CA3145936A1

CA3145936A1 - Vaccine combination and method for using the same

Info

Publication number: CA3145936A1
Application number: CA3145936A
Authority: CA
Inventors: Yung-Nien Chang
Original assignee: Papivax Biotech Inc
Current assignee: Papivax Biotech Inc
Priority date: 2022-01-18
Filing date: 2022-01-18
Publication date: 2023-07-18

Abstract

A vaccine combination may include first and second vaccines. The first vaccine may include a first fusion protein or a first polynucleotide encoding the first fusion protein.
The first fusion protein may include an E7 protein of HPV-16; an E7 protein of HPV-18; an E6 protein of HPV-16; an E6 protein of HPV-18; and a heat shock protein. The second vaccine may include second and third fusion proteins, or a second polynucleotide encoding the second and third fusion proteins. The second fusion protein may include an E6 protein of HPV-16 and an E7 protein of HPV-16. The third fusion protein may include an E6 protein of HPV-18 and an E7 protein of HPV-18. A
functional variant may be employed for one or more of the proteins. Amino acid sequences of junction regions in the first fusion protein may be different from those in the second and third fusion proteins.

Description

VACCINE COMBINATION AND METHOD FOR USING THE SAME
REFERENCE TO SEQUENCE LISTING
[0001] Accompanying this application is a sequence listing in an American Standard Code for Information Interchange (ASCII) text file named "211223-US86679-Sequence Listing-v1F.txt", created December 07, 2021, and having a size of 18,253 bytes.

[0002] [blank]

Date Recue/Date Received 2023-06-06 BACKGROUND
1. Field

[0003] The present disclosure generally relates to vaccine combinations, particularly for a human papillomavirus (HPV)-associated disease, and more specifically to improving the vaccine combination by the particular design of a priming vaccine and a boosting vaccine.
2. Related Art

[0004] HPV is a common etiological agent in several human cancers, including cervical, anal, penile, vulvar, vaginal, and head and neck cancers. Current vaccines against HPV, such as Gardasil and Cervarix , have shown clinical efficacy in preventing HPV
infection, but they are ineffective in treating patients with existing HPV infection or HPV-associated cancers. As such, development of therapeutic vaccines for patients infected with HPV or even suffering from HPV-associated diseases are highly demanded.

[0005] Deoxyribonucleic acid (DNA) vaccination is a technique for protecting against infection or treating disease by injection with a genetically engineered plasmid containing a DNA sequence encoding one or more antigens. DNA vaccines have theoretical advantages over conventional vaccines, including safety, speed, and predictability of manufacture; temperature stability; flexibility in design; and the ability to induce a wider range of immune response types.

[0006] An effective vaccine usually requires more than one-time immunization in the form of prime-boost. Traditionally the same vaccines are given multiple times as homologous boosts.
Some findings suggest that prime-boost can be done with different types of vaccines containing the same antigens. In many cases such heterologous prime-boost can be more immunogenic than homologous prime-boost (Curr Opin Immunol. 2009 Jun; 21(3): 346-351).
Heterologous prime-boost may include administration of two different vectors or delivery systems expressing the same Date Recue/Date Received 2022-01-18 or overlapping antigenic inserts. It has been known that using certain vector combinations could increase both antibody and T cell immunity. However, while a priming vaccine and a boosting vaccine, which both can be either a fusion protein of antigens or a vector encoding the same, may have the same antigen arrangement in the fusion protein, the enhanced immunity generated by the prime-boost regimen may also include boosting an immune response against the junction-associated epitopes in the fusion protein of antigens and may lead to an impaired immune response against the target pathogen or other undesired effects.

[0007] Furthermore, before providing a newly developed DNA vaccine to the clinics, the potential to induce autoimmunity by vaccinating with novel sequences is a great concern that should be addressed. Such adverse reaction to vaccines may be viewed as a result of the interaction between susceptibility of the vaccinated subject and various vaccine components. The significant similarity between certain pathogenic elements contained in the vaccine and specific human proteins may lead to immune cross-reactivity, wherein the reaction of the immune system towards the pathogenic antigens may harm the similar human proteins (self-antigens), essentially causing autoimmune disease (Cell Mol Irnmunol. 2018 Jun;15(6):586-594). Therefore, in addition to elevating the immunogenicity of vaccines, it is essential as well to avoid potential induction of autoimmunity due to cross-reactivity when developing vaccines.

[0008] In view of the reasons mentioned above, there exists an unmet need for providing a vaccine for treating HPV-associated diseases with enhanced immunogenicity and improved safety, as reflected in a reduced risk to generate an immune response against the junction-associated epitopes potentially in the fusion protein expressed by or contained in the vaccine and to induce cross-reactivity against self-antigens.
BRIEF SUMMARY OF THE DISCLOSURE

[0009] In a first aspect of the present disclosure, a vaccine combination may be provided. The vaccine combination may include a first vaccine and a second vaccine. The first vaccine may Date Recue/Date Received 2022-01-18 include a first fusion protein or a first polynucleotide encoding the first fusion protein. The first fusion protein, in an order from N to C terminus, may include: (i) an E7 protein of human papillomavirus type 16 (HPV-16) or a functional variant thereof (ii) an E7 protein of human papillomavirus type 18 (HPV-18) or a functional variant thereof; (iii) an E6 protein of HPV-16 or a functional variant thereof; (iv) an E6 protein of HPV-18 or a functional variant thereof; and (v) a heat shock protein or a functional variant thereof The E7 protein of HPV-16 or a functional variant thereof may comprise SEQ ID NO: 1 at a beginning of the protein and SEQ ID NO: 2 at an end of the protein. The E7 protein of HPV-18 or a functional variant thereof may comprise SEQ
ID NO: 3 at a beginning of the protein and SEQ ID NO: 4 at an end of the protein. The E6 protein of HPV-16 or a functional variant thereof may comprise SEQ ID NO: 5 at a beginning of the protein and SEQ ID NO: 6 at an end of the protein. The E6 protein of HPV-18 or a functional variant thereof may comprise SEQ ID NO: 7 at a beginning of the protein and SEQ ID NO: 8 at an end of the protein. The second vaccine may include a second fusion protein and a third fusion protein, or a second polynucleotide encoding the second fusion protein and the third fusion protein.
The second fusion protein may include an E6 protein of HPV-16 or a functional variant thereof;
and an E7 protein of HPV-16 or a functional variant thereof The third fusion protein may include an E6 protein of HPV-18 or a functional variant thereof; and an E7 protein of HPV-18 or a functional variant thereof. Amino acid sequences of junction regions in the first fusion protein may be different from those in the second fusion protein and the third fusion protein.

