM3 and LAG3.
b. Anti-Immune Checkpoint Molecule Antibody
As described above, the immune checkpoint inhibitor can be an antibody. The antibody can bind or react with an antigen (i.e., the immune checkpoint molecule described above.) Accordingly, the antibody may be considered an anti-immune checkpoint molecule antibody or an immune checkpoint molecule antibody. The antibody can be encoded by a nucleic acid sequence contained in
The antibody can include a heavy chain polypeptide and a light chain polypeptide. The heavy chain polypeptide can include a variable heavy chain (VH) region and/or at least one constant heavy chain (CH) region. The at least one constant heavy chain region can include a constant heavy chain region 1 (CH1), a constant heavy chain region 2 (CH2), and a constant heavy chain region 3 (CH3), and/or a hinge region.
In some embodiments, the heavy chain polypeptide can include a VH region and a CH1 region. In other embodiments, the heavy chain polypeptide can include a VH region, a CH1 region, a hinge region, a CH2 region, and a CH3 region.
The heavy chain polypeptide can include a complementarity determining region (“CDR”) set. The CDR set can contain three hypervariable regions of the VH region. Proceeding from N-terminus of the heavy chain polypeptide, these CDRs are denoted “CDR1,” “CDR2,” and “CDR3,” respectively. CDR1, CDR2, and CDR3 of the heavy chain polypeptide can contribute to binding or recognition of the antigen.
The light chain polypeptide can include a variable light chain (VL) region and/or a constant light chain (CL) region. The light chain polypeptide can include a complementarity determining region (“CDR”) set. The CDR set can contain three hypervariable regions of the VL region. Proceeding from N-terminus of the light chain polypeptide, these CDRs are denoted “CDR1,” “CDR2,” and “CDR3,” respectively. CDR1, CDR2, and CDR3 of the light chain polypeptide can contribute to binding or recognition of the antigen.
The antibody may comprise a heavy chain and a light chain complementarity determining region (“CDR”) set, respectively interposed between a heavy chain and a light chain framework (“FR”) set which provide support to the CDRs and define the spatial relationship of the CDRs relative to each other. The CDR set may contain three hypervariable regions of a heavy or light chain V region. Proceeding from the N-terminus of a heavy or light chain, these regions are denoted as “CDR1,” “CDR2,” and “CDR3,” respectively. An antigen-binding site, therefore, may include six CDRs, comprising the CDR set from each of a heavy and a light chain V region.
The antibody can be an immunoglobulin (Ig). The Ig can be, for example, IgA, IgM, IgD, IgE, and IgG. The immunoglobulin can include the heavy chain polypeptide and the light chain polypeptide. The heavy chain polypeptide of the immunoglobulin can include a VH region, a CH1 region, a hinge region, a CH2 region, and a CH3 region. The light chain polypeptide of the immunoglobulin can include a VL region and CL region.
Additionally, the proteolytic enzyme papain preferentially cleaves IgG molecules to yield several fragments, two of which (the F(ab) fragments) each comprise a covalent heterodimer that includes an intact antigen-binding site. The enzyme pepsin is able to cleave IgG molecules to provide several fragments, including the F(ab′)2 fragment, which comprises both antigen-binding sites. Accordingly, the antibody can be the Fab or F(ab′)2. The Fab can include the heavy chain polypeptide and the light chain polypeptide. The heavy chain polypeptide of the Fab can include the VH region and the CH1 region. The light chain of the Fab can include the VL region and CL region.
The antibody can be a polyclonal or monoclonal antibody. The antibody can be a chimeric antibody, a single chain antibody, an affinity matured antibody, a human antibody, a humanized antibody, or a fully human antibody. The humanized antibody can be an antibody from a non-human species that binds the desired antigen having one or more complementarity determining regions (CDRs) from the non-human species and framework regions from a human immunoglobulin molecule.
(1) PD-1 Antibody
The anti-immune checkpoint molecule antibody can be an anti-PD-1 antibody (also referred to herein as “PD-1 antibody”), a variant thereof, a fragment thereof, or a combination thereof. The PD-1 antibody can be Nivolumab. The anti-PD-1 antibody can inhibit PD-1 activity, thereby inducing, eliciting, or increasing an immune response against a tumor or cancer and decreasing tumor growth.
(2) PD-L1 Antibody
The anti-immune checkpoint molecule antibody can be an anti-PD-L1 antibody (also referred to herein as “PD-L1 antibody”), a variant thereof, a fragment thereof, or a combination thereof. The anti-PD-L1 antibody can inhibit PD-L1 activity, thereby inducing, eliciting, or increasing an immune response against a tumor or cancer and decreasing tumor growth.
(3) CTLA4 Antibody
The anti-immune checkpoint molecule antibody can be an anti-CTLA4 antibody (also referred to herein as “CTLA4 antibody”), a variant thereof, a fragment thereof, or a combination thereof. The anti-CTLA4 antibody can inhibit CTLA4 activity, thereby inducing, eliciting, or increasing an immune response against a tumor or cancer and decreasing tumor growth.
(4) TIM3 Antibody
The anti-immune checkpoint molecule antibody can be an anti-TIM3 antibody (also referred to herein as “TIM3 antibody”), a variant thereof, a fragment thereof, or a combination thereof. The anti-TIM3 antibody can inhibit TIM3 activity, thereby inducing, eliciting, or increasing an immune response against a tumor or cancer and decreasing tumor growth.
(5) LAG3 Antibody
The anti-immune checkpoint molecule antibody can be an anti-LAG3 antibody (also referred to herein as “LAG3 antibody”), a variant thereof, a fragment thereof, or a combination thereof. The anti-LAG3 antibody can inhibit LAG3 activity, thereby inducing, eliciting, or increasing an immune response against a tumor or cancer and decreasing tumor growth.

