WO2022122026A1

WO2022122026A1 - A modified oncolytic virus, composition and use thereof

Info

Publication number: WO2022122026A1
Application number: PCT/CN2021/137194
Authority: WO
Inventors: Min Liang
Original assignee: Genesail (Shanghai) Co., Ltd.; Genesailnova (Shanghai) Co., Ltd.
Priority date: 2020-12-11
Filing date: 2021-12-10
Publication date: 2022-06-16
Also published as: CN117222436A

Abstract

Provided is a modified oncolytic virus having a first heterologous polynucleotide encoding a first molecule capable of inhibiting the interaction between PD-1 and PD-L1 and a second heterologous polynucleotide encoding a second molecule capable of inhibiting TGF-β signaling. Also provided is a pharmaceutical composition comprising the modified oncolytic virus and a method of treating a cancer comprising administering to a subject the modified oncolytic virus or the pharmaceutical composition

Description

A MODIFIED ONCOLYTIC VIRUS, COMPOSITION AND USE THEREOF

FIELD OF TECHNOLOGY

The present disclosure relates generally to modified oncolytic viruses, the composition comprising the modified oncolytic viruses and its use in the treatment of tumor.

BACKGROUND OF THE INVENTION

Tumor is diagnosed in more than 14 million people every year worldwide. Despite of numerous advances in medical research, tumor accounts for approximately 16%of all deaths.

Malignant tumors are often resistant to conventional therapies and represent significant therapeutic challenges. For example, micro-metastasis can establish at a very early stage in the development of primary tumors. Therefore, at the time of diagnosis, many tumor patients already have microscopic metastasis. Tumor-reactive T cells can seek out and destroy the micro-metastasis and spare the surrounding healthy tissues. However, naturally existing T cell responses against malignancies is often not sufficient to cause regression of the primary or metastatic tumors.

Oncolytic viruses have shown potential as anti-tumor agents. Unlike conventional gene therapy, oncolytic viruses are able to spread through tumor tissue by virtue of viral replication and concomitant cell lysis. However, Oncolytic viruses itself are not sufficient to treat the primary or metastatic tumors either.

Therefore, the need for enhancing the potency of oncolytic viruses and clearing metastatic tumor cells is particularly acute.

SUMMARY OF THE INVENTION

In one aspect, the present disclosure relates to a modified oncolytic virus comprising a virus genome having a first heterologous polynucleotide encoding a first molecule capable of inhibiting the interaction between PD-1 and PD-L1 and a second heterologous polynucleotide encoding a second molecule capable of inhibiting TGF-βsignaling.

In certain embodiments, the oncolytic virus is selected from the group consisting of vaccinia virus, adenovirus, reovirus, measles, herpes simplex virus, Semliki Forest virus, Venezuelan equine encephalitis, Parvovirus, Chicken Anemia Virus, Measles Virus, Coxsackie Virus, Vesicular Stomatitis Virus, Seneca Valley Virus, Maraba virus, Newcastle disease virus and Myxoma virus. In certain embodiments, the oncolytic virus is vaccinia virus.

In certain embodiments, the modified oncolytic virus is attenuated and can replicate in a tumor cell.

In certain embodiments, the virus genome comprises at least one deletion or disruption that renders the virus capable of selective replication in a tumor cell. In certain embodiments, the deletion or the disruption is in an Open Reading Frame (ORF) encoding at least a part of an enzyme that is both essential for replication of the virus and preferentially expressed in a tumor cell than in a non-tumor cell. In certain embodiments, the enzyme is a kinase. In certain embodiments, the enzyme is thymidine kinase.

In certain embodiments, the oncolytic virus is derived from the Western Reserve strain.

In certain embodiments, the first heterologous polynucleotide and the second heterologous polynucleotide is inserted in the place of the deletion.

In certain embodiments, the first heterologous polynucleotide and the second heterologous polynucleotide are configured such that they are expressed in the same or different stages of replicative cycle of the modified oncolytic virus.

In certain embodiments, the first molecule is a first fusion protein and the second molecule is a second fusion protein. In certain embodiments, the first heterologous polynucleotide comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a first promoter –a polynucleotide encoding the first fusion protein –a first stop codon, and the second heterologous polynucleotide comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a second promoter –a polynucleotide encoding the second fusion protein –a second stop codon.

In certain embodiments, the first fusion protein expressed from the first heterologous polynucleotide and the second fusion protein expressed from the second heterologous polynucleotide are expressed as separate proteins. In certain embodiments, the first heterologous polynucleotide is immediately upstream or immediately downstream of the second heterologous polynucleotide. In certain embodiments, wherein the first promoter is capable of driving expression of the first fusion protein, and the second promoter is capable of driving expression of the second fusion protein, wherein the first and the second promoters are in a head-to-head orientation.

In certain embodiments, the first and the second promoters are the same or different. In certain embodiments, the first and the second promoters are both early and late promoter. In certain embodiments, the early and late promoter is pSE/L.

In certain embodiments, the first and second stop codons are the same or different.

In certain embodiments, the first fusion protein comprises PD-1 extracellular domain (PD-1 ECD) . In certain embodiments, the first fusion protein further comprises a first immunoglobulin Fc region. In certain embodiments, the first immunoglobulin Fc region is a first human IgG1 Fc region.

In certain embodiments, the PD-1 ECD is operably linked to the first immunoglobulin Fc region at the C terminal of the PD-1 ECD.

In certain embodiments, the first fusion protein further comprises a signal peptide.

In certain embodiments, the signal peptide is operably linked to the PD-1 ECD at the C terminal of the signal peptide. In certain embodiments, the signal peptide is CD33 signal peptide.

In certain embodiments, the PD-1 ECD comprises an amino acid sequence of SEQ ID NO: 1 or a homologous sequence thereof having at least 80%sequence identity. In certain embodiments, the amino acid sequence is encoded by a nucleic acid sequence of SEQ ID NO: 7 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the first human IgG1 Fc region comprises an amino acid sequence of SEQ ID NO: 3 or a homologous sequence thereof having at least 80%sequence identity. In certain embodiments, the amino acid sequence is encoded by a nucleic acid sequence of SEQ ID NO: 9 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the CD33 signal peptide comprises an amino acid sequence of SEQ ID NO: 4 or a homologous sequence thereof having at least 80%sequence identity. In certain embodiments, the amino acid sequence is encoded by a nucleic acid sequence comprising SEQ ID NO: 11 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the first fusion protein comprises an amino acid sequence of SEQ ID NO: 5 or a homologous sequence thereof having at least 80%sequence identity. In certain embodiments, he amino acid sequence is encoded by a nucleic acid sequence comprising SEQ ID NO: 13 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the first molecule is an anti-PD-1 antibody and the second molecule is a second fusion protein.