[0010] In some embodiments, the E7 protein of HPV-16 may comprise SEQ ID
NO: 9; the E7 protein of HPV-18 may comprise SEQ ID NO: 10; the E6 protein of HPV-16 may comprise SEQ ID NO: 11; and the E6 protein of HPV-18 may comprise SEQ ID NO: 12.

[0011] In some embodiments, the E7 protein of HPV-16 may be encoded by SEQ
ID NO: 13;
the E7 protein of HPV-18 may be encoded by SEQ ID NO: 14; the E6 protein of HPV-16 may be encoded by SEQ ID NO: 15; and the E6 protein of HPV-18 may be encoded by SEQ
ID NO: 16.

[0012] In some embodiments, the first polynucleotide may include SEQ ID NO:
17.

Date Recue/Date Received 2022-01-18

[0013] In some embodiments, the first polynucleotide may include SEQ ID NO:
18.

[0014] In some embodiments, the second polynucleotide may be contained within a recombinant virus.

[0015] In some embodiments, the recombinant virus may be TA-HPV.

[0016] In a second aspect of the present disclosure, a method for treating an HPV-associated disease in a subject in need thereof may be provided. The method may include administering the aforementioned vaccine combination to the subject. The first vaccine may be administered as a priming vaccine, and the second vaccine may be administered as a boosting vaccine.

[0017] In some embodiments, the method may further include administering the first vaccine to the subject as a boosting vaccine after the administration of the first vaccine as a priming vaccine and prior to the administration of the second vaccine as a boosting vaccine.

[0018] In some embodiments, the first vaccine may comprise the first polynucleotide. In some embodiments, the first vaccine may be administered at a dose ranging from 10 micrograms per subject to 20 milligrams per subject.

[0019] In some embodiments, the second vaccine may comprise TA-HPV. In some embodiments, the second vaccine may be administered at a dose ranging from 1 x 104 plaque-forming units (pfu) to 2 x 109 pfu.

[0020] In some embodiments, the method may further include administering a chemotherapy, radiotherapy, chemo-radiotherapy, cryotherapy, thermotherapy, targeted therapy, cellular therapy, gene therapy, or immunotherapy in combination with the administration of the vaccine combination.

[0021] In some embodiments, the chemotherapy, radiotherapy, chemo-radiotherapy, cryotherapy, thermotherapy, targeted therapy, cellular therapy, gene therapy, or immunotherapy may be administered prior to and/or simultaneously with the administration of the first vaccine.

[0022] In some embodiments, the immunotherapy may comprise administering an immune checkpoint inhibitor to the subject.
Date Recue/Date Received 2022-01-18

[0023] In some embodiments, the immune checkpoint inhibitor may be an immune modulator targeting programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4), inducible costimulator (ICOS), T-cell immunoglobulin and mucin domain 3 (TIM-3), lymphocyte activation gene 3 (LAG-3) or T cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif (ITIM) domain (TIGIT).

[0024] In some embodiments, the immune checkpoint inhibitor may be an anti-PD-1 antibody.
BRIEF DESCRIPTION OF THE DRAWINGS

[0025] So that the manner in which the above-recited features of the present disclosure can be understood in detail, a more particular description of the disclosure, briefly summarized above, may be had by reference to embodiments, some of which are illustrated in the appended drawings.
It is to be noted, however, that the appended drawings illustrate only typical embodiments of this disclosure and are therefore not to be considered limiting of its scope, for the disclosure may admit to other equally effective embodiments.

[0026] FIG. lA is a schematic illustration showing a DNA construct encoding the first fusion protein of the first vaccine of the vaccine combination according to an embodiment of the present disclosure.

[0027] FIG. 1B is a schematic illustration showing a cassette for expression of an HPV-16 E6-E7 fusion protein and an HPV-18 E6-E7 fusion protein inserted into the genome of a vaccinia virus of the vaccine combination according to an embodiment of the present disclosure.

[0028] FIG. 2A is a schematic illustration of the experimental design for characterizing HPV
antigen-specific CD8+ T cell-mediated immune responses in mice vaccinated with the vaccine combination of the present disclosure in a prime and boost strategy (two DNA
doses and one recombinant virus dose, DDV regimen) or a DNA vaccine alone in a prime and boost strategy (three DNA doses, DDD regimen), in accordance with an embodiment of the present disclosure.

[0029] FIG. 2B is a bar chart showing the percentage of HPV-16 E7-specific CD8+ T cells/

Date Recue/Date Received 2022-01-18 total CD8+ cells in peripheral blood mononuclear cells (PBMCs) collected from naïve mice or mice treated with the vaccine combination of the present disclosure (DDV
regimen) or the DNA
vaccine alone (DDD regimen) using HPV-16 E7 (aa 49-57) peptide-loaded tetramer staining, using a two-tailed Student's t-test, in accordance with an embodiment of the present disclosure.