5. CONSTRUCTS AND PLASMIDS

The immunogenic composition can comprise nucleic acid constructs or plasmids that encode the above described antigens and/or antibodies. The nucleic acid constructs or plasmids can include or contain one or more heterologous nucleic acid sequences. Provided herein are genetic constructs that can comprise a nucleic acid sequence that encodes the above described antigens and/or antibodies. The genetic construct can be present in the cell as a functioning extrachromosomal molecule. The genetic construct can be a linear minichromosome including centromere, telomeres or plasmids or cosmids. The genetic constructs can include or contain one or more heterologous nucleic acid sequences.
The genetic construct can be useful for transfecting cells with nucleic acid encoding the above described antigens and/or antibodies, which the transformed host cell is cultured and maintained under conditions wherein expression of the above described antigens and/or antibodies takes place.
Coding sequences can be optimized for stability and high levels of expression. In some instances, codons are selected to reduce secondary structure formation of the RNA such as that formed due to intramolecular bonding.
The genetic constructs can be in the form of plasmids expressing the above described antigens and/or antibodies in any order.
Expression Vectors
The vector can be a circular plasmid or a linear nucleic acid. The circular plasmid and linear nucleic acid are capable of directing expression of a particular nucleotide sequence in an appropriate subject cell. The vector can have a promoter operably linked to the antigen-encoding nucleotide sequence, which may be operably linked to termination signals. The vector can also contain sequences required for proper translation of the nucleotide sequence. The vector comprising the nucleotide sequence of interest may be chimeric, meaning that at least one of its components is heterologous with respect to at least one of its other components. The expression of the nucleotide sequence in the expression cassette may be under the control of a constitutive promoter or of an inducible promoter, which initiates transcription only when the host cell is exposed to some particular external stimulus. In the case of a multicellular organism, the promoter can also be specific to a particular tissue or organ or stage of development.
RNA Vectors
In one embodiment, the nucleic acid is an RNA molecule. Accordingly, in one embodiment, the invention provides an RNA molecule encoding one or more MAYV antigens. The RNA may be plus-stranded. Accordingly, in some embodiments, the RNA molecule can be translated by cells without needing any intervening replication steps such as reverse transcription. A RNA molecule useful with the invention may have a 5′ cap (e.g. a 7-methylguanosine). This cap can enhance in vivo translation of the RNA. The 5′ nucleotide of a RNA molecule useful with the invention may have a 5′ triphosphate group. In a capped RNA this may be linked to a 7-methylguanosine via a 5′-to-5′ bridge. A RNA molecule may have a 3′ poly-A tail. It may also include a poly-A polymerase recognition sequence (e.g. AAUAAA) near its 3′ end. A RNA molecule useful with the invention may be single-stranded. In some embodiments, the RNA molecule is a naked RNA molecule. In one embodiment, the RNA molecule is comprised within a vector.
In one embodiment, the RNA has 5′ and 3′ UTRs. In one embodiment, the 5′ UTR is between zero and 3000 nucleotides in length. The length of 5′ and 3′ UTR sequences to be added to the coding region can be altered by different methods, including, but not limited to, designing primers for PCR that anneal to different regions of the UTRs. Using this approach, one of ordinary skill in the art can modify the 5′ and 3′ UTR lengths required to achieve optimal translation efficiency following transfection of the transcribed RNA.
The 5′ and 3′ UTRs can be the naturally occurring, endogenous 5′ and 3′ UTRs for the gene of interest. Alternatively, UTR sequences that are not endogenous to the gene of interest can be added by incorporating the UTR sequences into the forward and reverse primers or by any other modifications of the template. The use of UTR sequences that are not endogenous to the gene of interest can be useful for modifying the stability and/or translation efficiency of the RNA. For example, it is known that AU-rich elements in 3′ UTR sequences can decrease the stability of RNA. Therefore, 3′ UTRs can be selected or designed to increase the stability of the transcribed RNA based on properties of UTRs that are well known in the art.
In one embodiment, the 5′ UTR can contain the Kozak sequence of the endogenous gene. Alternatively, when a 5′ UTR that is not endogenous to the gene of interest is being added by PCR as described above, a consensus Kozak sequence can be redesigned by adding the 5′ UTR sequence. Kozak sequences can increase the efficiency of translation of some RNA transcripts, but does not appear to be required for all RNAs to enable efficient translation. The requirement for Kozak sequences for many RNAs is known in the art. In other embodiments, the 5′ UTR can be derived from an RNA virus whose RNA genome is stable in cells. In other embodiments, various nucleotide analogues can be used in the 3′ or 5′ UTR to impede exonuclease degradation of the RNA.
In one embodiment, the RNA has both a cap on the 5′ end and a 3′ poly(A) tail which determine ribosome binding, initiation of translation and stability of RNA in the cell.
In one embodiment, the RNA is a nucleoside-modified RNA. Nucleoside-modified RNA have particular advantages over non-modified RNA, including for example, increased stability, low or absent innate immunogenicity, and enhanced translation.
Circular and Linear Vectors
The vector may be a circular plasmid, which may transform a target cell by integration into the cellular genome or exist extrachromosomally (e.g., autonomous replicating plasmid with an origin of replication).
The vector can be pVAX, pcDNA3.0, or provax, or any other expression vector capable of expressing DNA encoding the antigen and enabling a cell to translate the sequence to an antigen that is recognized by the immune system.
Also provided herein is a linear nucleic acid immunogenic composition, or linear expression cassette (“LEC”), that is capable of being efficiently delivered to a subject via electroporation and expressing one or more desired antigens. The LEC may be any linear DNA devoid of any phosphate backbone. The DNA may encode one or more antigens. The LEC may contain a promoter, an intron, a stop codon, and/or a polyadenylation signal. The expression of the antigen may be controlled by the promoter. The LEC may not contain any antibiotic resistance genes and/or a phosphate backbone. The LEC may not contain other nucleotide sequences unrelated to the desired antigen gene expression.
The LEC may be derived from any plasmid capable of being linearized. The plasmid may be capable of expressing the antigen. The plasmid can be pNP (Puerto Rico/34) or pM2 (New Caledonia/99). The plasmid may be WLV009, pVAX, pcDNA3.0, or provax, or any other expression vector capable of expressing DNA encoding the antigen and enabling a cell to translate the sequence to an antigen that is recognized by the immune system.
The LEC can be perM2. The LEC can be perNP. perNP and perMR can be derived from pNP (Puerto Rico/34) and pM2 (New Caledonia/99), respectively.
Promoter, Intron, Stop Codon, and Polyadenylation Signal
The vector can comprise heterologous nucleic acid encoding the above described antigens and/or antibodies and can further comprise an initiation codon, which can be upstream of the one or more cancer antigen coding sequence(s), and a stop codon, which can be downstream of the coding sequence(s) of the above described antigens and/or antibodies.
The vector may have a promoter. A promoter may be any promoter that is capable of driving gene expression and regulating expression of the isolated nucleic acid. Such a promoter is a cis-acting sequence element required for transcription via a DNA dependent RNA polymerase, which transcribes the antigen sequence described herein. Selection of the promoter used to direct expression of a heterologous nucleic acid depends on the particular application. The promoter may be positioned about the same distance from the transcription start in the vector as it is from the transcription start site in its natural setting. However, variation in this distance may be accommodated without loss of promoter function.
The initiation and termination codon can be in frame with the coding sequence(s) of the above described antigens and/or antibodies. The vector can also comprise a promoter that is operably linked to the coding sequence(s) of the above described antigens and/or antibodies. The promoter operably linked to the coding sequence(s) of the above described antigens and/or antibodies can be a promoter from simian virus 40 (SV40), a mouse mammary tumor virus (MMTV) promoter, a human immunodeficiency virus (HIV) promoter such as the bovine immunodeficiency virus (BIV) long terminal repeat (LTR) promoter, a Moloney virus promoter, an avian leukosis virus (ALV) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter, Epstein Barr virus (EBV) promoter, or a Rous sarcoma virus (RSV) promoter. The promoter can also be a promoter from a human gene such as human actin, human myosin, human hemoglobin, human muscle creatine, or human metalothionein. The promoter can also be a tissue specific promoter, such as a muscle or skin specific promoter, natural or synthetic. Examples of such promoters are described in US patent application publication no. US20040175727, the contents of which are incorporated herein in its entirety.
The vector can also comprise a polyadenylation signal, which can be downstream of the coding sequence(s) of the above described antigens and/or antibodies. The polyadenylation signal can be a SV40 polyadenylation signal, LTR polyadenylation signal, bovine growth hormone (bGH) polyadenylation signal, human growth hormone (hGH) polyadenylation signal, or human β-globin polyadenylation signal. The SV40 polyadenylation signal can be a polyadenylation signal from a pCEP4 vector (Invitrogen, San Diego, Calif.).
The vector can also comprise an enhancer upstream of the the above described antigens and/or antibodies. The enhancer can be necessary for expression. The enhancer can be human actin, human myosin, human hemoglobin, human muscle creatine or a viral enhancer such as one from CMV, HA, RSV or EBV. Polynucleotide function enhances are described in U.S. Pat. Nos. 5,593,972, 5,962,428, and WO94/016737, the contents of each are fully incorporated by reference.
The vector may include an enhancer and an intron with functional splice donor and acceptor sites. The vector may contain a transcription termination region downstream of the structural gene to provide for efficient termination. The termination region may be obtained from the same gene as the promoter sequence or may be obtained from different genes.
Multiple Vectors
The immunogenic composition may comprise a plurality of copies of a single nucleic acid molecule such a single plasmid, or a plurality of copies of two or more different nucleic acid molecules such as two or more different plasmids. For example an immunogenic composition may comprise plurality of two, three, four, five, six, seven, eight, nine or ten or more different nucleic acid molecules. Such compositions may comprise plurality of two, three, four, five, six, or more different plasmids.
Immunogenic compositions may comprise nucleic acid molecules, such as plasmids, that collectively contain coding sequence for a single antigen. In one embodiment, the antigen is FAP. Immunogenic compositions may comprise nucleic acid molecules, such as plasmids, that collectively contain coding sequence for multiple antigens. As an example, in one embodiment, the antigens are multiple antigens selected from TERT and an additional cancer antigen. In one exemplary embodiment, the antigens are WT-1 and TERT. In one exemplary embodiment, the antigens are PSMA and TERT. In another exemplary embodiment, the antigens are TERT, WT-1 and PSMA. Immunogenic compositions may comprise nucleic acid molecules, such as plasmids, that collectively contain coding sequence for one or more antigen and one or more cancer antigen.
Origin of Replication
The vector can also comprise a mammalian origin of replication in order to maintain the vector extrachromosomally and produce multiple copies of the vector in a cell. The vector can be pVAX1, pCEP4 or pREP4 from Invitrogen (San Diego, Calif.), which can comprise the Epstein Barr virus origin of replication and nuclear antigen EBNA-1 coding region, which can produce high copy episomal replication without integration. The vector can be pVAX1 or a pVax1 variant with changes such as the variant plasmid described herein. The variant pVax1 plasmid is a 2998 basepair variant of the backbone vector plasmid pVAX1 (Invitrogen, Carlsbad Calif.). The CMV promoter is located at bases 137-724. The T7 promoter/priming site is at bases 664-683. Multiple cloning sites are at bases 696-811. Bovine GH polyadenylation signal is at bases 829-1053. The Kanamycin resistance gene is at bases 1226-2020. The pUC origin is at bases 2320-2993.
Based upon the sequence of pVAX1 available from Invitrogen, the following mutations were found in the sequence of pVAX1 that was used as the backbone for plasmids 1-6 set forth herein:
C>G241 in CMV promoter
C>T 1942 backbone, downstream of the bovine growth hormone polyadenylation signal (bGHpolyA)
A>- 2876 backbone, downstream of the Kanamycin gene
C>T 3277 in pUC origin of replication (Ori) high copy number mutation (see Nucleic Acid Research 1985)
G>C 3753 in very end of pUC Ori upstream of RNASeH site
Base pairs 2, 3 and 4 are changed from ACT to CTG in backbone, upstream of CMV promoter.
The backbone of the vector can be pAV0242. The vector can be a replication defective adenovirus type 5 (Ad5) vector.
The vector can also comprise a regulatory sequence, which can be well suited for gene expression in a mammalian or human cell into which the vector is administered. The one or more cancer antigen sequences disclosed herein can comprise a codon, which can allow more efficient transcription of the coding sequence in the host cell.
The vector can be pSE420 (Invitrogen, San Diego, Calif.), which can be used for protein production in Escherichia coli (E. coli). The vector can also be pYES2 (Invitrogen, San Diego, Calif.), which can be used for protein production in Saccharomyces cerevisiae strains of yeast. The vector can also be of the MAXBAC™ complete baculovirus expression system (Invitrogen, San Diego, Calif.), which can be used for protein production in insect cells. The vector can also be pcDNA I or pcDNA3 (Invitrogen, San Diego, Calif.), which maybe used for protein production in mammalian cells such as Chinese hamster ovary (CHO) cells. The vector can be expression vectors or systems to produce protein by routine techniques and readily available starting materials including Sambrook et al., Molecular Cloning and Laboratory Manual, Second Ed., Cold Spring Harbor (1989), which is incorporated fully by reference.