In certain embodiments, the anti-PD-1 antibody comprises: a HCDR1 having an amino acid sequence of SEQ ID NO: 23 or a homologous sequence thereof having at least 80%sequence identity, a HCDR2 having an amino acid sequence of SEQ ID NO: 24 or a homologous sequence thereof having at least 80%sequence identity, a HCDR3 having an amino acid sequence of SEQ ID NO: 25 or a homologous sequence thereof having at least 80%sequence identity, a LCDR1 having an amino acid sequence of SEQ ID NO: 26 or a homologous sequence thereof having at least 80%sequence identity, a LCDR2 having an amino acid sequence of SEQ ID NO: 27 or a homologous sequence thereof having at least 80%sequence identity, and a LCDR3 having an amino acid sequence of SEQ ID NO: 28 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the HCDR1 is encoded by a nucleic acid sequence of SEQ ID NO: 31 or a homologous sequence thereof having at least 80%sequence identity, the HCDR2 is encoded by a nucleic acid sequence of SEQ ID NO: 32 or a homologous sequence thereof having at least 80%sequence identity, the HCDR3 is encoded by a nucleic acid sequence of SEQ ID NO: 33 or a homologous sequence thereof having at least 80%sequence identity, the LCDR1 is encoded by a nucleic acid sequence of SEQ ID NO: 34 or a homologous sequence thereof having at least 80%sequence identity, the LCDR2 is encoded by a nucleic acid sequence of SEQ ID NO: 35 or a homologous sequence thereof having at least 80%sequence identity, and the LCDR3 is encoded by a nucleic acid sequence of SEQ ID NO: 36 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the anti-PD-1 antibody comprises a heavy chain variable region having an amino acid sequence of SEQ ID NO: 29 or a homologous sequence thereof having at least 80%sequence identity, and a light chain variable region having an amino acid sequence of SEQ ID NO: 30 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the anti-PD-1 antibody heavy chain variable region is encoded by a nucleic acid sequence of SEQ ID NO: 37 or a homologous sequence thereof having at least 80%sequence identity, and the anti-PD-1 antibody light chain variable region is encoded by a nucleic acid sequence of SEQ ID NO: 38 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the anti-PD-1 antibody comprises a full length heavy chain having an amino acid sequence of SEQ ID NO: 21 or a homologous sequence thereof having at least 80%sequence identity, and a full length light chain having an amino acid sequence of SEQ ID NO: 20 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the anti-PD-1 antibody full length heavy chain is encoded by a nucleic acid sequence of SEQ ID NO: 39 or a homologous sequence thereof having at least 80%sequence identity, and the anti-PD-1 antibody full length light chain is encoded by a nucleic acid sequence of SEQ ID NO: 40 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the first heterologous polynucleotide further comprises a third heterologous polynucleotide and a fourth heterologous polynucleotide, wherein the third heterologous polynucleotide comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a third promoter –a polynucleotide encoding the anti-PD-1 antibody heavy chain –a third stop codon, and wherein the fourth heterologous polynucleotide comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a fourth promoter –a polynucleotide encoding the anti-PD-1 antibody light chain –a fourth stop codon; and the second heterologous polynucleotide further comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a second promoter –a polynucleotide encoding the second fusion protein –a second stop codon.

In certain embodiments, the third heterologous polynucleotide is immediately upstream or immediately downstream of the fourth heterologous polynucleotide. In certain embodiments, the first heterologous polynucleotide is immediately upstream or immediately downstream of the second heterologous polynucleotide.

In certain embodiments, the third promoter is capable of driving expression of the anti-PD-1 antibody heavy chain, and the fourth promoter is capable of driving expression of the anti-PD-1 antibody light chain, wherein the third and the fourth promoters are in a head-to-head orientation.

In certain embodiments, the anti-PD-1 antibody expressed from the first heterologous polynucleotide and the second fusion protein expressed from the second heterologous polynucleotide are expressed as separate proteins.

In certain embodiments, the second, the third and the fourth promoters are the same or different. In certain embodiments, the second, the third and the fourth promoters are both early and late promoter. In certain embodiments, the early and late promoter is pSE/L.

In certain embodiments, the second, the third and fourth stop codons are the same or different.

In certain embodiments, the second fusion protein comprises TGF-βreceptor II extracellular domain (TGFBRII ECD) . In certain embodiments, the second fusion protein further comprises a second immunoglobulin Fc region. In certain embodiments, the immunoglobulin Fc region is a second human IgG1 Fc region.

In certain embodiments, the TGFBRII ECD is operably linked to the second immunoglobulin Fc region at the C terminal of the TGFBRII ECD.

In certain embodiments, the second fusion protein further comprises a signal peptide. In certain embodiments, the signal peptide is operably linked to the TGFBRII ECD at the C terminal of the signal peptide. In certain embodiments, the signal peptide is CD33 signal peptide.

In certain embodiments, the TGFBRII ECD comprises an amino acid sequence of SEQ ID NO: 2 or a homologous sequence thereof having at least 80%sequence identity. In certain embodiments, the amino acid sequence is encoded by a nucleic acid sequence of SEQ ID NO: 8 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the second human IgG1 Fc region comprises an amino acid sequence of SEQ ID NO: 3 or a homologous sequence thereof having at least 80%sequence identity. In certain embodiments, the amino acid sequence is encoded by a nucleic acid sequence of SEQ ID NO: 10 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the CD33 signal peptide comprises an amino acid sequence of SEQ ID NO: 4 or a homologous sequence thereof having at least 80%sequence identity. In certain embodiments, the amino acid sequence is encoded by a nucleic acid sequence comprising SEQ ID NO: 12 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the second fusion protein comprises an amino acid sequence of SEQ ID NO: 6 or a homologous sequence thereof having at least 80%sequence identity. In certain embodiments, the amino acid sequence is encoded by a nucleic acid sequence comprising SEQ ID NO: 14 or a homologous sequence thereof having at least 80%sequence identity.

In certain embodiments, the first fusion protein and the second fusion protein are capable of forming a dimer. In certain embodiments, the dimer is formed via the association of the first immunoglobulin Fc region and the second immunoglobulin Fc region.

In certain embodiments, the modified oncolytic virus provided herein has a nucleic acid sequence of SEQ ID NO: 17 or SEQ ID NO: 22.

In one aspect, the present disclosure provides a pharmaceutical composition, comprising the modified oncolytic virus provided herein and a pharmaceutically acceptable carrier.

In one aspect, the present disclosure provides a method of treating a tumor, comprising administering to a subject an effective amount of the modified oncolytic virus provided herein or the pharmaceutical composition provided herein.

In certain embodiments, the subject is human.

In certain embodiments, the tumor is a solid tumor.

In certain embodiments, the tumor is melanoma, non-small cell lung cancer, renal cell carcinoma, Hodgkin lymphoma, squamous cell carcinoma of the head and neck, bladder cancer, colorectal cancer, triple negative breast cancer, hepatocellular carcinoma, pancreatic cancer, ovarian cancer, colon cancer, pharyngeal squamous cell carcinoma, or ovarian teratoma.

In certain embodiments, the route of administering is topical. In certain embodiments, the route of administering is intra-tumor injection.