[0030] FIG. 2C is a bar chart of the number of HPV-16 E7-specific IFN-7+
CD8+ T cells/3 x 105 splenocytes from mice vaccinated with the vaccine combination of the present disclosure (DDV regimen) or the DNA vaccine alone (DDD regimen) after stimulation with either HPV-16 E6 (aa 50-57), peptide HPV-16 E7 (aa 49-57) peptide or HPV-18 E6 (aa 67-75) peptide, in accordance with an embodiment of the present disclosure.

[0031] FIG. 3A is a schematic illustration of the experimental design for characterizing the HPV antigen-specific immune response and antitumor effects in TC-1 tumor-bearing mice treated with the vaccine combination of the present disclosure in a prime and boost strategy with or without anti-PD-1 antibody, in accordance with an embodiment of the present disclosure.

[0032] FIG. 3B is a bar chart showing the percentage of HPV-16 E7-specific CD8+ T cells/
total CD 8+ T cells in peripheral blood mononuclear cells (PBMCs) prepared from untreated mice, mice treated with anti-PD-1 antibody alone, mice treated with the vaccine combination of the present disclosure (DDV), or mice treated with the vaccine combination of the present disclosure in combination with anti-PD-1 antibody (Anti-PD-1+DDV), using HPV-16 E7 (aa 49-57) peptide-loaded tetramer staining, using a two-tailed Student's t-test, in accordance with an embodiment of the present disclosure.

[0033] FIG. 3C is a curve chart showing TC-1 tumor volumes in the untreated mice, the mice treated with anti-PD-1 antibody alone, the mice treated with the vaccine combination of the present disclosure (DDV), or the mice treated with the vaccine combination of the present disclosure in combination with anti-PD-1 antibody (Anti-PD-1+DDV), in accordance with an embodiment of the present disclosure.

[0034] FIG. 3D is a Kaplan-Meier survival curve showing the probability of survival in the Date Recue/Date Received 2022-01-18 untreated mice, the mice treated with anti-PD-1 antibody alone, the mice treated with the vaccine combination of the present disclosure (DDV), or the mice treated with the vaccine combination of the present disclosure in combination with anti-PD-1 antibody (Anti-PD-1+DDV), in accordance with an embodiment of the present disclosure.

[0035] In accordance with common practice, the various described features are not drawn to scale and are drawn to emphasize features relevant to the present disclosure.
Like reference characters denote like elements throughout the figures and text.
DETAILED DESCRIPTION

[0036] The present disclosure will now be described more fully hereinafter with reference to the accompanying drawings, in which exemplary embodiments of the disclosure are shown. This disclosure may, however, be embodied in many different forms and should not be construed as limited to the exemplary embodiments set forth herein. Rather, these exemplary embodiments are provided so that this disclosure will be thorough and complete, and will fully convey the scope of the disclosure to those skilled in the art. Like reference numerals refer to like elements throughout.

[0037] The terminology used herein is for the purpose of describing particular exemplary embodiments only and is not intended to be limiting of the disclosure. As used herein, the singular forms "a", "an", and "the" are intended to include the plural forms as well, unless the context clearly indicates otherwise. It will be further understood that the terms "comprises" and/or "comprising," or "includes" and/or "including" or "has" and/or "having", when used herein, specify the presence of stated features, regions, integers, steps, operations, elements, and/or components, but do not preclude the presence or addition of one or more other features, regions, integers, steps, operations, elements, components, and/or groups thereof.

[0038] The term "functional variant", as used herein, refers to a protein (i) having at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more identical in amino acid sequence to the wild-type protein; and (ii) retaining the immunogenicity of the wild-type protein, for example, Date Recue/Date Received 2022-01-18 the ability to induce protein-specific CD8+ T cells.

[0039] The term "in combination with", as used herein, includes the administration of two or more vaccines or therapeutic agents simultaneously, or sequentially in any order within no specific time limits, unless otherwise indicated, in the course of treating the same disease in the same patient.

[0040] Unless otherwise defined, all terms (including technical and scientific telins) used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. It will be further understood that terms, such as those defined in commonly used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of the relevant art and the present disclosure, and will not be interpreted in an idealized or overly formal sense unless expressly so defined herein.

[0041] A vaccine combination of the present disclosure is provided for a subject having a human papillomavirus (HPV)-associated disease. The subject having an HPV-associated disease may be a mammal (e.g., human, mice, etc.) suffering from, but not limited to, warts, papilloma, intraepithelial neoplasia, penile cancer, vaginal cancer, vulva cancer, anal cancer, oropharyngeal cancer, non-melanoma skin cancer, conjunctival cancer, or cervical cancer.

[0042] The vaccine combination may include a first vaccine and a second vaccine. The first vaccine includes a first fusion protein or a first polynucleotide that is designed to encode the first fusion protein. The first fusion protein includes a plurality of HPV antigens and a heat shock protein having a specific arrangement and thereby encompasses specific junction regions between the HPV antigens and between the HPV antigen and the heat shock protein. The second vaccine includes a second fusion protein and a third fusion protein, or a second polynucleotide that is designed to encode the second fusion protein and the third fusion protein. The second fusion protein includes two HPV antigens having a specific arrangement and thereby encompasses a specific junction region between the HPV antigens. The third fusion protein also includes two HPV
antigens having a specific arrangement and thereby encompasses a specific junction region Date Recue/Date Received 2022-01-18 between the HPV antigens. The amino acid sequences of the junction regions in the first fusion protein are different from those in the second fusion protein and the third fusion protein.