6. PHARMACEUTICAL COMPOSITIONS

The immunogenic composition can be in the form of a pharmaceutical composition. The pharmaceutical composition can comprise the immunogenic composition. The pharmaceutical compositions can comprise about 5 nanograms to about 10 mg of a nucleic acid molecule encoding an antigen of the invention. In some embodiments, pharmaceutical compositions according to the present invention comprise about 25 nanogram to about 5 mg of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 50 nanograms to about 1 mg of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 0.1 to about 500 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 1 to about 350 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 5 to about 250 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 10 to about 200 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 15 to about 150 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 20 to about 100 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 25 to about 75 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 30 to about 50 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 35 to about 40 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 100 to about 200 microgram of nucleic acid. In some embodiments, the pharmaceutical compositions comprise about 10 microgram to about 100 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions comprise about 20 micrograms to about 80 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions comprise about 25 micrograms to about 60 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions comprise about 30 nanograms to about 50 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions comprise about 35 nanograms to about 45 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 0.1 to about 500 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 1 to about 350 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 25 to about 250 micrograms of nucleic acid. In some embodiments, the pharmaceutical compositions contain about 100 to about 200 microgram nucleic acid.
In some embodiments, pharmaceutical compositions according to the present invention comprise at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 nanograms of nucleic acid. In some embodiments, the pharmaceutical compositions can comprise at least 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295, 300, 305, 310, 315, 320, 325, 330, 335, 340, 345, 350, 355, 360, 365, 370, 375, 380, 385, 390, 395, 400, 405, 410, 415, 420, 425, 430, 435, 440, 445, 450, 455, 460, 465, 470, 475, 480, 485, 490, 495, 500, 605, 610, 615, 620, 625, 630, 635, 640, 645, 650, 655, 660, 665, 670, 675, 680, 685, 690, 695, 700, 705, 710, 715, 720, 725, 730, 735, 740, 745, 750, 755, 760, 765, 770, 775, 780, 785, 790, 795, 800, 805, 810, 815, 820, 825, 830, 835, 840, 845, 850, 855, 860, 865, 870, 875, 880, 885, 890, 895. 900, 905, 910, 915, 920, 925, 930, 935, 940, 945, 950, 955, 960, 965, 970, 975, 980, 985, 990, 995 or 1000 micrograms of nucleic acid. In some embodiments, the pharmaceutical composition can comprise at least 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 mg or more of nucleic acid.
In other embodiments, the pharmaceutical composition can comprise up to and including 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 nanograms of nucleic acid. In some embodiments, the pharmaceutical composition can comprise up to and including 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295, 300, 305, 310, 315, 320, 325, 330, 335, 340, 345, 350, 355, 360, 365, 370, 375, 380, 385, 390, 395, 400, 405, 410, 415, 420, 425, 430, 435, 440, 445, 450, 455, 460, 465, 470, 475, 480, 485, 490, 495, 500, 605, 610, 615, 620, 625, 630, 635, 640, 645, 650, 655, 660, 665, 670, 675, 680, 685, 690, 695, 700, 705, 710, 715, 720, 725, 730, 735, 740, 745, 750, 755, 760, 765, 770, 775, 780, 785, 790, 795, 800, 805, 810, 815, 820, 825, 830, 835, 840, 845, 850, 855, 860, 865, 870, 875, 880, 885, 890, 895. 900, 905, 910, 915, 920, 925, 930, 935, 940, 945, 950, 955, 960, 965, 970, 975, 980, 985, 990, 995, or 1000 micrograms of nucleic acid. In some embodiments, the pharmaceutical composition can comprise up to and including 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 mg of nucleic acid.
The pharmaceutical composition can further comprise other agents for formulation purposes according to the mode of administration to be used. In cases where pharmaceutical compositions are injectable pharmaceutical compositions, they are sterile, pyrogen free and particulate free. In one embodiment, an isotonic formulation is used. Generally, additives for isotonicity can include sodium chloride, dextrose, mannitol, sorbitol and lactose. In some cases, isotonic solutions such as phosphate buffered saline are used. Stabilizers include gelatin and albumin. In some embodiments, a vasoconstriction agent is added to the formulation.
The immunogenic composition can further comprise a pharmaceutically acceptable excipient. The pharmaceutically acceptable excipient can be functional molecules as vehicles, adjuvants, carriers, or diluents. The pharmaceutically acceptable excipient can be a transfection facilitating agent, which can include surface active agents, such as immune-stimulating complexes (ISCOMS), Freunds incomplete adjuvant, LPS analog including monophosphoryl lipid A, muramyl peptides, quinone analogs, vesicles such as squalene and squalene, hyaluronic acid, lipids, liposomes, calcium ions, viral proteins, polyanions, polycations, or nanoparticles, or other known transfection facilitating agents.
The transfection facilitating agent is a polyanion, polycation, including poly-L-glutamate (LGS), or lipid. The transfection facilitating agent is poly-L-glutamate. In one embodiment, the poly-L-glutamate is present in the immunogenic composition at a concentration less than 6 mg/ml. The transfection facilitating agent can also include surface active agents such as immune-stimulating complexes (ISCOMS), Freunds incomplete adjuvant, LPS analog including monophosphoryl lipid A, muramyl peptides, quinone analogs and vesicles such as squalene and squalene, and hyaluronic acid can also be used administered in conjunction with the genetic construct. In some embodiments, the immunogenic composition can also include a transfection facilitating agent such as lipids, liposomes, including lecithin liposomes or other liposomes known in the art, as a DNA-liposome mixture (see for example WO9324640), calcium ions, viral proteins, polyanions, polycations, or nanoparticles, or other known transfection facilitating agents. In one embodiment, the transfection facilitating agent is a polyanion, polycation, including poly-L-glutamate (LGS), or lipid. Concentration of the transfection agent in the immunogenic composition is less than 4 mg/ml, less than 2 mg/ml, less than 1 mg/ml, less than 0.750 mg/ml, less than 0.500 mg/ml, less than 0.250 mg/ml, less than 0.100 mg/ml, less than 0.050 mg/ml, or less than 0.010 mg/ml.
The pharmaceutically acceptable excipient can be an adjuvant. The adjuvant can be other genes that are expressed in alternative plasmid or are delivered as proteins in combination with the plasmid above in the immunogenic composition. The adjuvant can be selected from the group consisting of: α-interferon (IFN-α), β-interferon (IFN-β), γ-interferon, platelet derived growth factor (PDGF), TNFα, TNFβ, GM-CSF, epidermal growth factor (EGF), cutaneous T cell-attracting chemokine (CTACK), epithelial thymus-expressed chemokine (TECK), mucosae-associated epithelial chemokine (MEC), IL-12, IL-15, MI-IC, CD80, CD86 including IL-15 having the signal sequence deleted and optionally including the signal peptide from IgE. The adjuvant can be IL-12, IL-15, IL-28, CTACK, TECK, platelet derived growth factor (PDGF), TNFα, TNFβ, GM-CSF, epidermal growth factor (EGF), IL-1, IL-2, IL-4, IL-5, IL-6, IL-10, IL-12, IL-18, or a combination thereof. In an exemplary embodiment, the adjuvant is IL-12.
Other genes which can be useful adjuvants include those encoding: MCP-1, MIP-la, MIP-1p, IL-8, RANTES, L-selectin, P-selectin, E-selectin, CD34, GlyCAM-1, MadCAM-1, LFA-1, VLA-1, Mac-1, p150.95, PECAM, ICAM-1, ICAM-2, ICAM-3, CD2, LFA-3, M-CSF, G-CSF, IL-4, mutant forms of IL-18, CD40, CD40L, vascular growth factor, fibroblast growth factor, IL-7, nerve growth factor, vascular endothelial growth factor, Fas, TNF receptor, Flt, Apo-1, p55, WSL-1, DR3, TRAMP, Apo-3, AIR, LARD, NGRF, DR4, DR5, KILLER, TRAIL-R2, TRICK2, DR6, Caspase ICE, Fos, c-jun, Sp-1, Ap-1, Ap-2, p38, p65Rel, MyD88, IRAK, TRAF6, IkB, Inactive NIK, SAP K, SAP-1, JNK, interferon response genes, NFkB, Bax, TRAIL, TRAILrec, TRAILrecDRC5, TRAIL-R3, TRAIL-R4, RANK, RANK LIGAND, Ox40, Ox40 LIGAND, NKG2D, MICA, MICB, NKG2A, NKG2B, NKG2C, NKG2E, NKG2F, TAP1, TAP2 and functional fragments thereof.

7. COMBINATIONAL IMMUNOGENIC COMPOSITIONS FOR TREATING PARTICULAR CANCERS

The immunogenic composition can be in the form of various combinations of the TERT antigen with one or more cancer antigens as described above to treat particular cancer or tumors. Depending upon the combination of one or more cancer antigens, various cancers or other tumor types may be targeted with the immunogenic composition. These cancers can include melanoma, blood cancers (e.g., leukemia, lymphoma, myeloma), lung carcinomas, esophageal squamous cell carcinomas, bladder cancer, colorectal cancer, esophagus, gastric cancer, hepatocarcinoma, head and neck, brain, anal cancer, non-small cell lung carcinoma, pancreatic cancer, synovial carcinoma, prostate cancer, testicular cancer, liver cancer, cervical cancer, recurrent respiratory papillomatosis, skin cancer and stomach cancer.
a. Melanoma
The immunogenic composition can combine a TERT antigen and one or more cancer antigens such as tyrosinase, PRAME, or GP100-Trp2 to treat or prevent melanoma. The immunogenic composition can further combine one or more cancer antigen tyrosinase, PRAME, or GP100-Trp2 with any one or more cancer antigens NY-ESO-1, MAGE-A1, or WTI for treating or preventing melanoma. Other combinations of cancer antigens may also be applied for treating or preventing melanoma.
b. Head and Neck Cancer
The immunogenic composition can comprise can combine a TERT antigen and one or more cancer antigen HPV 16 E6/E7 to treat or prevent head and neck cancer. The immunogenic composition can further combine cancer antigen HPV 16 E6/E7 with any one or more cancer antigens NY-ESO-1, MAGE-A1, or WTI for treating or preventing head and neck cancer. Other combinations of cancer antigens may also be applied for treating or preventing head and neck cancer.
c. Recurrent Respiratory Papillomatosis/Anal Cancer
The immunogenic composition can combine a TERT antigen and one or more cancer antigen one or more cancer antigens such as HPV 6, HPV11, or HPV 16 to treat or prevent recurrent respiratory papilloatosis or anal cancer. The immunogenic composition can further combine one or more cancer antigens HPV 6, HPV11 or HPV16 with one or more cancer antigens, NY-ESO-1, MAGE-A1, or WTI for treating or preventing recurrent respiratory papilloatosis or anal cancer. Other combinations of cancer antigens may also be applied for treating or preventing recurrent respiratory papilloatosis or anal cancer.
d. Cervical Cancer
The immunogenic composition can combine a TERT antigen and one or more cancer antigen one or more cancer antigens such as HPV 16 E6/E7 or HPV 18 E6/E7 to treat or prevent cervical cancer. The immunogenic composition can further combine one or more cancer antigens such as HPV 16 E6/E7 or HPV 18 E6/E7 with one or more cancer antigens NY-ESO-1, MAGE-A1, or WTI for treating or preventing cervical. Other combinations of cancer antigens may also be applied for treating or preventing cervical cancer.
e. Liver Cancer
The immunogenic composition can combine a TERT antigen and one or more cancer antigen such as HBV core antigen, HBV surface antigen, HCVNS34A, HCVNS5A, HCV NS5B, or HCVNS4B to treat or prevent liver cancer. The immunogenic composition can further combine one or more cancer antigens HBV core antigen, HBV surface antigen, HCVNS34A, HCVNS5A, HCV NS5B, or HCVNS4B with one or more of cancer antigens NY-ESO-1, MAGE-A1, or WTI for treating or preventing liver cancer. Other combinations of cancer antigens may also be applied for treating or preventing liver cancer.
f. Glioblastoma
The immunogenic composition can comprise a TERT antigen and one or more cancer antigen CMV to treat or prevent glioblastoma. The immunogenic composition can further combine CMV with one or more of cancer antigens NY-ESO-1, MAGE-A1, or WTI for treating or preventing glioblastoma. Other combinations of cancer antigens may also be applied for treating or preventing glioblastoma.
g. Prostate
The immunogenic composition can combine a TERT antigen and one or more cancer antigens such as PSA, PSMA, or STEAP to treat or prevent prostate cancer. The immunogenic composition can further combine one or more cancer antigens PSA, PSMA, or STEAP with one or more of cancer antigens NY-ESO-1, MAGE-A1, or WTI for treating or preventing prostate cancer. Other combinations of cancer antigens may also be applied for treating or preventing prostate cancer.
h. Blood Cancers (e.g., Leukemia, Lymphoma, Myeloma)
The immunogenic composition can combine a TERT antigen and one or more cancer antigens such as PRAME and WT-1 to treat or prevent blood cancers such as leukemia, lymphoma and myeloma. The immunogenic composition can further combine one or more cancer antigens PRAME and WT-1 with one or more of cancer antigens NY-ESO-1, or MAGE-A1 for treating or preventing blood cancers such as leukemia, lymphoma and myeloma. Other combinations of cancer antigens may also be applied for treating or preventing blood cancers such as leukemia, lymphoma and myeloma cancer.
i. Ovarian Cancers
The immunogenic composition can combine a TERT antigen and one or more cancer antigens such as a follicle stimulating hormone receptor (FSHR) antigen to treat or prevent ovarian cancer. The immunogenic composition can further combine FSHR with one or more of cancer antigens NY-ESO-1, or MAGE-A1 for treating or preventing ovarian cancer. Other combinations of cancer antigens may also be applied for treating or preventing ovarian cancer.
j. Other Cancers
The immunogenic composition can combine a TERT antigen and one or more cancer antigens such as FAP to treat or prevent cancers. The immunogenic composition can further combine FAP with one or more of cancer antigens NY-ESO-1, or MAGE-A1 for treating or preventing cancers. Other combinations of cancer antigens may also be applied for treating or preventing cancers.