BRIEF DESCRIPTION OF THE FIGURES

Figure 1 shows the vaccinia virus construction of WR-GO-001 comprising insertion of nucleic acid sequences encoding the human PD-1 G22-170 ECD Fc fusion protein and TGF-beta RII 23-166 ECD Fc fusion protein.

Figure 2 shows the vaccinia virus construction of WR-GO-002 comprising insertion of nucleic acid sequences encoding the TGF-beta RII 23-166 ECD Fc fusion protein.

Figure 3 shows the vaccinia virus construction of WR-GO-003 comprising insertion of nucleic acid sequences encoding the human PD-1 G22-170 ECD Fc fusion protein.

Figure 4 shows the vaccinia virus construction of WR-GO-004 comprising insertion of nucleic acid sequences encoding the anti-PD-1 antibody and TGF-beta RII 23-166 ECD Fc fusion protein.

Figures 5A-5C show the expression of human PD-1 Fc chimera protein, human TGF-beta Receptor II Fc chimera protein and Anti-human PD-1 antibody in both supernatant and intracellular samples of Hela cells infected by WR-GO-002, WR-GO-003 or WR-GO-004 was measured using ELISA method.

Figures 6A-6H show the cytotoxicity of WR-GO-001, WR-GO-002, WR-GO-003 and WR-GO-004 in MC38 and CT26 cell lines.

Figures 7A-7D show the cytotoxicity assay results of WR-GO-003 in human tumor cell lines (FaDu , PA1 PANC-1) and human normal cell line (HUVEC) .

Figures 8A-8D show the cytotoxicity assay results of WR-GO-004 in human tumor cell lines (FaDu, PA1 PANC-1) and human normal cell line (HUVEC) .

Figures 9A and 9B show the fold change of VPs of WR-GO-003 or WR-GO-004 in FaDu.

DETAILED DESCRIPTION

In one aspect, the present disclosure relates to a modified oncolytic virus comprising a virus genome having a first heterologous polynucleotide encoding a first molecule capable of inhibiting the interaction between PD-1 and PD-L1 and a second heterologous polynucleotide encoding a second molecule capable of inhibiting TGF-β signaling.

Oncolytic Virus

The term “oncolytic virus” as used herein refers to a virus capable of selectively replicating in and slowing the growth or inducing the death of tumor cells, either in vitro or in vivo, while having no or minimal effect on normal cells. In certain embodiments, an oncolytic virus contains a viral genome packaged into a viral particle (or virion) and is infectious (i.e., capable of infecting and entering into a host cell or subject) . In certain embodiments, the oncolytic virus can be a DNA virus or an RNA virus, and can be in any suitable form such as a DNA viral vector, a RNA viral vector or viral particles.

The term “selectively replicate” as used herein refers to that the replication rate of the oncolytic virus is significantly higher in tumor cells than in non-tumor cells (e.g. healthy cells) . In certain embodiments, the oncolytic virus shows at least 50%, 60%, 70%, 80%, 90%, 1 fold, 2 folds, 3 folds, 4 folds, 5 folds, 10 folds, 50 folds, 100 folds or 1000 folds higher rate of lysis in tumor cells than in non-tumor cells (e.g., healthy cells) .

In certain embodiments, the oncolytic virus of the present disclosure can selectively replicate in liver tumor cells (e.g., Hepal-6 cells, Hep3B cells, 7402 cells, and 7721 cells) , breast tumor cells (e.g., MCF-7 cells) , tongue tumor cells (e.g., TCa8113 cells) , adenoid cystic tumor cells (e.g., ACC-M cells) , prostate tumor cells (e.g., LNCaP cells) , human embryo kidney cells (e.g., HEK293 cells) , lung tumor cells (e.g., A549 cells) , or cervical tumor cells (e.g., Hela cells) .

The oncolytic viruses of the present disclosure can be derived from poxvirus (e.g., vaccinia virus) , adenovirus (e.g., Delta-24, Delta-24-RGD, ICOVIR-5, ICOVIR-7, Onyx-015, ColoAdl, H101, and AD5/3-D24-GMCSF) , reovirus (e.g., Reolysin) , measles virus, herpes simplex virus (e.g., HSV, OncoVEX GMCSF) , Newcastle Disease virus (e.g., 73-T PV701 and HDV-HUJ strains as well as those described in the following literatures: Phuangsab et al., 2001, Cancer Lett. 172 (1) : 27-36; Lorence et al., 2007, Curr. Cancer Drug Targets 7 (2) : 157-67; and Freeman et al., 2006, Mol. Ther. 13 (1) : 221-8) , retrovirus (e.g., influenza virus) , myxoma virus, rhabdovirus (e.g., vesicular stomatitis virus; those described in the following literatures: Stojdl et al., 2000, Nat. Med. 6 (7) : 821-5 and Stojdl et al., 2003, Cancer Cell 4 (4) : 263-75) , picornavirus (e.g., Seneca Valley virus; SW-001 and NTX-010) , coxsackievirus or parvovirus.

In certain embodiments, the oncolytic virus of the present disclosure is derived from a poxvirus. The term “poxvirus” as used herein refers to a virus belonging to the Poxviridae subfamily. In certain embodiments, the poxvirus is a virus belonging to the Chordopoxviridae subfamily. In certain embodiments, the poxvirus is a virus belonging to the Orthopoxvirus subfamily. Sequences of the genome of various poxviruses, for example, the vaccinia virus, cowpox virus, Canarypox virus, Ectromelia virus, Myxoma virus genomes are available in the art and specialized databases such as Genbank (accession number NC_006998, NC_003663, NC_005309, NC_004105, NC_001132, respectively) .

In certain embodiments, the oncolytic virus of the present disclosure is derived from a vaccinia virus. Vaccinia viruses are members of the poxvirus family characterized by an approximately 190kb double-stranded DNA genome that encodes numerous viral enzymes and factors that enable the virus to replicate independently from the host cell machinery. In certain embodiments, the vaccinia virus of the present disclosure is derived from Elstree, Copenhagen, Western Reserve or Wyeth strains. In certain embodiments, the vaccinia virus of the present disclosure is the Western Reserve (WR) strain. Western Reserve strain has been well characterized and its complete sequence is available on the NCBI site (www. ncbi. nlm. nih. gov) with access number of AY243312.

The term “modified oncolytic virus” as used herein refers to an oncolytic virus that has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein. In certain embodiments, the modified oncolytic virus provided herein is is genetically altered by deletion and/or addition of nucleic acid sequences. In certain embodiments, the modified oncolytic virus provided herein comprises deletion of thymidine kinase (TK) gene. In certain embodiments, the modified oncolytic virus provided herein comprises addition of nucleic acid sequences encoding anti-human PD-1 antibody, PD-1 ECD-IgG1 Fc fusion protein and/or TGFBRII ECD -IgG1 Fc fusion protein.

In certain embodiments, the modified oncolytic virus of the present disclosure is attenuated. In certain embodiments, the modified oncolytic virus has reduced (e.g. at least 90%, 80%, 70%, 60%, 50%less) or undetectable virulence compared to its wild type counterpart in the normal cells (e.g., healthy cells) .