[0043] Specifically, the specific arrangement of HPV antigens of the first fusion protein, the second fusion protein and the third fusion protein are described as follows:

[0044] The first fusion protein, in an order from N to C terminus, may include (i) an E7 protein of human papillomavirus type 16 (HPV-16) or a functional variant thereof, wherein the E7 protein of HPV-16 or a functional variant thereof comprises SEQ ID NO: 1 at the beginning of the protein and SEQ ID NO: 2 at the end of the protein; (ii) an E7 protein of human papillomavirus type 18 (HPV-18) or a functional variant thereof, wherein the E7 protein of HPV-18 or a functional variant thereof comprises SEQ ID NO: 3 at the beginning of the protein and SEQ ID NO:
4 at the end of the protein; (iii) an E6 protein of HPV-16 or a functional variant thereof, wherein the E6 protein of HPV-16 or a functional variant thereof comprises SEQ ID NO: 5 at the beginning of the protein and SEQ ID NO: 6 at the end of the protein; (iv) an E6 protein of HPV-18 or a functional variant thereof, wherein the E6 protein of HPV-18 or a functional variant thereof comprises SEQ ID NO:
7 at the beginning of the protein and SEQ ID NO: 8 at the end of the protein;
and (v) a heat shock protein or a functional variant thereof. Thereby, junctions are formed between the adjacent HPV
antigens (e.g., E7 protein of HPV-16 and E7 protein HPV-18; E7 protein HPV-18 and E6 protein of HPV-16; and E6 protein of HPV-16 and E6 protein HPV-18) and between the E6 protein of HPV-18 and the heat shock protein in the first fusion protein.

[0045] The second fusion protein, in an order from N to C terminus, may include an E6 protein of HPV-16 or a functional variant thereof; and an E7 protein of HPV-16 or a functional variant thereof. The third fusion protein, in an order from N to C terminus, may include an E6 protein of HPV-18 or a functional variant thereof; and an E7 protein of HPV-18 or a functional variant thereof Thereby, a junction is formed between the adjacent HPV antigens (i.e., E6 protein of HPV-16 and E7 protein of HPV-16; or E6 protein of HPV-18 and E7 protein of HPV-18) in the second fusion protein or the third fusion protein.
Date Recue/Date Received 2022-01-18

[0046] Due to the aforementioned arrangement of the first fusion protein, the second fusion protein and the third fusion protein, the amino acid sequences of the junction regions in the first fusion protein are different from those in the second fusion protein and the third fusion protein.

[0047] Examples of the first polynucleotide of the first vaccine and the second polynucleotide of the second vaccine according to the vaccine combination are illustrated in FIG. I A and FIG. 1B, respectively.

[0048] FIG. IA illustrates an exemplary first polynucleotide (denoted as PBI-11) that encodes the first fusion protein. The first polynucleotide includes a fusion gene encoding the first fusion protein, which in an order from N to C terminus comprises: a signal peptide (denoted as -S"), an E7 protein of HPV-16 (denoted as E7(16)), an E7 protein of HPV-18 (denoted as E708)), an E6 protein of HPV-16 (denoted as E6(16)), an E6 protein of HPV-18 (denoted as E6(18)), and a 70 kilodalton heat shock protein (HSP70).

[0049] The first fusion protein thereby has junction regions formed between the adjacent HPV
antigens (e.g., E7 protein HPV-16 and E7 protein HPV-18, E7 protein HPV-18 and E6 protein of HPV-16. E6 protein of HPV-16 and E6 protein of HPV-18).

[0050] In some embodiments, the E7 protein of HPV-16 may comprise SEQ ID
NO: 9, the E7 protein of HPV-18 may comprise SEQ ID NO: 10, the E6 protein of HPV-16 may comprise SEQ
ID NO: 11, and the E6 protein of HPV-18 may comprise SEQ ID NO: 12.

[0051] In some embodiments, the E7 protein of HPV-16 may be encoded by SEQ
ID NO: 13, the E7 protein of HPV-18 may be encoded by SEQ ID NO: 14, the E6 protein of HPV-16 may be encoded by SEQ ID NO: 15, and the E6 protein of HPV-18 may be encoded by SEQ
ID NO: 16.

[0052] In some embodiments, pBI-11 may be used as the first vaccine of the instant vaccine combination. pBI-11, which has a nucleotide sequence as set forth in SEQ ID
NO: 17, is a DNA
construct including a fusion gene which includes: a subsequence encoding a signal peptide; an optimized HPV subsequence (FIG. 1A, fragments 101) encoding an E7 protein of HPV-16 as set forth in SEQ ID NO: 9, an E7 protein of HPV-18 as set forth in SEQ ID NO: 10, an E6 protein of Date Recue/Date Received 2022-01-18 HPV-16 as set forth in SEQ ID NO: 11, and an E6 protein of HPV-18 as set forth in SEQ ID NO:
12; and a subsequence encoding an HSP70.

[0053] In some embodiments, alternatively and/or additively, pBI-12 may be used as the first vaccine of the instant vaccine combination. pBI-12, which has a nucleotide sequence as set forth in SEQ ID NO: 18, is a DNA construct comprising a fusion gene which includes:
an optimized signal sequence encoding a signal peptide; an optimized HPV subsequence encoding an E7 protein of HPV-16 as set forth in SEQ ID NO: 9, an E7 protein of HPV-18 as set forth in SEQ ID NO: 10, an E6 protein of HPV-16 as set forth in SEQ NO: 11, and an E6 protein of HPV-18 as set forth in SEQ ID NO: 12; and a subsequence encoding an HSP70.

[0054] In some embodiments, the first vaccine may comprise the first polynucleotide, and the first vaccine may be administered at a dose ranging from 10 micrograms per subject to 20 milligrams per subject.