8. METHOD OF VACCINATION

Provided herein is a method for treating or prevent cancer using the pharmaceutical formulations for providing genetic constructs and proteins of the one or more cancer antigens as described above, which comprise epitopes that make them particular effective immunogens against which an immune response to the one or more cancer antigens can be induced. The method of administering the immunogenic composition, or vaccination, can be provided to induce a therapeutic and/or prophylactic immune response. The vaccination process can generate in the mammal an immune response against one or more of the cancer antigens as disclosed herein. The immunogenic composition can be administered to an individual to modulate the activity of the mammal's immune system and enhance the immune response. The administration of the immunogenic composition can be the transfection of the one or more cancer antigens as disclosed herein as a nucleic acid molecule that is expressed in the cell and thus, delivered to the surface of the cell upon which the immune system recognizes and induces a cellular, humoral, or cellular and humoral response. The administration of the immunogenic composition can be used to induce or elicit an immune response in mammals against one or more of the cancer antigens as disclosed herein by administering to the mammals the immunogenic composition as discussed herein.
Upon administration of the immunogenic composition to the mammal, and thereupon the vector into the cells of the mammal, the transfected cells will express and secrete one or more of the cancer antigens as disclosed herein. These secreted proteins, or synthetic antigens, will be recognized as foreign by the immune system, which will mount an immune response that can include: antibodies made against the one or more cancer antigens, and T-cell response specifically against the one or more cancer antigens. In some examples, a mammal administered the immunogenic composition discussed herein will have a primed immune system and when challenged with the one or more cancer antigens as disclosed herein, the primed immune system will allow for rapid clearing of subsequent cancer antigens as disclosed herein, whether through the humoral, cellular, or both cellular and humoral immune responses. The immunogenic composition can be administered to an individual to modulate the activity of the individual's immune system, thereby enhancing the immune response.
Methods of administering the immunogenic composition are described in U.S. Pat. Nos. 4,945,050 and 5,036,006, both of which are incorporated herein in their entirety by reference.
The vaccine can be administered to a mammal to elicit an immune response in a mammal. The mammal can be human, non-human primate, cow, pig, sheep, goat, antelope, bison, water buffalo, bovids, deer, hedgehogs, elephants, llama, alpaca, mice, rats, or chicken.
The immunogenic composition dose can be between 1 μg to 10 mg active component/kg body weight/time and can be 20 μg to 10 mg component/kg body weight/time. The immunogenic composition can be administered every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 days. The number of immunogenic composition doses for effective treatment can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more doses.
a. Method of Generating an Immune Response with the Immunogenic Composition
The immunogenic composition can be used to generate an immune response in a mammal, including therapeutic or prophylactic immune response. The immune response can generate antibodies and/or killer T cells which are directed to the one or more cancer antigens as disclosed herein. Such antibodies and T cells can be isolated.
Some embodiments provide methods of generating immune responses against one or more of the cancer antigens as disclosed herein, which comprise administering to an individual the immunogenic composition. Some embodiments provide methods of prophylactically vaccinating an individual against a cancer or tumor expressing one or more of the cancer antigens as described above, which comprise administering the immunogenic composition. Some embodiments provide methods of therapeutically vaccinating an individual that has been suffering from the cancer or tumor expressing one or more of the cancer antigens, which comprise administering the immunogenic composition. Diagnosis of the cancer or tumor expressing the one or more cancer antigens as disclosed herein prior to administration of the immunogenic composition can be done routinely.
b. Method of Cancer Treatment with the Immunogenic Composition
The immunogenic composition can be used to generate or elicit an immune response in a mammal that is reactive or directed to a cancer or tumor (e.g., melanoma, head and neck, cervical, liver, prostate, blood cancers, esophageal squamous, gastric) of the mammal or subject in need thereof. The elicited immune response can prevent cancer or tumor growth.
The elicited immune response can prevent and/or reduce metastasis of cancerous or tumor cells. Accordingly, the immunogenic composition can be used in a method that treats and/or prevents cancer or tumors in the mammal or subject administered the immunogenic composition. Depending upon the antigen used in the immunogenic composition, the treated cancer or tumor based growth can be any type of cancer such as, but not limited to, melanoma, blood cancers (e.g., leukemia, lymphoma, myeloma), lung carcinomas, esophageal squamous cell carcinomas, bladder cancer, colorectal cancer, esophagus, gastric cancer, hepatocarcinoma, head and neck, brain, anal cancer, non-small cell lung carcinoma, pancreatic cancer, synovial carcinoma, prostate cancer, testicular cancer, liver cancer, cervical cancer, recurrent respiratory papillomatosis, skin cancer and stomach cancer.
In some embodiments, the administered immunogenic composition can mediate clearance or prevent growth of tumor cells by inducing (1) humoral immunity via B cell responses to generate antibodies that block monocyte chemoattractant protein-1 (MCP-1) production, thereby retarding myeloid derived suppressor cells (MDSCs) and suppressing tumor growth; (2) increase cytotoxic T lymphocyte such as CD8⁺ (CTL) to attack and kill tumor cells; (3) increase T helper cell responses; (4) and increase inflammatory responses via IFN-γ and TFN-α or a combination of the aforementioned.
In some embodiments, the immune response can generate a humoral immune response and/or an antigen-specific cytotoxic T lymphocyte (CTL) response that does not cause damage to or inflammation of various tissues or systems (e.g., brain or neurological system, etc.) in the subject administered the immunogenic composition.
In some embodiments, the administered immunogenic composition can increase tumor free survival, reduce tumor mass, increase tumor survival, or a combination thereof in the subject. The administered immunogenic composition can increase tumor free survival by 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, and 60% in the subject. The administered immunogenic composition can reduce tumor mass by 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, and 70% in the subject after immunization. The administered immunogenic composition can prevent and block increases in monocyte chemoattractant protein 1 (MCP-1), a cytokine secreted by myeloid derived suppressor cells, in the subject. In some embodiments, the administered immunogenic composition can prevent and block increases in MCP-1 within the cancerous or tumor tissue in the subject, thereby reducing vascularization of the cancerous or tumor tissue in the subject.
The administered immunogenic composition can increase tumor survival by 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, and 70% in the subject. In some embodiments, the immunogenic composition can be administered to the periphery (as described in more detail below) to establish an antigen-specific immune response targeting the cancerous or tumor cells or tissue to clear or eliminate the cancer or tumor expressing the one or more cancer antigens without damaging or causing illness or death in the subject administered the immunogenic composition.
The administered immunogenic composition can increase a cellular immune response in the subject by about 50-fold to about 6000-fold, about 50-fold to about 5500-fold, about 50-fold to about 5000-fold, about 50-fold to about 4500-fold, about 100-fold to about 6000-fold, about 150-fold to about 6000-fold, about 200-fold to about 6000-fold, about 250-fold to about 6000-fold, or about 300-fold to about 6000-fold. In some embodiments, the administered immunogenic composition can increase the cellular immune response in the subject by about 50-fold, 100-fold, 150-fold, 200-fold, 250-fold, 300-fold, 350-fold, 400-fold, 450-fold, 500-fold, 550-fold, 600-fold, 650-fold, 700-fold, 750-fold, 800-fold, 850-fold, 900-fold, 950-fold, 1000-fold, 1100-fold, 1200-fold, 1300-fold, 1400-fold, 1500-fold, 1600-fold, 1700-fold, 1800-fold, 1900-fold, 2000-fold, 2100-fold, 2200-fold, 2300-fold, 2400-fold, 2500-fold, 2600-fold, 2700-fold, 2800-fold, 2900-fold, 3000-fold, 3100-fold, 3200-fold, 3300-fold, 3400-fold, 3500-fold, 3600-fold, 3700-fold, 3800-fold, 3900-fold, 4000-fold, 4100-fold, 4200-fold, 4300-fold, 4400-fold, 4500-fold, 4600-fold, 4700-fold, 4800-fold, 4900-fold, 5000-fold, 5100-fold, 5200-fold, 5300-fold, 5400-fold, 5500-fold, 5600-fold, 5700-fold, 5800-fold, 5900-fold, or 6000-fold.
The administered immunogenic composition can increase interferon gamma (IFN-γ) levels in the subject by about 50-fold to about 6000-fold, about 50-fold to about 5500-fold, about 50-fold to about 5000-fold, about 50-fold to about 4500-fold, about 100-fold to about 6000-fold, about 150-fold to about 6000-fold, about 200-fold to about 6000-fold, about 250-fold to about 6000-fold, or about 300-fold to about 6000-fold. In some embodiments, the administered immunogenic composition can increase IFN-γ levels in the subject by about 50-fold, 100-fold, 150-fold, 200-fold, 250-fold, 300-fold, 350-fold, 400-fold, 450-fold, 500-fold, 550-fold, 600-fold, 650-fold, 700-fold, 750-fold, 800-fold, 850-fold, 900-fold, 950-fold, 1000-fold, 1100-fold, 1200-fold, 1300-fold, 1400-fold, 1500-fold, 1600-fold, 1700-fold, 1800-fold, 1900-fold, 2000-fold, 2100-fold, 2200-fold, 2300-fold, 2400-fold, 2500-fold, 2600-fold, 2700-fold, 2800-fold, 2900-fold, 3000-fold, 3100-fold, 3200-fold, 3300-fold, 3400-fold, 3500-fold, 3600-fold, 3700-fold, 3800-fold, 3900-fold, 4000-fold, 4100-fold, 4200-fold, 4300-fold, 4400-fold, 4500-fold, 4600-fold, 4700-fold, 4800-fold, 4900-fold, 5000-fold, 5100-fold, 5200-fold, 5300-fold, 5400-fold, 5500-fold, 5600-fold, 5700-fold, 5800-fold, 5900-fold, or 6000-fold.
The immunogenic composition dose can be between 1 μg to 10 mg active component/kg body weight/time and can be 20 μg to 10 mg component/kg body weight/time. The immunogenic composition can be administered every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 days. The number of immunogenic composition doses for effective treatment can be 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
(1) Combinational Therapies with Immune Checkpoint Targeting Antibodies
The present invention is also directed to a method of increasing an immune response in a mammal using the immunogenic composition as described above. The immunogenic composition as described above can comprise the cancer antigen and a PD1 antibody and/or PDL1 antibody as described above. The combination can be in a single formulation or can be separate and administered in sequence (either cancer antigen first and then immune checkpoint antibody or immune checkpoint antibody first and then cancer antigen). In some embodiments, the cancer antigen can be administered to the subject about 30 seconds, 1 minute, 2 minutes, 3 minutes, 4 minutes, 5 minutes, 10 minutes, 15 minutes, 20 minutes, 25 minutes, 30 minutes, 35 minutes, 40 minutes, 45 minutes, 50 minutes, 55 minutes, 60 minutes, 0.25 hours, 0.5 hours, 0.75 hours, 1 hours, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours, 23 hours, 24 hours, 36 hours, 48 hours, 60 hours, 72 hours, 84 hours, 96 hours, 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 21 days, 22 days, 23 days, 24 days, 25 days, 26 days, 27 days, 28 days, 29 days, 30 days, 31 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, or 8 weeks before the immune checkpoint antibody is administered to the subject. In other embodiments, the immune checkpoint antibody can be administered to the subject about 30 seconds, 1 minute, 2 minutes, 3 minutes, 4 minutes, 5 minutes, 10 minutes, 15 minutes, 20 minutes, 25 minutes, 30 minutes, 35 minutes, 40 minutes, 45 minutes, 50 minutes, 55 minutes, 60 minutes, 0.25 hours, 0.5 hours, 0.75 hours, 1 hours, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours, 23 hours, 24 hours, 36 hours, 48 hours, 60 hours, 72 hours, 84 hours, 96 hours, 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 21 days, 22 days, 23 days, 24 days, 25 days, 26 days, 27 days, 28 days, 29 days, 30 days, 31 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, or 8 weeks before the cancer antigen is administered to the subject.
The combination of the cancer antigen and immune checkpoint antibody induces the immune system more efficiently than an immunogenic composition comprising the cancer antigen alone. This more efficient immune response provides increased efficacy in the treatment and/or prevention of a particular cancer. Depending upon the antigen used in the immunogenic composition combined with the immune checkpoint antibody, the treated cancer or tumor based growth can be any type of cancer such as, but not limited to, melanoma, blood cancers (e.g., leukemia, lymphoma, myeloma), lung carcinomas, esophageal squamous cell carcinomas, bladder cancer, colorectal cancer, esophagus, gastric cancer, hepatocarcinoma, head and neck, brain, anal cancer, non-small cell lung carcinoma, pancreatic cancer, synovial carcinoma, prostate cancer, testicular cancer, liver cancer, cervical cancer, recurrent respiratory papillomatosis, skin cancer and stomach cancer.
In some embodiments, the immune response can be increased by about 0.5-fold to about 15-fold, about 0.5-fold to about 10-fold, or about 0.5-fold to about 8-fold. Alternatively, the immune response in the subject administered the immunogenic composition can be increased by at least about 0.5-fold, at least about 1.0-fold, at least about 1.5-fold, at least about 2.0-fold, at least about 2.5-fold, at least about 3.0-fold, at least about 3.5-fold, at least about 4.0-fold, at least about 4.5-fold, at least about 5.0-fold, at least about 5.5-fold, at least about 6.0-fold, at least about 6.5-fold, at least about 7.0-fold, at least about 7.5-fold, at least about 8.0-fold, at least about 8.5-fold, at least about 9.0-fold, at least about 9.5-fold, at least about 10.0-fold, at least about 10.5-fold, at least about 11.0-fold, at least about 11.5-fold, at least about 12.0-fold, at least about 12.5-fold, at least about 13.0-fold, at least about 13.5-fold, at least about 14.0-fold, at least about 14.5-fold, or at least about 15.0-fold.
In still other alternative embodiments, the immune response in the subject administered the immunogenic composition can be increased about 50% to about 1500%, about 50% to about 1000%, or about 50% to about 800%. In other embodiments, the immune response in the subject administered the immunogenic composition can be increased by at least about 50%, at least about 100%, at least about 150%, at least about 200%, at least about 250%, at least about 300%, at least about 350%, at least about 400%, at least about 450%, at least about 500%, at least about 550%, at least about 600%, at least about 650%, at least about 700%, at least about 750%, at least about 800%, at least about 850%, at least about 900%, at least about 950%, at least about 1000%, at least about 1050%, at least about 1100%, at least about 1150%, at least about 1200%, at least about 1250%, at least about 1300%, at least about 1350%, at least about 1450%, or at least about 1500%.
The immunogenic composition dose can be between 1 μg to 10 mg active component/kg body weight/time, and can be 20 μg to 10 mg component/kg body weight/time. The immunogenic composition can be administered every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 days. The number of immunogenic composition doses for effective treatment can be 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
(2) Cancer
The immunogenic composition can be used to generate or elicit an immune response in a mammal that is reactive or directed to a tumor in the mammal or subject in need thereof. The elicited immune response can prevent tumor growth. The elicited immune response can reduce tumor growth. The elicited immune response can prevent and/or reduce metastasis of cancerous or tumor cells. Accordingly, the immunogenic composition can be used in a method that treats and/or prevents cancer in the mammal or subject administered the immunogenic composition.
In some embodiments, the administered immunogenic composition can mediate clearance or prevent growth of tumor cells by inducing (1) humoral immunity via B cell responses to generate antibodies that block monocyte chemoattractant protein-1 (MCP-1) production, thereby retarding myeloid derived suppressor cells (MDSCs) and suppressing melanoma growth; (2) increase cytotoxic T lymphocyte such as CD8⁺ (CTL) to attack and kill melanoma cells; (3) increase T helper cell responses; (4) and increase inflammatory responses via IFN-γ and TFN-α or a combination of the aforementioned.
In some embodiments, the administered immunogenic composition can increase tumor free survival, reduce tumor mass, increase tumor-free survival, or a combination thereof in the subject. The administered immunogenic composition can increase tumor-free survival by 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, and 45% in the subject. The administered immunogenic composition can reduce tumor mass by 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, and 60% in the subject after immunization. The administered immunogenic composition can reduce vascularization of the tumor tissue in the subject. The administered immunogenic composition can increase tumor survival by 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, and 60% in the subject.