The modified oncolytic virus of the present disclosure can be derived from any oncolytic virus known in the art to be oncolytic by its propensity to selectivity replicate and kill tumor cells as compared to non-tumor cells. The oncolytic virus may be naturally oncolytic or may be rendered oncolytic by genetic engineering, such as by modifying one or more genes so as to increase tumor selectivity and/or preferential replication in tumor cells. Examples of such genes for modification include those involved in DNA replication, nucleic acid metabolism, host tropism, surface attachment, virulence, host cell lysis and virus spread (see for example Kirn et al., 2001, Nat. Med. 7: 781; Wong et al., 2010, Viruses 2: 78-106) .

In certain embodiments, the virus genome of the modified oncolytic virus of the present disclosure comprises at least one deletion or disruption that renders the virus capable of selective replication in a tumor cell. For example, the deletion or disruption may reduce the expression or function of an enzyme essential for virus replication, such that the virus becomes less capable to replicate in the absence of such an enzyme. In some embodiments, the virus replication depends on the presence and/or level of such an enzyme in a cell, the higher the level of the enzyme, the higher replicate capability or rate of the virus.

In certain embodiments, the deletion or the disruption is in an Open Reading Frame (ORF) . The term “open reading frame” or an “ORF” or “encoding sequence” as used herein refers to a DNA sequence that is capable of being translated into an amino acid sequence. An ORF usually begins with a start codon (e.g., ATG) , followed by amino-acid encoding codons, and ends with a stop codon (e.g., TGA, TAA, TAG) .

In certain embodiments, the ORF encodes at least a part of an enzyme that is essential for replication of the virus and is preferentially expressed in a tumor cell than in a non-tumor cell. The term “express” as used herein refers to a process wherein a protein or a peptide sequence is produced from its encoding DNA or RNA sequence. In certain embodiments, the enzyme is a kinase.

In certain embodiments, the deletion in the ORF constitutes 100%, more than 99%, more than 98%, more than 95%, more than 90%, more than 85%, more than 80%, more than 75%, more than 70%, more than 65%, more than 60%, more than 55%, more than 50%, more than 45%, more than 40%, more than 35%, more than 30%, more than 25%, more than 20%, more than 15%, or more than 10%of the full length of the ORF. In certain embodiments, the deletion in the ORF constitutes at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 300, 500, 800, 1000, 1200, 1500, 1800, 2000, 2200, 2400, 2500 or more nucleotides (optionally contiguous) .

In certain embodiments, the ORF for thymidine kinase (TK) is deleted or disrupted. TK is involved in the synthesis of deoxyribonucleotides. TK is needed for viral replication in normal cells as these cells have generally low concentration of nucleotides whereas it is dispensable in tumor cells, which contain high nucleotide concentration. In poxvirus, the thymidine kinase-encoding gene is located at locus J2R. In certain embodiments, TK is completely deleted.

In certain embodiments, the ORF of ribonucleotide reductase (RR) is deleted or disrupted. RR catalyzes the reduction of ribonucleotides to deoxyribonucleotides, which is a crucial step in DNA biosynthesis. The viral enzyme is composed of two heterologous subunits, designated Rl and R2, which are encoded respectively by the I4L and F4L locus. Sequences for the I4L and F4L genes and their locations in the genome of various poxvirus are available in public databases, for example via GenBank accession number DQ437594, DQ437593, DQ377804, AH015635, AY313847, AY313848, NC_003391, NC_003389, NC_003310, M-35027, AY243312, DQ011157, DQ011156, DQ011155, DQ011154, DQ011153, Y16780, X71982, AF438165, U60315, AF410153, AF380138, U86916, L22579, NC_006998, DQ121394 and NC_008291. In the context of the invention, either the I4L gene (encoding the Rl large subunit) or the F4L gene (encoding the R2 small subunit) or both may be deleted or disturbed.

In certain embodiments, the virus genome of the modified oncolytic virus further comprises an additional deletion or disruption that further increases the tumor-specificity of the virus. In certain embodiments, the additional deletion or disruption is in an ORF encoding at least part of a tumor-specific protein that is preferentially or specifically expressed in a tumor cell. A representative example of tumor-specific protein is VGF. VGF is a secreted protein which is expressed early after cell infection by virus and its function seems important for virus spread in normal cells. Another example is the A56R gene coding for hemagglutinin (Zhang et al., 2007, Cancer Res. 67: 10038-46) . One further example is F2L gene which encodes the viral dUTPase involved in both maintaining the fidelity of DNA replication and providing the precursor for the production of TMP by thymidylate synthase (Broyles et al., 1993, Virol. 195: 863-5) . Sequence of the vaccinia virus F2L gene is available in GenBank via accession number M25392.

The term “fusion” or “fused” when used with respect to amino acid sequences (e.g. peptide, polypeptide or protein) refers to combination of two or more amino acid sequences, for example by chemical bonding or recombinant means, into a single amino acid sequence which does not exist naturally. A fusion amino acid sequence may be produced by genetic recombination of two encoding polynucleotide sequences, and can be expressed by a method of introducing a construct containing the recombinant polynucleotides into a host cell.

The term “heterologous” as used herein means that the sequence is not endogenous to the wild type virus.

The term “encode” or “encoding for” as used herein refers to being capable of being transcribed into mRNA and/or translated into a peptide or protein.

PD-1 extracellular domain (PD-1 ECD)

In certain embodiments, the first molecule is a first fusion protein and the second molecule is a second fusion protein. In certain embodiments, the first fusion protein is capable of binding to PD-L1. In certain embodiments, the first fusion protein is capable of blocking PD-L1 function in tumor cells.

The term “PD-1” as used herein refers to programmed cell death protein, which belongs to the superfamily of immunoglobulin and functions as coinhibitory receptor to negatively regulate the immune system. PD-1 is a member of the CD28/CTLA-4 family, and has two known ligands including PD-L1 and PD-L2. Representative amino acid sequence of human PD-1 is disclosed under the GenBank accession number: NP_005009.2, and the representative nucleic acid sequence encoding the human PD-1 is shown under the GenBank accession number: NM_005018.3.

The term “PD-1” as used herein is intended to encompass any form of PD-1 that retains a useful activity, for example, 1) native unprocessed PD-1 molecule, “full-length” PD-1 chain or naturally occurring variants of PD-1, including, for example, splice variants or allelic variants; 2) any form of PD-1 that results from processing in the cell; or 3) full length, a fragment (e.g., a truncated form, an extracellular/transmembrane domain) or a modified form (e.g. a mutated form, a glycosylated/PEGylated, a His-tag/immunofluorescence fused form) of PD-1 subunit generated through recombinant method. Preferably, the PD-1 polypeptides as described herein, as well as protein complexes or fusion proteins comprising the same, are soluble.