[0055] FIG. 1B illustrates an exemplary second polynucleotide that encodes the second fusion protein and the third fusion protein. As shown in FIG. 1B, a cassette for expression of the second fusion protein and the third fusion protein is contained within the vaccinia virus genome (denoted as TA-HPV). The second polynucleotide includes a first open reading frame for encoding an E6 and an E7 protein of HPV-16 (denoted as HPV16 E67 in FIG. 1B); and a second open reading frame for encoding an E6 and an E7 protein of HPV-18 (denoted as HPV18 E67 in FIG. 1B).

[0056] In some embodiments, the second polynucleotide may be contained in a recombinant virus.

[0057] In some embodiments, the recombinant virus which contains the second polynucleotide may be, but not limited to TA-HPV. The TA-HPV may be administered at a dose ranging from 1 x 104 pfu to 2 x 109 pfu. The TA-HPV may be administered preferably at a dose ranging from 2 x 104 pfu to 5 x 107 pfu.

[0058] In some embodiments, the vaccine combination of the present disclosure may be administered to a subject for treating an HPV-associated disease.

Date Recue/Date Received 2022-01-18

[0059] In some embodiments, the first vaccine of the vaccine combination may be administered as a priming vaccine and the second vaccine of the vaccine combination may be administered subsequently as a boosting vaccine, so as to provide a combination therapy being used in a heterologous prime-boost regimen to enhance a subject's immune responses against HPV.
For example, the first vaccine may comprise the first polynucleotide and be administered at a dose ranging from 10 micrograms per subject to 20 milligrams per subject, and the second vaccine may comprise TA-HPV and be administered at a dose ranging from 1 x 104 pfu to 2 x 109 pfu.

[0060] In some embodiments, the first vaccine of the vaccine combination may be administered as a priming vaccine and be administered subsequently as a boosting vaccine, and after the administration of the first vaccine as the boosting vaccine, the second vaccine of the vaccine combination may be administered subsequently also as a boosting vaccine, so as to provide a combination therapy being used in a heterologous prime-boost regimen to enhance a subject's immune responses against HPV.

[0061] In some embodiments, the vaccine combination may further include an immune checkpoint inhibitor. The immune checkpoint inhibitor may be administered simultaneously and/or sequentially in any order with the administration of the first vaccine and/or the second vaccine. For example, the immune checkpoint inhibitor may be administered prior to and/or simultaneously with the administration of the first vaccine.

[0062] In some embodiments, the immune checkpoint inhibitor may be an immune modulator that targets programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4), inducible costimulator (ICOS). T-cell immunoglobulin and mucin domain 3 (TIM-3), lymphocyte activation gene 3 (LAG-3) or T cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif (ITIM) domain (TIGIT).
For instance, the immune checkpoint may be an antibody targeting PD-1 (also called "anti-PD-1 antibody").

[0063] In some embodiments, the first vaccine and the second vaccine of the vaccine Date Recue/Date Received 2022-01-18 combination may further include an ingredient, such as an adjuvant, to create a stronger immune response in the subject receiving the vaccine.
Example 1: Design and synthesis of the vaccine combination

[0064] A pBI-I DNA construct has been described previously as pNGVL4a-SigE7(detox)HSP70 (C. Trimple et al. Vaccine 2003, 21:4036-4042). In one example, the pBI-11 DNA construct was derived by Gibson assembly of a synthesized DNA fragment encoding a fusion protein of a signal peptide, an E7 protein of HPV-16, an E7 protein of HPV-18, an E6 protein of HPV-16, an E6 protein of HPV-18, and a 5' portion of HSP70 (up to the Tthl I
1I site), flanked 5' by anEcoRI and Kozak site and 3' with a Tth111I site. The synthesized DNA
fragment was cloned into the pBI-1 to replace the fragment between EcoRI and Tth111I in frame with HSP70. The expressing genes for the E7 protein of HPV-16, the E7 protein of HPV-18, the E6 protein of HPV-16, and the E6 protein of HPV-18 in pBI-11 were codon-optimized and encoded by SEQ ID NO:
1-4 respectively. In another example, the pBI-12 DNA construct also included a synthesized DNA
fragment encoding a fusion protein of the signal peptide, an E7 protein of HPV-16, an E7 protein of HPV-18, an E6 protein of HPV-16, an E6 protein of HPV-18, and a HSP70. The expressing genes for the signal peptide, HPV-I6 E7, HPV-I8 E7, HPV-I6 E6, and HPV-18 E6 in pBI-I2 were codon-optimized. The synthesized DNA fragment of pBI-12 was cloned into the pBI-1 to replace the fragment between EcoRI and Tth111I in frame with HSP70.

[0065] The genes in the synthesized DNA fragment of each DNA construct that have been either optimized for gene expression (FIG. 1A, fragments 101) or based on native papillomaviral sequences (FIG. IA, fragments 103) are shown in FIG. 1A.

[0066] TA-HPV is a recombinant vaccinia viral vaccine expressing oncogenes E6 and E7 of HPV types 16 and 18. The HPV-16 and HPV-18 oncogenes E6 and E7 may be inserted in a head-to-head orientation under the control of the p7.5 and H6 promoters (denoted as P7.5 and FI6, respectively, in FIG. 1B) at a neutral site in the vaccinia virus Wyeth strain genome (L. K.

Date Recue/Date Received 2022-01-18 Borysiewicz et al., Lancet., 1996 Jun 1;347(9014):1523-7). For both the HPV-16 and HPV-18 genes, the E6 termination codon may be altered to create an E6/E7 fused open reading frame and defined mutation introduced to inactivate the Rb-binding site in E7.
Example 2: The arrangement of the HPV antigens in the fusion protein encoded in the vaccine combination does not include peptides with sequences common to host proteins that can induce cross-reactive immunity against self-antigens.