9. ROUTES OF ADMINISTRATION

The immunogenic composition or pharmaceutical composition can be administered by different routes including orally, parenterally, sublingually, transdermally, rectally, transmucosally, topically, via inhalation, via buccal administration, intrapleurally, intravenous, intraarterial, intraperitoneal, subcutaneous, intramuscular, intranasal intrathecal, and intraarticular or combinations thereof. For veterinary use, the composition can be administered as a suitably acceptable formulation in accordance with normal veterinary practice. The veterinarian can readily determine the dosing regimen and route of administration that is most appropriate for a particular animal. The immunogenic composition can be administered by traditional syringes, needleless injection devices, “microprojectile bombardment gone guns”, or other physical methods such as electroporation (“EP”), “hydrodynamic method”, or ultrasound.
The vector of the immunogenic composition can be administering to the mammal by several well known technologies including DNA injection (also referred to as DNA vaccination) with and without in vivo electroporation, liposome mediated, nanoparticle facilitated, recombinant vectors such as recombinant adenovirus, recombinant adenovirus associated virus and recombinant vaccinia. The one or more cancer antigens of the immunogenic composition can be administered via DNA injection and along with in vivo electroporation.
a. Electroporation
The immunogenic composition or pharmaceutical composition can be administered by electroporation. Administration of the immunogenic composition via electroporation can be accomplished using electroporation devices that can be configured to deliver to a desired tissue of a mammal a pulse of energy effective to cause reversible pores to form in cell membranes. In one embodiment, the pulse of energy is a constant current similar to a preset current input by a user. The electroporation device can comprise an electroporation component and an electrode assembly or handle assembly. The electroporation component can include and incorporate one or more of the various elements of the electroporation devices, including: controller, current waveform generator, impedance tester, waveform logger, input element, status reporting element, communication port, memory component, power source, and power switch. The electroporation can be accomplished using an in vivo electroporation device, for example CELLECTRA® EP system (Inovio Pharmaceuticals, Inc., Blue Bell, Pa.) or Elgen electroporator (Inovio Pharmaceuticals, Inc.) to facilitate transfection of cells by the plasmid.
Examples of electroporation devices and electroporation methods that can facilitate administration of the immunogenic compositions of the present invention, include those described in U.S. Pat. No. 7,245,963 by Draghia-Akli, et al., U.S. Patent Pub. 2005/0052630 submitted by Smith, et al., the contents of which are hereby incorporated by reference in their entirety. Other electroporation devices and electroporation methods that can be used for facilitating administration of the include those provided in co-pending and co-owned U.S. patent application Ser. No. 11/874,072, filed Oct. 17, 2007, which claims the benefit under 35 USC 119(e) to U.S. Provisional Application Ser. No. 60/852,149, filed Oct. 17, 2006, and 60/978,982, filed Oct. 10, 2007, all of which are hereby incorporated in their entirety.
U.S. Pat. No. 7,245,963 by Draghia-Akli, et al. describes modular electrode systems and their use for facilitating the introduction of a biomolecule into cells of a selected tissue in a body or plant. The modular electrode systems can comprise a plurality of needle electrodes; a hypodermic needle; an electrical connector that provides a conductive link from a programmable constant-current pulse controller to the plurality of needle electrodes; and a power source. An operator can grasp the plurality of needle electrodes that are mounted on a support structure and firmly insert them into the selected tissue in a body or plant. The biomolecules are then administering via the hypodermic needle into the selected tissue. The programmable constant-current pulse controller is activated and constant-current electrical pulse is applied to the plurality of needle electrodes. The applied constant-current electrical pulse facilitates the introduction of the biomolecule into the cell between the plurality of electrodes. The entire content of U.S. Pat. No. 7,245,963 is hereby incorporated by reference in its entirety.
U.S. Patent Pub. 2005/0052630 submitted by Smith, et al. describes an electroporation device which can be used to effectively facilitate the introduction of a biomolecule into cells of a selected tissue in a body or plant. The electroporation device comprises an electro-kinetic device (“EKD device”) whose operation is specified by software or firmware. The EKD device produces a series of programmable constant-current pulse patterns between electrodes in an array based on user control and input of the pulse parameters, and allows the storage and acquisition of current waveform data. The electroporation device also comprises a replaceable electrode disk having an array of needle electrodes, a central injection channel for an injection needle, and a removable guide disk. The entire content of U.S. Patent Pub. 2005/0052630 is hereby fully incorporated by reference.
The electrode arrays and methods described in U.S. Pat. No. 7,245,963 and U.S. Patent Pub. 2005/0052630 can be adapted for deep penetration into not only tissues such as muscle, but also other tissues or organs. Because of the configuration of the electrode array, the injection needle (to deneurological system the biomolecule of choice) is also inserted completely into the target organ, and the injection is administered perpendicular to the target issue, in the area that is pre-delineated by the electrodes. In one embodiment, the electrodes are 20 mm long and 21 gauge, as described in U.S. Pat. No. 7,245,963 and U.S. Patent Pub. 2005/005263.
Additionally, contemplated in some embodiments that incorporate electroporation devices and uses thereof, there are electroporation devices that are those described in the following patents: U.S. Pat. No. 5,273,525 issued Dec. 28, 1993, U.S. Pat. No. 6,110,161 issued Aug. 29, 2000, U.S. Pat. No. 6,261,281 issued Jul. 17, 2001, and U.S. Pat. No. 6,958,060 issued Oct. 25, 2005, and U.S. Pat. No. 6,939,862 issued Sep. 6, 2005. Furthermore, patents covering subject matter provided in U.S. Pat. No. 6,697,669 issued Feb. 24, 2004, which concerns administration of DNA using any of a variety of devices, and U.S. Pat. No. 7,328,064 issued Feb. 5, 2008, drawn to method of injecting DNA are contemplated herein. The above-patents are incorporated by reference in their entirety.