PD-L1, also named B7-H1/CD274, a ligand of PD-1, is expressed on antigen presenting cells and tumor cells. Binding of PD-L1 to PD-1 inhibits T cell activation and counterbalances T cell stimulatory signals, such as the binding of B7 to CD28. PD-L1 is not expressed by normal epithelial tissues, but it is aberrantly expressed on a wide array of human cancers. In this context, activation of PD-L1 signaling may promote cancer progression by disabling the host anti-tumor response. Its expression on tumor cells has been associated with poorer prognosis in renal cell carcinoma, lung cancer, breast cancer, pancreatic cancer, ovarian cancer, urothelial cancer, gastric cancer, esophageal cancer, colon cancer, pharyngeal squamous cell carcinoma, ovarian teratoma and hepatocellular carcinoma. Representative amino acid sequence of human PD-L1 is disclosed under the NCBI accession number: NP_054862.1, and the representative nucleic acid sequence encoding the human PD-L1 is shown under the NCBI accession number: NM_014143.3.

Binding of the PD-1 ECD of the present disclosure to PD-L1 inhibits PD-L1 function, such as those reduce the activity of PD-L1 by at least 5%, 10%, 20%, 40%, 50%, 80%, 90%, 95%or more.

The activity or function (e.g. of PD-L1) may be reduced as a result of, for example, inhibition of binding between the functional protein and its ligand (e.g. binding between PD-1 and PD-L1) , inhibition of its biological activation (e.g. PD-L1’s activation) , and/or reduction of the level (e.g. PD-L1 level) .

In certain embodiments, the first fusion protein comprises a PD-1 protein truncation capable of specifically binding to PD-L1. In certain embodiments, the PD-1 protein truncation comprises extracellular domain of PD-1 protein (PD-1 ECD) . In certain embodiments, the PD-1 ECD is residues 22-170 of PD-1 protein ECD (PD-1 ECD G22-170) , which has the amino acid sequence of SEQ ID NO: 1, corresponding to nucleic acid sequence of SEQ ID NO: 7.

Amino acid sequence of PD-1 ECD G22-170 (SEQ ID NO: 1)

Nucleic acid sequence of PD-1 ECD G22-170 (SEQ ID NO: 7)

The term “specific binding” or “specifically binds” as used herein refers to a non-random binding reaction between two molecules, such as for example between an antibody and an antigen. In certain embodiments, the antibodies or antigen-binding fragments provided herein specifically bind human and/or monkey PD-1 with a binding affinity (KD) of ≤10 ^-6 M (e.g., ≤5x10 ^-7 M, ≤2x10 ^-7 M, ≤10 ^-7 M, ≤5x10 ^-8 M, ≤2x10 ^-8 M, ≤10 ^-8 M, ≤5x10 ^-9 M, ≤2x10 ^-9 M, ≤10 ^-9 M, ≤10 ^-10 M) . KD as used herein refers to the ratio of the dissociation rate to the association rate (k _off/k _on) , which may be determined using surface plasmon resonance methods for example using instrument such as Biacore.

The term “identity” as used herein, with respect to amino acid sequence (or nucleic acid sequence) , refers to the percentage of amino acid (or nucleic acid) residues in a candidate sequence that are identical to the amino acid (or nucleic acid) residues in a reference sequence, after aligning the sequences and, if necessary, introducing gaps, to achieve the maximum number of identical amino acids (or nucleic acids) . Conservative substitution of the amino acid residues are not considered as identical residues. Alignment for purposes of determining percent amino acid (or nucleic acid) sequence identity can be achieved, for example, using publicly available tools such as BLASTN, BLASTp (available on the website of U.S. National Center for Biotechnology Information (NCBI) , see also, Altschul S.F. et al, J. Mol. Biol., 215: 403–410 (1990) ; Stephen F. et al, Nucleic Acids Res., 25: 3389–3402 (1997) ) , ClustalW2 (available on the website of European Bioinformatics Institute, see also, Higgins D.G. et al, Methods in Enzymology, 266: 383-402 (1996) ; Larkin M.A. et al, Bioinformatics (Oxford, England) , 23 (21) : 2947-8 (2007) ) , and ALIGN or Megalign (DNASTAR) software. Those skilled in the art may use the default parameters provided by the tool, or may customize the parameters as appropriate for the alignment, such as for example, by selecting a suitable algorithm.

In certain embodiments, the PD-1 ECD has an amino acid sequence of SEQ ID NO: 1 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

In certain embodiments, the PD-1 ECD is encoded by a nucleic acid sequence of SEQ ID NO: 7 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

Anti-PD-1 antibody

The term “antibody” as used herein includes any immunoglobulin, monoclonal antibody, polyclonal antibody, multispecific antibody, or bispecific (bivalent) antibody that binds to a specific antigen. A native intact antibody comprises two heavy chains and two light chains. Each heavy chain consists of a variable region and a first, second, and third constant region, while each light chain consists of a variable region and a constant region. Mammalian heavy chains are classified as α, δ, ε, γ, and μ, and mammalian light chains are classified as λ or κ. The antibody has a “Y” shape, with the stem of the Y consisting of the second and third constant regions of two heavy chains bound together via disulfide bonding. Each arm of the Y includes the variable region and first constant region of a single heavy chain bound to the variable and constant regions of a single light chain, wherein the first constant region of the heavy chain is linked to the second constant region via a hinge region. The variable regions of the light and heavy chains are responsible for antigen binding specificity. The variable regions in both chains generally contain three highly variable loops called the complementarity determining regions (CDRs) (light (L) chain CDRs including LCDR1, LCDR2, and LCDR3, heavy (H) chain CDRs including HCDR1, HCDR2, and HCDR3) . CDR boundaries for the antibodies and antigen-binding fragments disclosed herein may be defined or identified by the conventions of Kabat, Chothia, or Al-Lazikani (see Al-Lazikani, B., Chothia, C., Lesk, A.M., J. Mol. Biol., 273 (4) , 927 (1997) ; Chothia, C. et al., J Mol Biol. Dec 5; 186 (3) : 651-63 (1985) ; Chothia, C. and Lesk, A.M., J. Mol. Biol., 196, 901 (1987) ; Chothia, C. et al., Nature. Dec 21-28; 342 (6252) : 877-83 (1989) ; Kabat E.A. et al., National Institutes of Health, Bethesda, Md. (1991) for specifics) . The three CDRs are interposed between flanking stretches known as framework regions (FRs) , which are more highly conserved than the CDRs and form a scaffold to support the structure of the variable regions. The constant regions of the heavy and light chains are irrelevant to antigen binding specificity, but exhibit various effector functions. Antibodies are assigned to classes based on the amino acid sequence of the constant region of their heavy chain. The five major classes or isotypes of antibodies are IgA, IgD, IgE, IgG, and IgM, which are characterized by the presence of α, δ, ε, γ, and μheavy chains, respectively. Several of the major antibody classes are divided into subclasses such as IgG1 (γ1 heavy chain) , IgG2 (γ2 heavy chain) , IgG3 (γ3 heavy chain) , IgG4 (γ4 heavy chain) , IgA1 (α1 heavy chain) , or IgA2 (α2 heavy chain) .