[0067] To identify vaccine epitopes that might induce cross-reactivity against self-antigens, the sequence of the first fusion protein encoded by the first vaccine to those of human proteins were compared. Considering that peptide antigens are presented as fragments of either 8-11 amino acids on MHC class Ito CD8 T cells, or 12-20 amino acids on MHC class II to CD4 T
cells, a search for all 8-mers generated from the HPV16/18 E6/E7 peptides plus the junctional regions in pBI-11 encoded fusion protein against human protein sequences in UniProtTm, which contains the Swiss-ProtTM and TrEMBLI'm databases, was carried out.

[0068] Specifically, in order to search for potential novel peptides that may be identical to endogenous peptides, all linear sequences of 5-8 amino acids in length (5-mers to 8-mers) from amino acid 24-550 of pBI-11 were generated. The linear sequences span the last 7 amino acids of the signal peptide, HPV-16 E7, HPV-18 E7, HPV-18 E6, HPV-16 E6, and the first 11 amino acids of HSP70. In total, 520 8-mers, 521 7-mers, 522 6-mers, and 523 5-mers were generated.

[0069] Furthermore, the sequences were submitted to the UniProtTm protein database (https://www.uniprot.org/) in groups of 80-100 sequences using the Peptide Search Tool provided at the website and searched for exact matches against the Swiss-ProtTm and TrEMBLI'm databases filtered for human proteins. The results revealed no exact match between the pBI-11 encoded fusion protein and endogenous human peptide sequences that are at least 8 amino acids in length.

[0070] An alternative searching approach was also conducted. The Immune Epitope Database (https://www.iedb.org/) was searched by using the same region of the pBI-11 protein sequence.
Date Recue/Date Received 2022-01-18 "Substring" for Linear Epitope to obtain any epitope sequences that are mapped to the pBI-10.1 sequence (disclosed in U.S. Patent Application No. 17/534,256, filed on November 23, 2021) were selected. The search identified a B cell epitope derived from HPV-16 E7 in pBI-11 (see Table 1 below). This epitope is also present in pBI-1, which has been tested for its safety in human subjects.
Taken together, these results indicate that the arrangement of the fusion protein encoded by the first vaccine of the instant application (e.g., pBI-11 or pBI-12) is unlikely to generate peptides that could induce cross-reactive T cell immunity against self-antigens.

[0071] Table 1. Peptide epitope from pBI-11 protein identified in the Immune Epitope Database HPV Protein Epitope' 'Human Protein Uniprot ID
HPV16 E7 RTLED Glutamate decarboxylase 2 (GAD2) A0A3B3IU09

[0072] In addition, pBI-11 encodes a fusion protein of the signal peptide, HPV-16 E7, HPV-18 E7, HPV-16 E6, and HPV-18 E6 (E7(16)/E7(18)/E6(16)/E6(l8), see FIG. 1A), arranged in an order different from that in TA-HPV (see FIG. 1B). Such arrangement can further avoid boosting immune response against junction-associated epitopes potentially contained within the fusion protein encoded by pBI-11.

[0073] As a result, the vaccine combination of the instant application reduces the risk to induce cross-reactive immune response against self-antigens and the possibility to generate immunity against junction-associated epitopes in the fusion protein comprised within or encoded by the vaccine, and thus has an improved safety.
Example 3: HPV antigen-specific CD8+ T cell-mediated immune responses generated by the pBI-11 vaccine can be further enhanced by boost with TA-HPV vaccinia virus vaccine.

[0074] In vivo T cell activation assays were performed to compare immune response in mice vaccinated with either pBI-11 alone, or pBI-11 in combination with TA-HPV.

[0075] FIG. 2A is a schematic illustration of the experiment design. 6- to 8-week-old female C57BL/6 mice purchased from Taconic Biosciences (Germantown, NY) were vaccinated pBI-11 Date Recue/Date Received 2022-01-18 (25 mg/50 ml/mouse) through intramuscular (I.M.) injection. The mice were divided into a control group (naive group), a DDD group and a DDV group. Each mouse in each group was boosted with the same regimen 7 days later. One week after the second vaccination, the DDD
group of the mice (denoted as DDD in FIG.2A) was vaccinated with pBI-11 (25 mg/50 ml/mouse) through I.M.
injection. The DDV group of mice (denoted as DDV in FIG. 2A) was vaccinated with TA-HPV (1 x 106 pfu/50 ml/mouse) through I.M. injection. Six days after the last vaccination, peripheral blood was collected from the vaccinated or naive mice for HPV-16 E7 tetramer staining. Fourteen days after the last vaccination, splenocytes were prepared from the vaccinated mice and stimulated with either HPV-16 E6 (aa 50 to 57), HPV-16 E7 (aa 49 to 57), or HPV-18 E6 (aa 67 to 75) peptide in the presence of GolgiPlug rim (BD Pharmingen, San Diego, CA). It is known that the presentation of epitope HPV-16 E6 (aa 50 to 57) is suppressed by the immunodominant epitope of HPV-16 E7 (aa 49 to 57). Intracellular IFN-y cytokine staining assay was performed to detect antigen-specific CD8+ T cells. The cells were acquired with a FACSCaliburTm flow cytometer, and data were analyzed with CellQuest Pro software (BD Biosciences, Mountain View, CA).

[0076] As shown in FIG. 2B, mice vaccinated with the DDV regimen had significantly higher percentages of E7-specific CD8+ T cells than mice vaccinated with pBI-11 alone (DDD) or naive mice.