10. METHOD OF PREPARING THE IMMUNOGENIC COMPOSITION

Provided herein are methods for preparing nucleic acid molecules that comprise the immunogenic compositions discussed herein. The nucleic acid molecules can be used to inoculate a cell culture in a large scale fermentation tank, using known methods in the art.
The nucleic acid molecules for use with the EP devices of the present invention can be formulated or manufactured using a combination of known devices and techniques. In one embodiment, they are manufactured using an optimized plasmid manufacturing technique that is described in a US published application no. 20090004716, which was filed on May 23, 2007. In some examples, the nucleic acid molecules used in these studies can be formulated at concentrations greater than or equal to 10 mg/mL. The manufacturing techniques also include or incorporate various devices and protocols that are commonly known to those of ordinary skill in the art, in addition to those described in U.S. Ser. No. 60/939,792, including those described in a licensed patent, U.S. Pat. No. 7,238,522, which issued on Jul. 3, 2007. The above-referenced application and patent, U.S. Ser. No. 60/939,792 and U.S. Pat. No. 7,238,522, respectively, are hereby incorporated in their entirety.
The present invention has multiple aspects, illustrated by the following non-limiting examples.

11. EXAMPLES

Example 1

Construction of pTyr

As shown in FIGS. 1A and 9 , Tyrosinase (Tyr) can be found in many different organisms. Accordingly, a consensus Tyr was generated by aligning sequences corresponding to Tyr from the organisms shown in FIG. 1A, and choosing the most common amino acid and/or nucleotide for the consensus Tyr. The corresponding Tyr sequences for each organism were obtained from GenBank (NCBI). As such, the consensus Tyr reflected the conserved elements of Tyr sequences across species.
The nucleic acid sequence encoding the consensus Tyr was adapted to include the IgE leader sequence. Specifically, the IgE leader sequence was fused in frame upstream of the consensus Tyr nucleic acid sequence (FIG. 1B). The resulting sequence was then inserted into the pVax1 expression vector to create a Tyrosinase construct or plasmid (pTyr) such that a Kozak sequence preceded the nucleotide sequence encoding the IgE leader sequence and the consensus Tyr.
Insertion of the consensus Tyr nucleic acid sequence into pVax1 was confirmed by restriction enzyme analysis. As shown in FIG. 1C, the consensus Tyr nucleic acid sequence was separated from the pVax1 plasmid on a DNA agarose gel (i.e., the lane labeled BamH1/Xho1), thereby confirming that the pVax1 vector contained the consensus Tyr nucleic acid sequence.
Expression of the consensus Tyr was confirmed by transfecting HeLa cells with pTyr. Western blotting with a human anti-Tyr antibody confirmed expression of the consensus Tyr protein in HeLa cells (FIG. 1D). GPF staining further showed expression of the consensus Tyr protein in transfected HeLa cells (FIG. 1E). In both the western blotting and staining experiments,

Example 2

Vaccination with pTyr Induced a Cell Mediated Immune Response

The above described pTyr was used to vaccinate mice to evaluate whether a cellular immune response was induced by pTyr. C57/B6 mice were immunized using the immunization strategy shown in FIG. 2A. Some mice were immunized with pVax1 while other mice were immunized with pTyr. The mice immunized with pTyr were further broken into the following groups: (1) 5 μg dosage of pTyr; (2) 20 μg dosage of pTyr; (3) 30 μg dosage of pTyr; and (4) 60 μg dosage of pTyr.
At day 35 of the immunization strategy, splenocytes were isolated from the C57B/6 mice and evaluated for induction of interferon-γ (IFN-γ) by IFN-γ ELISpot analysis. As shown in FIG. 2B, the 20 μg dosage of pTyr induced the highest levels of IFN-γ.
The cellular immune response to pTyr was further evaluated in immunized Balb/c and C57B/6 mice. Mice were immunized with either pVax1 or pTyr. Splenocytes were isolated two weeks after the third immunization and stimulated with the consensus Tyr peptide. After stimulation, the number of IFN-γ secreting splenocytes was calculated as the average number of spots in the triplicate stimulant wells. This assay indicated that C57/B6 mice were suitable for pTyr vaccination (data not shown).

Example 3

pTyr Vaccination Increased Cytokines IFN-γ and TNF-α

Cytokine production was examined in mice immunized with pTyr and pVax1. Mice were immunized using the strategy shown in FIG. 2A. At day 35 of the immunization strategy, cells isolated from the immunized mice were stimulated overnight with Tyr peptides. After stimulation, analysis of the polyfunctional responses was measured by FACS. Specifically, the analysis examined CD8⁺ and CD4⁺ T cells. FACS allowed for the identification of T cells positive for the cytokines IL-2, TNF-α, and IFN-γ. Of the CD44 hi cells, a significant percentage of CD8⁺ T cells produced IFN-γ in the mice immunized with pTyr as compared to mice immunized with pVax1 (FIG. 3 ).

Example 4

Tyr Specific Antibodies are Produced in Response to pTyr Vaccination

The humoral immune response was examined in mice vaccinated with pTyr. Specifically, C57BI/6 mice (n=4) were immunized three times at 2-week intervals with either pTyr or pVax1. Each immunization consisted of a 20 μg/intramuscular injection followed by electroporation with MID-EP. After the third immunization (i.e., day 35), serum was collected from the mice and antibody titers were measured by ELISA using total IgG-specific HRP labeled secondary antibodies. The sera were diluted as indicated in FIG. 4A. As shown in FIG. 4A, specific antibodies to Tyr were produced by the mice immunized with pTyr. Mice immunized with pTyr are represented by the filled circle in FIG. 4A while mice immunized with pVax1 are represented by the open triangle in FIG. 4A.
Additionally, the sera from the immunized mice were serially diluted at 1:20, 1:40, 1:80, 1:160, 1:320, and 1:640. Each serum dilution was added in triplicate to individual wells (50 μl/well) containing Tyr peptides. The peak increase in Tyr-specific titer, compared to the preimmune serum, was detected for all immunized groups of mice at recheck days 90 and 120. Representative results of three independent experiments at each serial dilution point are shown in FIG. 4B. These data further indicated that immunization with pTyr induced production of Tyr specific antibodies in mice immunized with pTyr.

Example 5

Mice Vaccinated with pTyr have Increased Survival to Tumor Challenge

pTry was further analyzed to determine if pTyr vaccination could provide protection from tumors. Specifically, C57BI/6 mice (10 per group) were immunized at 2-week intervals with either pTyr or pVax1. Each immunization consisted of a 20 μg/intramuscular injection followed by electroporation with MID-EP. One week after the third immunization (i.e., day 35), the immunized mice were challenged intradermally with B16 melanoma until the tumor diameter exceeded 200 mm².
Subsequently, tumor-free survival and tumor volume was evaluated in the immunized groups of mice. As shown in FIG. 5A (a Kaplan-Meier survival curve), mice immunized with pTyr were improved in tumor-free survival (i.e., 40% at days 40 and on after tumor challenge) as compared to mice vaccinated with pVax1 (p=0.05), which were all dead by day 20 after tumor challenge. Mice immunized with pTyr also had reduced tumor volume (i.e., about 50%) as compared to mice immunized with pVax1 (FIG. 5B). For both FIGS. 5A and 5B, mice immunized with pVax1 are represented by filled squares while mice immunized with pTyr are represented by filled circles. Accordingly, these data showed that pTyr vaccination provided protection against melanoma, namely increased tumor-free survival and reduction in tumor volume.

Example 6

MDSC Population is Reduced in Tumors from Mice Vaccinated with pTyr

MDSC populations were examined in mice immunized with pTyr and non-immunized mice to examine whether vaccination with pTyr altered levels of MDSCs in tumors from the respective groups of mice. Specifically, the percentage of Gr-1+ and CD11b+ cells were examined in the immunized and non-immunized mice.
As shown in FIGS. 6 and 7 , MDSC levels were significantly reduced within tumors from mice immunized with pTyr as compared to non-immunized mice (p=0.0004). The percentage of MDSC population in non-immunized mice was 40.00±4.826. The percentage of MDSC population in mice immunized with pTyr was 5.103±0.7718. Accordingly, these data showed that immunization with pTyr reduced MDSC populations within tumors of mice vaccinated with pTyr.