The term “antigen-binding fragment” as used herein refers to an antibody fragment formed from a portion of an antibody comprising one or more CDRs, but does not comprise an intact antibody structure. Examples of antigen-binding fragment include, without limitation, an Fab, an Fab’, an F (ab’) 2, an Fv fragment, a single-chain antibody molecule (scFv) , an scFv dimer, a camelized single domain antibody, and a nanobody. An antigen-binding fragment is capable of binding to the same antigen to which the parent antibody binds.

The term “Fab” as used herein refers to that portion of the antibody consisting of a single light chain (both variable and constant regions) bound to the variable region and first constant region of a single heavy chain by a disulfide bond.

The term “Fab’ ” as used herein refers to a Fab fragment that includes a portion of the hinge region.

The term “F (ab’) ₂” as used herein refers to a dimer of Fab’.

The term “Fv” as used herein refers to an Fv fragment consisting of the variable region of a single light chain and the variable region of a single heavy chain.

The term “Single-chain Fv antibody” or “scFv” as used herein refers to an engineered antibody consisting of a light chain variable region and a heavy chain variable region connected to one another directly or via a peptide linker sequence (see e.g., Huston JS et al., Proc Natl Acad Sci USA, 85: 5879 (1988) ) .

The term “scFv dimer” as used herein refers to a polymer formed by two scFvs.

The term “camelized single domain antibody” , also known as “heavy chain antibody” or “HCAb” (heavy-chain-only antibody) , refers to an antibody that contains two heavy chain variable regions but no light chains (see e.g., Riechmann L. and Muyldermans S., J Immunol Methods. Dec 10; 231 (1-2) : 25-38 (1999) ; Muyldermans S., J Biotechnol. Jun; 74 (4) : 277-302 (2001) ; WO94/04678; WO94/25591; and U.S. Patent No. 6,005,079) . Heavy chain antibodies were originally derived from Camelidae (camels, dromedaries, and llamas) . Although devoid of light chains, camelized antibodies have an authentic antigen-binding repertoire (see Hamers-Casterman C. et al., Nature. 363 (6428) : 446-8 (1993) ; Nguyen VK. et al., “Heavy-chain antibodies in Camelidae; a case of evolutionary innovation, ” Immunogenetics. 54 (1) : 39-47 (2002) ; and Nguyen VK. et al., Immunology. 109 (1) : 93-101 (2003) , which are incorporated herein by reference in their entirety) .

The term “nanobody” as used herein refers to an antibody consisting of a heavy chain variable region from a heavy chain antibody and two constant regions, CH2 and CH3.

In certain embodiments, the antibody provided herein is a fully human antibody, a humanized antibody, a chimeric antibody, a mouse antibody or rabbit antibody. In certain embodiments, the antibody provided herein is a polyclonal antibody, a monoclonal antibody or a recombinant antibody. In certain embodiments, the antibody provided herein is a monospecific antibody, a bispecific antibody or a multispecific antibody. In certain embodiments, the antibody provided herein may further be labeled. In certain embodiments, the antibody or antigen-binding fragment thereof is a fully human antibody, which is optionally produced by a transgenic rat, e.g., a transgenic rat in which the expression of endogenous rat immunoglobin gene is inactivated, and carrying recombinant human immunoglobin locus with J loci deletions and C-kappa mutations, and which can also be expressed by an engineered cell (e.g., CHO cell) .

The term “fully human” as used herein, with reference to antibody or antigen-binding fragment, refers to that the amino acid sequences of the antibody or the antigen-binding fragment correspond to that of an antibody produced by a human or a human immune cell, or derived from a non-human source such as a transgenic non-human animal that utilizes human antibody repertoires, or other human antibody-encoding sequences.

The term “humanized” as used herein, with reference to antibody or antigen-binding fragment, refers to an antibody or the antigen-binding fragment comprising CDRs derived from non-human animals, FR regions derived from human, and when applicable, constant regions derived from human. A humanized antibody or antigen-binding fragment is useful as human therapeutics in certain embodiments because it has reduced immunogenicity. In certain embodiments, the non-human animal is a mammal, for example, a mouse, a rat, a rabbit, a goat, a sheep, a guinea swine, or a hamster. In certain embodiments, the humanized antibody or antigen- binding fragment is composed of substantially all human sequences except for the CDR sequences which are non-human.

The term “chimeric” as used herein, with reference to antibody or antigen-binding fragment, refers to an antibody or antigen-binding fragment, having a portion of heavy and/or light chain derived from one species, and the rest of the heavy and/or light chain derived from a different species. In certain embodiments, a chimeric antibody may comprise a constant region derived from human and a variable region from a non-human species, such as from mouse or rabbit.

The term “conservative substitution” as used herein, with reference to amino acid sequence, refers to replacing an amino acid residue with a different amino acid residue having a side chain with similar physiochemical properties. For example, conservative substitutions can be made among amino acid residues with hydrophobic side chains (e.g. Met, Ala, Val, Leu, and Ile) , among residues with neutral hydrophilic side chains (e.g. Cys, Ser, Thr, Asn and Gln) , among residues with acidic side chains (e.g. Asp, Glu) , among amino acids with basic side chains (e.g. His, Lys, and Arg) , or among residues with aromatic side chains (e.g. Trp, Tyr, and Phe) . As known in the art, conservative substitution usually does not cause significant change in the protein conformational structure, and therefore could retain the biological activity of a protein.

Table 1 shows the CDR sequences of the anti-PD-1 antibody. The heavy chain and light chain variable region sequences are also provided below in Table 2.

Table 1. CDR amino acid sequences and nucleotide sequences

Table 2. Variable region amino acid sequences and nucleotide sequences

In certain embodiments, the anti-PD-1 antibody comprises:

a HCDR1 having an amino acid sequence of SEQ ID NO: 23 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity,

a HCDR2 having an amino acid sequence of SEQ ID NO: 24 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity,

a HCDR3 having an amino acid sequence of SEQ ID NO: 25 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity,

a LCDR1 having an amino acid sequence of SEQ ID NO: 26 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity,

a LCDR2 having an amino acid sequence of SEQ ID NO: 27 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity, and

a LCDR3 having an amino acid sequence of SEQ ID NO: 28 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

In certain embodiments, the HCDR1 is encoded by a nucleic acid sequence of SEQ ID NO: 31 or a homologous sequence thereof having at least 80%sequence identity,

the HCDR2 is encoded by a nucleic acid sequence of SEQ ID NO: 32 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity,

the HCDR3 is encoded by a nucleic acid sequence of SEQ ID NO: 33 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity,

the LCDR1 is encoded by a nucleic acid sequence of SEQ ID NO: 34 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity,

the LCDR2 is encoded by a nucleic acid sequence of SEQ ID NO: 35 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity, and

the LCDR3 is encoded by a nucleic acid sequence of SEQ ID NO: 36 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