[0077] Furthermore, FIG. 2C shows that mice in a prime-vaccinia boost (DDV) had significantly higher numbers of HPV-16 E7-specific T cells (P = 0.0428) and higher HPV-18 E6-specific T cells (P = 0.2116) than those that only received pBI-11. In fact, HPV16 E7-specific CD8+ T cell-mediated immune responses in mice vaccinated with TA-HPV alone was previously characterized (Virology 2018 Dec; 525:205-215). It is found that mice vaccinated with TA-HPV
alone did not generate appreciable HPV16 E7-specific CD8+ T cell-mediated immune responses (urology 2018 Dec; 525:205-215). However, our result indicates that TA-HPV
booster vaccination is capable of simultaneously enhancing HPV-16 and HPV-18 antigen-specific CD8 T cell immune responses generated after priming with pBI-11 DNA vaccine.

Date Recue/Date Received 2022-01-18

[0078] Based on the above results, the heterologous prime-boost vaccination using the first vaccine (e.g., pBI-11) in combination with the second vaccine (e.g., TA-HPV) according to the vaccine combination of the present disclosure induces an elevated HPV antigen-specific CD8+ T
cell-mediated immune responses compared to administration with the first vaccine (e.g., pBI-11) alone.
Example 4: The vaccine combination of the present disclosure can be combined with anti-PD-1 immune checkpoint blockade to improve therapeutic antitumor response.

[0079] The ability of the vaccine combination of the present disclosure in combination with an anti-PD-1 immune checkpoint inhibitor to generate therapeutic antitumor effects against HPV-associated diseases were examined in the HPV-16 E6/E7+ TC-1 tumor model.

[0080] FIG. 3A is a schematic illustration of the experiment design. 6- to 8-week-old female C57BL/6 mice were injected with 2 x 105 of TC-1 tumor cells subcutaneously on day 0. On day 3, the mice were divided into 4 groups (untreated group, anti-PD-1 group. DDV
group and anti-PD-1+DDV group). The mice in the anti-PD-1 group were injected with purified anti-mouse PD-1 monoclonal antibody (MAb; clone 29F.1Al2, 200mg/mouse) via intraperitoneal injection. The treatment was repeated every other day. The mice in the DDV group were vaccinated with pBI-11 (25mg/ 50m1/mouse) through LM. injection and boosted once 3 days later, and were further boosted with TA-HPV vaccinia virus 3 days later through skin scarification.
The mice in the anti-PD-1+DDV group were treated with both anti-mouse PD-1 MAb and pBI-11 DNA
vaccine prime followed by TA-HPV vaccinia virus boost. On day 27, PBMCs were collected for the characterization of HPV-16 E7-specific CD8 T cell-mediated immune responses using HPV-16 E7 peptide (aa 49 to 57)-loaded tetramer staining.

[0081] In one example, schematic illustration of the experiment in FIG. 3A
shows that the immune checkpoint inhibitor (e.g., anti-PD-1 antibody) was administered prior to heterologous prime-boost vaccination (e.g., DDV). However, in other examples, additively and/or alternatively, Date Recue/Date Received 2022-01-18 the immune checkpoint inhibitor may be administered during the course of heterologous prime-boost vaccination.

[0082] For tetramer staining, mouse PBMCs were stained with purified anti-mouse CD16/32 first and then stained with FITC-conjugated anti-mouse CD8a and PE-conjugated HPV-16 E7 (an 49-57) peptide-loaded H-2Db tetramer at 4 C for 1 hour. After washing, the cells were stained with 7-AAD. The cells were acquired with the FACSCaliburTM flow cytometer and analyzed with CellQuest Pro software (BD Biosciences, Mountain View, CA). The results of tetramer staining are shown in FIG. 3B.

[0083] The growth of the tumor was monitored twice a week by palpation and digital caliper measurement. Tumor volume was calculated using the formula [largest diameter x (perpendicular diameter)2] x 3.14/6 and is shown in FIG. 3C. The survival rate of the tumor-bearing mice was recorded, as illustrated in FIG. 3D, where both natural death and a tumor diameter greater than 2 cm leading to death were counted as death.

[0084] As shown in Fig. 3B, mice receiving DDV regimen, either alone or with anti-PD-1 antibody, displayed HPV-16 E7-specific CD8+T cell-mediated immune responses, whereas in the absence of vaccination with anti-PD-1 antibody, treatment of anti-PD-1 antibody did not elicit a detectable HPV-16 E7-specific CD8+ T cell response.

[0085] Furthermore, FIG. 3C demonstrated that addition of anti-PD-1 antibody treatment to the DDV regimen significantly enhanced the therapeutic antitumor effects. This suggests synergy of vaccination and anti-PD-1 antibody treatment and that the latter is not effective without a prior immune response. Additionally, FIG. 3D shows that the combinational treatment (anti-PD-1+DDV) translated into significantly (P = 0.0073 when compared to DDV, and P = 0.0002 when compared to anti-PD-1) better survival of the tumor-bearing mice.

[0086] In conclusion, the vaccine combination of the present disclosure including a first vaccine which comprises a first fusion protein with an indicated arrangement of HPV
antigens, or a first polynucleotide encoding the same; and a second vaccine which comprises a second fusion protein Date Recue/Date Received 2022-01-18 and a third fusion protein both with an arrangement of HPV antigens different from that in the first fusion protein, or a second polynucleotide encoding the second fusion protein and the third fusion protein, not only reduces the risk to induce cross-reactive immunity against self-antigens and to boost an immune response against junction-associated epitopes in the fusion protein contained in or encoded by the vaccine, but also exhibits a significant HPV antigen-specific immune response.
Moreover, the vaccine combination of the present disclosure in combination with an immune checkpoint inhibitor (e.g., anti-PD-1 antibody) elicits a stronger HPV antigen-specific antitumor response in vivo and further translates into more potent antitumor efficacy.