Example 7

MCP-1 Levels are Reduced by pTyr Vaccination

MDSCs can secrete the cytokine MCP-1, which promotes angiogenesis or vascularization by migration of endothelial cells. Given the above described effect of pTyr vaccination on MDSC levels in tumors, MCP-1 levels were examined after vaccination with pTyr.
As shown in FIG. 8A, MDSCs within the B16 melanoma can secrete MCP-1. As such, mice immunized with pTyr and mice immunized with pVax1 were challenged with the B16 melanoma to examine whether pTyr immunization altered MCP-1 levels. Naïve mice were included as a further control. After the challenge, MDSCs were isolated directly from the tumor tissue, and MCP-1 cytokine levels were analyzed ELISA. The experiment was performed in triplicate and repeated two times.
As shown in FIG. 8B, MDSCs within the B16 melanoma or tumor tissue significantly secreted MCP-1 (see pVax1 immunized mice). Mice immunized with pTyr, however, did not have a significant increase in MCP-1 levels. Rather, MCP-1 levels in mice immunized with pTyr were about 3-fold lower than mice immunized with pVax1. Accordingly, these data showed that pTyr vaccination reduced the level of MCP-1 secretion by MDSCs within tumors of mice immunized with pTyr.

Example 8

Construction of pPRAME

A consensus sequence was generated for PRAME and the nucleotide sequence encoding the consensus PRAME antigen was inserted into the BamHI and XhoI restriction enzyme sites of the expression vector or plasmid pVAX (also known as pVAX1 herein) to yield pGX1411 (also known as pPRAME herein) (see FIG. 10A).
To confirm that pPRAME resulted in expression of the consensus PRAME antigen, pVAX and pPRAME were transfected into RD cells and 293T cells. DAPI was used to stain nuclei and the consensus PRAME antigen was also fluorescently stained. This staining, along with a merge of the DAPI and consensus PRAME antigen staining, are shown in FIG. 10B. These staining demonstrated that the PRAME consensus antigen was expressed from pPRAME and no consensus PRAME antigen was detected in the cells transfected with pVAX (i.e., negative control).
Additionally, western blotting analysis of lysates from the transfected cells was used to confirm expression of the consensus PRAME antigen in transfected cells (FIG. 10C). Non-transfected cells and cells transfected with pVAX were used as negative controls (see lanes labeled “control” and “pVAX,” respectively in FIG. 10C). In FIG. 10C, beta-actin detection was used as a loading control. In summary, the staining of transfected cells and western blotting of lysates from transfected cells demonstrated that the vector pPRAME provided expression of the consensus PRAME antigen within cells.

Example 9

Interferon Gamma Response to Vaccination with pPRAME

The above described pPRAME was used to vaccinate mice to evaluate whether a cellular immune response was induced by pPRAME. C57BL/6 mice were separated into groups. A first group was naïve and did not receive pPRAME. Second, third, fourth, fifth, and sixth groups of mice received 5 μg, 10 μg, 15 μg, 25 μg, and 50 μg of pPRAME, respectively.
After immunization, splenocytes were isolated from the C57BL/6 mice and evaluated for induction of interferon gamma (IFN-γ) by IFN-γ ELISpot analysis. As shown in FIGS. 11A and 11B, each dosage of pPRAME induced production or secretion of IFN-γ unlike the negative control naïve mice. In particular, the IFN-γ levels were increased by about 3000-fold to about 4500-fold in vaccinated mice as compared to non-vaccinated mice. Accordingly, these data demonstrated that vaccination with pPRAME, which encodes the consensus PRAME antigen, induced a cellular immune response as evidenced by increased IFN-γ levels as compared non-vaccination.

Example 10

Construction of pNY-ESO-1

A consensus sequence was generated for NY-ESO-1 and the nucleotide sequence encoding the consensus NY-ESO-1 antigen was inserted into the BamHI and XhoI restriction enzyme sites of the expression vector or plasmid pVAX (also known as pVAX1 herein) to yield pGX1409 (also known as pNY-ESO-1 herein) (see FIG. 12A).
To confirm that pNY-ESO-1 resulted in expression of the consensus NY-ESO-1 antigen, pVAX and pNY-ESO-1 were transfected into cells. DAPI was used to stain nuclei and the consensus NY-ESO-1 antigen was also fluorescently stained. This staining, along with a merge of the DAPI and consensus NY-ESO-1 antigen staining, are shown in FIG. 12B. These staining demonstrated that the NY-ESO-1 consensus antigen was expressed from pNY-ESO-1 and no consensus NY-ESO-1 antigen was detected in the cells transfected with pVAX (i.e., negative control).
Additionally, western blotting analysis of lysates from 293T and RD transfected cells was used to confirm expression of the consensus NY-ESO-1 antigen in the transfected cells (FIG. 12C). Non-transfected cells and cells transfected with pVAX were used as negative controls (see lanes labeled “control” and “pVAX,” respectively in FIG. 12C). In FIG. 12C, alpha-actin detection was used as a loading control. In summary, the staining of transfected cells and western blotting of lysates from the transfected cells demonstrated that the vector pNY-ESO-1 provided expression of the consensus NY-ESO-1 antigen within cells.

Example 11

Interferon Gamma Response to Vaccination with pNY-ESO-1

The above described pNY-ESO-1 was used to vaccinate mice to evaluate whether a cellular immune response was induced by pNY-ESO-1. C57BL/6 mice were separated into groups. A first group was naïve and did not receive pNY-ESO-1. Second and third groups of mice received 25 μg and 50 μg pNY-ESO-1, respectively.
After immunization, splenocytes were isolated from the C57BL/6 mice and evaluated for induction of interferon gamma (IFN-γ) by IFN-γ ELISpot analysis. As shown in FIG. 13 , each dosage of pPRAME induced production or secretion of IFN-γ unlike the negative control naïve mice. In particular, the IFN-γ levels were increased by about 700-fold to about 1100-fold in vaccinated mice as compared to non-vaccinated mice. Accordingly, these data demonstrated that vaccination with pNY-ESO-1, which encodes the consensus NY-ESO-1 antigen, induced a cellular immune response as evidenced by increased IFN-γ levels as compared non-vaccination.

Example 12

Interferon Gamma Response to Vaccination with pNY-ESO-2

A consensus sequence was generated for NY-ESO-2 and the nucleotide sequence encoding the consensus NY-ESO-2 antigen was inserted into the multiple cloning site of the expression vector or plasmid pVAX (also known as pVAX1 herein) to yield pNY-ESO-2.
This pNY-ESO-2 was used to vaccinate mice to evaluate whether a cellular immune response was induced by pNY-ESO-2. C57BL/6 mice were separated into groups. A first group was naïve and did not receive pNY-ESO-2. Second and third groups of mice received 25 μg and 50 μg of pNY-ESO-2, respectively.
After immunization, splenocytes were isolated from the C57BL/6 mice and evaluated for induction of interferon gamma (IFN-γ) by IFN-γ ELISpot analysis. As shown in FIG. 14 , each dosage of pNY-ESO-2 induced production or secretion of IFN-γ unlike the negative control naïve mice. In particular, the IFN-γ levels were increased by about 400-fold to about 500-fold in vaccinated mice as compared to non-vaccinated mice. Accordingly, these data demonstrated that vaccination with pNY-ESO-2, which encodes the consensus NY-ESO-2 antigen, induced a cellular immune response as evidenced by increased IFN-γ levels as compared non-vaccination.
It is understood that the foregoing detailed description and accompanying examples are merely illustrative and are not to be taken as limitations upon the scope of the invention, which is defined solely by the appended claims and their equivalents.
Various changes and modifications to the disclosed embodiments will be apparent to those skilled in the art. Such changes and modifications, including without limitation those relating to the chemical structures, substituents, derivatives, intermediates, syntheses, compositions, formulations, or methods of use of the invention, may be made without departing from the spirit and scope thereof.

Example 13

Synthetic Consensus hTERT

The experiments presented herein were designed to evaluate the ability of a synthetic consensus hTERT, designed and manufactured using methods described herein, to break tolerance in non-human primates. A synthetic consensus hTERT (pGX1434) that is approximately 96% identical to the rhesus macaque TERT was designed. Rhesus macaques were either immunized with a plasmid encoding synthetic consensus hTERT or a plasmid encoding native RhTERT in the presence of IL12 adjuvant. The nucleotide sequence which encodes the synthetic consensus hTERT (pGX1434) is provided by SEQ ID NO: 45. The amino acid sequence of the synthetic consensus hTERT (pGX1434) is provided by SEQ ID NO: 46. Monkeys were immunized four times and cellular immune responses were evaluated by ELISpot assay. It was observed that, compared to native RhTERT, immunization with synthetic consensus hTERT elicited stronger immune responses (1200 SFU/10⁶ vs 400 SFU/10⁶).
A synthetic consensus hTERT was designed for human TERT with 5 mutations to abolish its function. Native RhTERT encode Rhesus TERT with 2 mutations. Both constructs were optimized. A schematic design of the TERT constructs are provided in FIG. 16 (top). FIG. 16 also shows the protein homology between the optimized TERT and native TERT identified in human, rhesus and mice (FIG. 16 (bottom)).
Experiments were done to characterize mouse TERT-specific IFN-γ responses against rhesus native peptides. Mice (n=8 per group) were immunized at weeks 0, 2 and 4 with native RhTERT and synthetic consensus hTERT via IM/electroporation. The DNA vaccine immunization schedule is shown in FIG. 17A. The frequency of TERT-specific IFN-γ spot-forming units (SFU) per million splenocytes isolated from vaccinated mice, was determined by IFN-γ ELISpot assay using rhesus peptides. It was observed that immunization with RhTERT and synthetic consensus hTERT elicited a robust cellular immune response (FIG. 17B).
Experiments were conducted to characterize rhesus TERT-specific IFN-γ responses Rhesus macaque (n=5 per group) were immunized at weeks 0, 4, 8 and 12 with Native RhTERT or synthetic consensus hTERT as well as rhIL-12 via IM/electroporation. The DNA vaccine immunization schedule is provide in FIG. 18A. The frequency of TERT-specific IFN-γ spot-forming units (SFU) per million splenocytes isolated from vaccinated mice, was determined by IFN-γ ELISpot assay using native rhesus peptides and SynCon hTERT peptide. It was observed that synthetic consensus hTERT exhibits better ability to break tolerance in non-human primates, as compared to RhTERT (FIG. 18B and FIG. 18C).
Further experiments were conducted to evaluate the effect of synthetic consensus hTERT (pGX1434) on T cell responses and tumor growth. Mice received 3 immunizations 2 weeks apart with 0, 20, 40, or 60 μg of pGX1434. T cell responses in the mice were evaluated at 5 weeks, demonstrating that pGX1434 induced a robust T cell response (FIG. 19 (left). To evaluate tumor growth, mice were implanted with 25×10⁴TC-1 cells. Mice then received 4 immunizations 1 week apart with 25 μg of pGX1434. Tumor volume was measured over 32 days, demonstrating that mice treated with pGX1434 had decreased tumor volume as compared to naïve mice (FIG. 19 (right), FIG. 20 and FIG. 21 ).
The experiments presented herein demonstrate that synthetic consensus hTERT was able to break tolerance, induce a strong cellular immune response, and reduce tumor growth. The synthetic consensus hTERT is superior to native self-antigen regarding the ability of eliciting a neo-antigen-like immune response to break tolerance.