In certain embodiments, the anti-PD-1 antibody comprises a heavy chain variable region having an amino acid sequence of SEQ ID NO: 29 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity, and a light chain variable region having an amino acid sequence of SEQ ID NO: 30 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

In certain embodiments, the anti-PD-1 antibody heavy chain variable region is encoded by a nucleic acid sequence of SEQ ID NO: 37 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity, and the anti-PD-1 antibody light chain variable region is encoded by a nucleic acid sequence of SEQ ID NO: 38 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

In certain embodiments, the anti-PD-1 antibody comprises a full length heavy chain having an amino acid sequence of SEQ ID NO: 21 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity, and a full length light chain having an amino acid sequence of SEQ ID NO: 20 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

In certain embodiments, the anti-PD-1 antibody and the fragments thereof provided herein further comprise an immunoglobulin constant region. In some embodiments, an immunoglobulin constant region comprises a heavy chain and/or a light chain constant region. The heavy chain constant region comprises CH1, hinge, and/or CH2-CH3 regions. In certain embodiments, the heavy chain constant region comprises an Fc region. In certain embodiments, the light chain constant region comprises Cκ or Cλ.

In some embodiments, the anti-PD-1 antibody and antigen-binding fragments thereof provided herein have a constant region of an immunoglobulin (Ig) , optionally a human Ig, optionally a human IgG. In certain embodiments, the anti-PD-1 antibodies and antigen-binding fragments thereof provided herein comprises a constant region of IgG1 isotype, which could induce ADCC or CDC, or a constant region of IgG4 or IgG2 isotype, which has reduced or depleted effector function. Effector functions can be evaluated using various assays such as Fc receptor binding assay, C1q binding assay, and cell lysis assay.

Table 3 shows the full length sequences of the anti-PD-1 antibody provided herein.

Table 3. Full length amino acid sequences and nucleotide sequences of the anti-PD-1 antibody

In certain embodiments, the anti-PD-1 antibody full length heavy chain is encoded by a nucleic acid sequence of SEQ ID NO: 39 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity, and the anti-PD-1 antibody full length light chain is encoded by a nucleic acid sequence of SEQ ID NO: 40 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

Binding of the anti-PD-1 antibody and antigen-binding fragments thereof provided herein to PD-1 inhibits the interaction between PD-1 and PD-L1, thereby reducing the activity of PD-L1, for example, by at least 5%, 10%, 20%, 40%, 50%, 80%, 90%, 95%or more.

The activity or function (e.g. of PD-L1) may be reduced as a result of, for example, inhibition of binding between the functional protein and its ligand (e.g. binding between anti-PD-1 antibody and PD-1) , inhibition of its biological activation (e.g. PD-L1’s activation) , and/or reduction of the level (e.g. PD-L1 level) .

TGF-β receptor extracellular domain (TGFBRII ECD)

In certain embodiments, the second molecule is a second fusion protein. In certain embodiments, the second fusion protein comprises TGF-β receptor II extracellular domain (TGFBRII ECD) .

The “Transforming Growth Factor-beta” or “TGF-β” superfamily are proteins comprised of extracellular cytokines found in the vast majority of human cells. TGF-β refers to any of the TGF-β family proteins that have either the full-length, native amino acid sequence of any of the TGF-betas from subjects (e.g. human) , including the latent forms and associated or unassociated complex of precursor and mature TGFβ. TGF-β has been demonstrated to play an important role in the regulation of the immune response, primarily through its suppressive function towards cells of the immune system. TGF-β is a suppressor of antigen-specific T cell proliferation at least through reduction of the cell-cycle rate, as opposed to induction of apoptosis. In particular, TGF-β acts on cytotoxic T lymphocytes (CTLs) to specifically inhibit the expression of at least five cytolytic gene products: perforin, granzyme A, granzyme B, Fas ligand, and interferon gamma that are important for CTL-mediated tumor cytotoxicity (Thomas and Massagué, Cancer Cell. 2005 Nov; 8 (5) : 369-80) . All ～40 TGF-β superfamily ligands share the same overall architecture with generic characteristics for each region of the protein. Reference to such TGF-β herein will be understood to be a reference to any one of the currently identified forms, including TGF-β1, TGF-β2, TGF-β3 isoforms and latent versions thereof, as well as to human TGF-β species identified in the future, including polypeptides derived from the sequence of any known TGF-β and being at least about 75%, preferably at least about 80%, more preferably at least about 85%, still more preferably at least about 90%, and even more preferably at least about 95%homologous with the sequence. The terms “Transforming Growth Factor-beta” , “transforming growth factor beta” , “TGFβ” , “TGFbeta” , “TGF-β” , “TGFB” and “TGF-beta” are used interchangeably in the present disclosure.

As used herein, the term “human TGF-β1” refers to a TGF-β1 protein encoded by a human TGFB1 gene (e.g., a wild-type human TGFB1 gene) . An exemplary wild-type human TGFβ1 protein is provided by GenBank Accession No. NP_000651.3. As used herein, the term “human TGF-β2” refers to a TGF-β2 protein encoded by a human TGFB2 gene (e.g., a wild-type human TGFB2 gene) . Exemplary wild-type human TGF-β2 proteins are provided by GenBank Accession Nos. NP_001129071.1 and NP_003229.1. As used herein, the term “human TGF-β3” refers to a TGF-β3 protein encoded by a human TGFB3 gene (e.g., a wild-type human TGFB3 gene) . Exemplary wild-type human TGF-β3 proteins are provided by GenBank Accession Nos. NP_003230.1, NP_001316868.1, and NP_001316867.1.

As used herein, the term “TGF-β receptor type II” or “TGFBRII” refers to a family of transforming growth factor-beta receptor II (TGFBRII) proteins. Members of the TGFBRII family are generally transmembrane proteins, composed of a ligand-binding extracellular domain with a cysteine-rich region, a transmembrane domain, and a cytoplasmic domain with predicted serine/threonine kinase activity. The nucleic acid sequence encoding TGFBRII isoform A precursor protein is shown under Genbank Reference Sequence NM_001024847.2, and the amino acid sequenced for human TGFBRII are shown under GenBank accession number NP_001020018.1. The nucleic acid sequence encoding TGFBRII isoform B precursor protein is shown under Genbank Reference Sequence NM_003242.6, and the amino acid sequenced for human TGFBRII are shown under GenBank accession number NP_003233.4. The nucleic acid sequence encoding TGFBRII isoform X1 protein is shown under Genbank Reference Sequence XM_011534043.2, and the amino acid sequenced for human TGFBRII are shown under GenBank accession number XP_011532345.1. The nucleic acid sequence encoding TGFBRII isoform X2 protein is shown under Genbank Reference Sequence XM_011534045.3, and the amino acid sequenced for human TGFBRII are shown under GenBank accession number XP_011532347.1. The nucleic acid sequence encoding TGFBRII isoform X2 protein is shown under Genbank Reference Sequence XM_017007106.1, and the amino acid sequenced for human TGFBRII are shown under GenBank accession number XP_016862595.1. The polypeptide of expressed TGFBRII lacks the signal sequence.