[0087] Those skilled in the art will readily observe that numerous modifications and alterations of the device and method may be made while retaining the teachings of the disclosure. Accordingly, the above disclosure should be construed as limited only by the metes and bounds of the appended claims.
Date Recue/Date Received 2022-01-18

Claims

1. A vaccine combination comprising a first vaccine comprising: a first fusion protein or a first polynucleotide encoding the first fusion protein, wherein the first fusion protein, in an order from N to C tenninus, comprises:
(i) an E7 protein of human papillomavirus type 16 (HPV-16) or a functional variant thereof, wherein the E7 protein of HPV-16 or a functional variant thereof is start with SEQ ID NO: 1 and end with SEQ ID NO: 2 from N to the C teuninus;
(ii) an E7 protein of human papillomavirus type 18 (HPV-18) or a functional variant thereof, wherein the E7 protein of HPV-18 or a functional variant thereof is start with SEQ ID NO: 3 and end with SEQ ID NO: 4 from N to C tenninus;
(iii) an E6 protein of HPV-16 or a functional variant thereof, wherein the E6 protein of HPV-16 or a functional variant thereof is start with SEQ
ID NO: 5 and end with SEQ ID NO: 6 from N to C terminus;
(iv) an E6 protein of HPV-18 or a functional variant thereof, wherein the E6 protein of HPV-18 or a functional variant thereof is start with SEQ ID NO: 7 and end with SEQ ID NO: 8 from N to C terminus; and (v) a heat shock protein or a functional variant thereof; and a second vaccine comprising: a second fusion protein and a third fusion protein, or a second polynucleotide encoding the second fusion protein and the third fusion protein, wherein the second fusion protein comprises:
an E6 protein of HPV-16 or a functional variant thereof; and an E7 protein of HPV-16 or a functional variant thereof; and wherein the third fusion protein comprises:
an E6 protein of HPV-18 or a functional variant thereof-, and an E7 protein of HPV-18 or a functional variant thereof, wherein amino acid sequences ofjunction regions in the first fusion protein are different from those in the second fusion protein and the third fusion protein.

2. The vaccine combination according to claim 1, wherein the E7 protein of HPV-16 comprises SEQ ID NO: 9;

Date Recue/Date Received 2023-06-06 wherein the E7 protein of HPV-18 comprises SEQ ID NO: 10;
wherein the E6 protein of HPV-16 comprises SEQ ID NO: 11; and wherein the E6 protein of HPV-18 comprises SEQ ID NO: 12.

3. The vaccine combination according to claim 1, wherein the E7 protein of HPV-16 is encoded by SEQ ID NO: 13;
wherein the E7 protein of HPV-18 is encoded by SEQ ID NO: 14;
wherein the E6 protein of HPV-16 is encoded by SEQ ID NO: 15; and wherein the E6 protein of HPV-18 is encoded by SEQ ID NO: 16.

4. The vaccine combination according to claim 1, wherein the first polynucleotide comprises SEQ ID NO: 17.

5. The vaccine combination according to claim 1, wherein the first polynucleotide comprises SEQ ID NO: 18.

6. The vaccine combination according to claim 1, wherein the second polynucleotide is contained within a recombinant virus.

7. The vaccine combination according to claim 6, wherein the recombinant virus is TA-HPV.

8. Use of the vaccine combination according to any one of claims 1-7 in the manufacture of a medicament for the treatment of an HPV-associated disease in a subject in need thereof, wherein the first vaccine is formulated for administration to the subject as a priming vaccine; and the second vaccine is foimulated for administration to the subject as a boosting vaccine.

9. The use according to claim 8, wherein the first vaccine is further formulated for administration to the subject as a boosting vaccine after the administration of the first vaccine as the priming vaccine and prior to the administration of the second vaccine as the boosting vaccine.

Date Recue/Date Received 2023-06-06

10. The use according to claim 8, wherein the first vaccine comprises the first polynucleotide, and wherein the first vaccine is formulated for administration at a dose ranging from 10 micrograms per subject to 20 milligrams per subject.

11. The use according to claim 8, wherein the second vaccine comprises TA-HPV, and wherein the second vaccine is formulated for administration at a dose ranging from 1 x 104 plaque-forming units (pfu) to 2 x 109 pfu.

12. The use according to claim 8, wherein the vaccine combination is further formulated for administration with a chemotherapy, radiotherapy, chemo-radiotherapy, cryotherapy, thermotherapy, targeted therapy, cellular therapy, gene therapy, or immunotherapy in combination with the administration of the vaccine combination.

13. The use according to claim 12, wherein the chemotherapy, radiotherapy, chemo-radiotherapy, cryotherapy, thermotherapy, targeted therapy, cellular therapy, gene therapy, or immunotherapy is formulated for administration prior to and/or simultaneously with the administration of the first vaccine.

14. The use according to claim 12, wherein the immunotherapy comprises an immune checkpoint inhibitor formulated for administration to the subject.

15. The use according to claim 14, wherein the immune checkpoint inhibitor is an immune modulator targeting programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD L1), cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4), inducible costimulator (ICOS), T-cell immunoglobulin and mucin domain 3 (TIM-3), lymphocyte activation gene 3 (LAG-3) or T cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif (ITIM) domain (TIGIT).

16. The use according to claim 14, wherein the immune checkpoint inhibitor is an anti-PD-1 antibody.

Date Recue/Date Received 2023-06-06 VACCINE COMBINATION AND METHOD FOR USING THE SAME
REFERENCE TO SEQUENCE LISTING
[0001] Accompanying this application is a sequence listing in an American Standard Code for Information Interchange (ASCII) text file named "211223-US86679-Sequence Listing-v1F.txt", created December 07, 2021, and having a size of 18,253 bytes. The sequence listing is hereby fully incorporated by reference herein.
[0002] [blank]

Date Recue/Date Received 2023-06-06