Example 14

SynCon hTERT Breaks Tolerance in NHP

Experiments were performed to assess immune responses induced by pGX1434 in NHPs+/−IL-12 (FIG. 22B, Groups 1 &2) and to evaluate immune responses induced by pGX1434 in the Wave 1 antigen combination (FIG. 22B, Group 3). Experiments were further designed to determine if SynCon design allows for breaking tolerance (FIG. 22B, Group 4) and to assess the ability of SynCon hTERT to break tolerance in NHPs (FIG. 22B, Groups 1-4).
The experimental design is provided in FIG. 22A. The formulation used for these experiments was: 3.0 mg/construct in 1.0 mL 20×SSC, with a 1 mL injection volume.
The results from the experiments are provided in FIG. 23 through FIG. 26 . Responses to native rhesus TERT were detected PD3 and PD4 in the pGX1434+pGX6006 group (FIG. 23 ). pGX1406 induces more robust TERT responses compared to pGX1434 when combined in the multivalent Wave 1 formulation with 0.20 mg pGX6006 (FIG. 25 ). SynCon PSMA and SynCon WT-1 specific responses PD4 are similar for groups containing pGX1434 and pGX1406.
The multivalent formulation of WT-1, TERT, and PSMA induced robust immune responses in mice by IFNγ ELISpot and in the CD8+ T cell compartment (FIG. 27 ) and mice immunized with a combination of WT1, PSMA and consensus mTERT showed a reduced tumor burden and increased survival (FIG. 28 ).
The experiments presented herein demonstrate that synthetic consensus hTERT was able to break tolerance and induce a strong cellular immune response in non-human primates.

Example 15

Sequences


SEQ
ID
NO:	Antigen	Type	Plasmid

1	Consensus Tyrosinase	Nucleic acid
2	Consensus Tyrosinase	Amino acid
3	Consensus Tyrosinase-related protein 1	Nucleic acid
4	Consensus Tyrosinase-related protein 1	Amino acid
5	Consensus Tyrosinase-related protein 2	Nucleic acid
6	Consensus Tyrosinase-related protein 2	Amino acid
7	Consensus Melanoma-associated	Nucleic acid
	antigen 4
8	Consensus Melanoma-associated	Amino acid
	antigen 4
9	Consensus Growth hormone releasing	Nucleic acid
	hormone
10	Consensus Growth hormone releasing	Amino acid
	hormone
11	Consensus Melan-A	Nucleic acid
12	Consensus Melan-A	Amino acid
13	Consensus NY-ESO-1	Nucleic acid
14	Consensus NY-ESO-1	Amino acid
15	Consensus NY-ESO-2	Nucleic acid
16	Consensus NY-ESO-2	Amino acid
17	Consensus PRAME	Nucleic acid
18	Consensus PRAME	Amino acid
19	Con WT1-L with modified Zinc Fingers	Nucleic acid	pGX1404
20	Con WT1-L with modified Zinc Fingers	Amino acid	pGX1404
21	Con WT1-S without Zinc fingers	Nucleic acid
22	Con WT1-S without Zinc fingers	Amino acid
23	hTERT operably linked to IgE	Nucleic acid	pGX1406
24	hTERT operably linked to IgE	Amino acid	pGX1406
25	gB consensus	Nucleic acid
26	gB consensus	Amino acid
27	gM consensus	Nucleic acid
28	gM consensus	Amino acid
29	gN consensus	Nucleic acid
30	gN consensus	Amino acid
31	gH consensus	Nucleic acid
32	gH consensus	Amino acid
33	gL consensus	Nucleic acid
34	gL consensus	Amino acid
35	gO consensus	Nucleic acid
36	gO consensus	Amino acid
37	UL128 consensus	Nucleic acid
38	UL128 consensus	Amino acid
39	UL130 consensus	Nucleic acid
40	UL130 consensus	Amino acid
41	UL131a consensus	Nucleic acid
42	UL131a consensus	Amino acid
43	UL83 consensus	Nucleic acid
44	UL83 consensus	Amino acid
45	Synthetic Consensus hTERT operably	Nucleic acid	pGX1434
	linked to IgE
46	Synthetic Consensus hTERT operably	Amino acid	pGX1434
	linked to IgE
47	Synthetic Consensus hTERT	Nucleic acid	pGX1434
48	Synthetic Consensus hTERT	Amino acid	pGX1434
49	Synthetic Consensus mTERT operably	Nucleic acid	pGX1418
	linked to IgE
50	Synthetic Consensus mTERT operably	Amino acid	pGX1418
	linked to IgE
51	Synthetic Consensus mTERT	Nucleic acid	pGX1418
52	Synthetic Consensus mTERT	Amino acid	pGX1418
53	Synthetic Consensus rhTERT operably	Nucleic acid	pGX1473
	linked to IgE
54	Synthetic Consensus rhTERT operably	Amino acid	pGX1473
	linked to IgE
55	Synthetic Consensus rhTERT	Nucleic acid	pGX1473
56	Synthetic Consensus rhTERT	Amino acid	pGX1473
57	mut rhTERT	Nucleic acid	pGX1447
58	mut rhTERT	Amino acid	pGX1447
59	Consensus FAP	Nucleic acid
60	Consensus FAP	Amino acid
61	Consensus FSHR	Nucleic acid
62	Consensus FSHR	Amino acid
63	Consensus PSA	Nucleic acid
64	Consensus PSA	Amino acid
65	Consensus PSMA	Nucleic acid	pGX1108
66	Consensus PSMA	Amino acid	pGX1108
67	Consensus STEAP	Nucleic acid
68	Consensus STEAP	Amino acid
69	Consensus PSCA	Nucleic acid
70	Consensus PSCA	Amino acid

Claims

1. An immunogenic composition comprising a nucleic acid molecule encoding a consensus TERT antigen, wherein the consensus TERT antigen comprises an amino acid sequence selected from the group consisting of:

a) an amino acid sequence selected from the group consisting of SEQ ID NO: 46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, and SEQ ID NO:56,

b) an amino acid sequence that is 95% identical or greater to an amino acid sequence selected from the group consisting of SEQ ID NO: 46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, and SEQ ID NO:56, and

c) a fragment of an amino acid sequence selected from the group consisting of SEQ ID NO: 46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, and SEQ ID NO:56, wherein the fragment comprises at least 95% of the full length amino acid sequence.

2. The immunogenic composition of claim 1, wherein the immunogenic composition further comprises one or more nucleotide sequences encoding one or more amino acid sequence selected from the group consisting of

a) an amino acid sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO; 58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70;

b) an amino acid sequence that is 95% identical or greater to the amino acid selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO; 58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, and

c) a fragment of an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO; 58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, wherein the fragment comprises at least 95% of the full length amino acid sequence.

3. The immunogenic composition of claim 1 further comprising a nucleic acid encoding one or more antigens selected from the group consisting of: MAGE A1, gp100, a viral antigen, and combinations thereof.

4. The immunogenic composition of claim 3, wherein the viral antigen is selected from the group consisting of a Hepatitis B virus (HBV) antigen, a Hepatitis C virus (HCV) antigen, a Human Papilloma Virus (HPV) antigen, a HBV core antigen, a HBV surface antigen, a HCV NS34A antigen, a HCV NS5A antigen, a HCV NS5B antigen, an HCV NS4B antigen, a HPV type 6 E6 antigen, a HPV type 6 E7 antigen, a HPV type 11 E6 antigen, a HPV type 11 E7 antigen, a HPV type 16 E6 antigen, a HPV type 16 E7 antigen, a HPV type 18 E6 antigen, an HPV type 18 E7 antigen and combinations thereof.

5-7. (canceled)

8. The immunogenic composition of claim 1, further comprising an immune checkpoint inhibitor.

9. The immunogenic composition of claim 1, wherein the nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of

a) a nucleotide sequence selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53 and SEQ ID NO: 55,

b) a nucleotide sequence that is 95% identical or greater to a nucleotide sequence selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53 and SEQ ID NO: 55, and

c) a fragment of a nucleotide sequence selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53 and SEQ ID NO: 55, wherein the fragment comprises at least 95% of the full length nucleotide sequence.

10. The immunogenic composition of claim 2, wherein the immunogenic composition comprises one or more nucleotide sequences selected from the group consisting of:

a) a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 and SEQ ID NO:69;

b) a nucleotide sequence that is 95% identical or greater to a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 and SEQ ID NO:69, and

c) a fragment of a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67 and SEQ ID NO:69, wherein the fragment comprises at least 95% of the full length nucleotide sequence.

11. The immunogenic composition of claim 1, wherein the nucleic acid molecule is a plasmid.

12. (canceled)

13. The immunogenic composition of claim 1, further comprising an adjuvant.

14. The immunogenic composition of claim 13, wherein the adjuvant is IL-12, IL-15, IL-28, or RANTES.

15. A method of treating or preventing cancer in a subject in need thereof, the method comprising administering the immunogenic composition of claim 1 to the subject.

16. (canceled)

17. The method of claim 15, further comprising administering an immune checkpoint inhibitor to the subject.

18. The method of claim 17, wherein the immunogenic composition and immune checkpoint inhibitor are administered in a single formulation to the subject.

19. The method of claim 17, wherein the immunogenic composition and immune checkpoint inhibitor are administered separately to the subject.

20. The method of claim 15, wherein the cancer is selected from the group consisting of: melanoma, head and neck cancer, prostate cancer, liver cancer, cervical cancer, recurrent respiratory papillomatosis (RRP), anal cancer, a blood cancer, ovarian cancer and a combination thereof.

21. A nucleic acid molecule comprising one or more nucleotide sequences selected from the group consisting of:

22. The nucleic acid molecule of claim 21, further comprising one or more nucleotide sequences selected from the group consisting of:

23. The nucleic acid molecule of claim 21, wherein the nucleic acid molecule is a plasmid.

24. An amino acid molecule comprising one or more amino acid sequence selected from the group consisting of:

25. The amino acid molecule of claim 24, further comprising one or more amino acid sequence selected from the group consisting of: a) an amino acid sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO; 58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70;