The term “TGF-β receptor type II” or “TGFBRII” as used herein is intended to encompass any form of TGF-β receptor type II that retains a useful activity, for example, 1) native unprocessed TGF-β receptor type II molecule, “full-length” TGF-β receptor type II chain or naturally occurring variants of TGF-βreceptor type II, including, for example, splice variants or allelic variants; 2) any form of TGF-β receptor type II that results from processing in the cell; or 3) full length, a fragment (e.g., a truncated form, an extracellular/transmembrane domain) or a modified form (e.g. a mutated form, a glycosylated/PEGylated, a His-tag/immunofluorescence fused form) of TGF-β receptor type II subunit generated through recombinant method. Preferably, the TGF-β type II polypeptides as described herein, as well as protein complexes or fusion proteins comprising the same, are soluble.

Binding of the TGFBRII of the present disclosure to TGF-β inhibits TGF-β function, such as those reduce the activity of TGF-β by at least 5%, 10%, 20%, 40%, 50%, 80%, 90%, 95%or more.

The activity or function (e.g. of TGF-β) may be reduced as a result of, for example, inhibition of binding between the functional protein and its ligand (e.g. binding between TGFBRII and TGF-β) , inhibition of its biological activation (e.g. TGF-β’s activation) , and/or reduction of the level (e.g. TGF-β level) .

In certain embodiments, the second fusion protein comprises a TGFBRII protein truncation capable of specifically binding to TGF-β. In certain embodiments, the TGFBRII protein truncation comprises extracellular domain of TGFBRII protein (TGFBRII ECD) . In certain embodiments, the TGFBRII ECD is residues 23-166 of TGFBRII ECD protein (TGFBRII ECD G23-166) , which has the amino acid sequence of SEQ ID NO: 2, corresponding to nucleic acid sequence of SEQ ID NO: 8.

Amino acid sequence of TGFBRII ECD G23-166 (SEQ ID NO: 2)

Nucleic acid sequence of TGFBRII ECD G23-166 (SEQ ID NO: 8)

In certain embodiments, the TGFBRII ECD has an amino acid sequence of SEQ ID NO: 2 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

In certain embodiments, the TGFBRII ECD is encoded by a nucleic acid sequence of SEQ ID NO: 8 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

Immunoglobulin Fc region

In certain embodiments, the first fusion protein further comprises an immunoglobulin Fc region.

In certain embodiments, the second fusion protein further comprises an immunoglobulin Fc region.

As used herein, an immunoglobulin “Fc” region refers to that portion of an antibody consisting of the second and third constant regions of a first heavy chain bound to the second and third constant regions of a second heavy chain via disulfide bonding. The Fc portion of the antibody is responsible for various effector functions such as antibody-dependent cell-mediated cytotoxicity (ADCC) , and complement dependent cytotoxicity (CDC) , but does not function in antigen binding.

In certain embodiments, the first fusion protein comprises a first immunoglobulin Fc region.

In certain embodiments, the second fusion protein comprises a second immunoglobulin Fc region.

In certain embodiments, the first or second immunoglobulin Fc region comprises one or more amino acid substitution (s) that improves pH-dependent binding to neonatal Fc receptor (FcRn) . Such a variant can have an extended pharmacokinetic half-life, as it binds to FcRn at acidic pH which allows it to escape from degradation in the lysosome and then be translocated and released out of the cell.

In certain embodiments, the first or second immunoglobulin Fc region comprises one or more amino acid substitution (s) that alters the antibody-dependent cellular cytotoxicity (ADCC) . Certain amino acid residues at CH2 domain of the Fc region can be substituted to provide for enhanced ADCC activity. Alternatively or additionally, carbohydrate structures on the antibody can be changed to enhance ADCC activity. In certain embodiments, the first or second immunoglobulin Fc region comprises one or more amino acid substitution (s) that alters Complement Dependent Cytotoxicity (CDC) , for example, by improving or diminishing C1q binding and/or CDC.

When the first heterologous polynucleotide encodes the first fusion protein, and the second heterologous polynucleotide encodes the second fusion protein, the first and the second immunoglobulin Fc region are capable of associating into dimers, for example, via formation of knob-into-hole, hydrophobic interaction, electrostatic interaction, hydrophilic interaction, or increased flexibility.

In certain embodiments, the first or second immunoglobulin Fc region comprises one or more amino acid substitution (s) in the interface of the Fc region to facilitate and/or promote heterodimerization. These modifications comprise introduction of a protuberance into a first Fc polypeptide and a cavity into a second Fc polypeptide (or vice versa) , wherein the protuberance can be positioned in the cavity so as to promote interaction of the first and second Fc polypeptides to form a heterodimer or a complex.

The PD-1 ECD of the present disclosure is operably linked to the first immunoglobulin Fc region at the C terminal of the PD-1 ECD. The TGFBRII ECD of the present disclosure is operably linked to the second immunoglobulin Fc region at the C terminal of the TGFBRII ECD.

The PD-1 ECD or TGFBRII ECD of the present disclosure can be linked either directly or indirectly to the first or second immunoglobulin Fc region, respectively. In certain embodiments, the PD-1 ECD is linked to the first immunoglobulin Fc region via a linker. In certain embodiments, the TGFBRII ECD is linked to the second immunoglobulin Fc region via a linker. In certain embodiments, the linker is a polypeptide linker. In certain embodiments, the linker is a bi-functional cross-linker such as disuccinimidyl glutarate, or 1-ethyl-3- [3-dimethylaminopropyl] carbodiimide hydrochloride) , which can link at one end the amino group of a first polypeptide and at the other end the carboxyl end of a second polypeptide. A skilled artisan can select a suitable linker from those known in the art, as long as the linked fusion protein retains sufficient biological activities.

In certain embodiments, the first or second immunoglobulin Fc region is derived from human IgG Fc region. In certain embodiments, the first and second immunoglobulin Fc regions are the same. In certain embodiments, the human IgG Fc region is human IgG1, IgG2, IgG3, or IgG4 Fc region.

In certain embodiments, the first and second immunoglobulin Fc regions are human IgG1 Fc regions and have an amino acid sequence of SEQ ID NO: 3 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

Amino acid sequence of human IgG1 Fc regions (SEQ ID NO: 3)

In certain embodiments, the human IgG1 Fc regions is encoded by a nucleic acid sequence of SEQ ID NO: 9 or 10 or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

Nucleic acid sequence of human IgG1 Fc regions (SEQ ID NO: 9)

Nucleic acid sequence of human IgG1 Fc regions (SEQ ID NO: 10)

In certain embodiments, the PD-1 ECD is operably linked to the human IgG1 Fc region at the C terminal of the PD-1 ECD. In certain embodiments, the human IgG1 Fc region is encoded by nucleic acid sequence of SEQ ID NO: 9.

In certain embodiments, the TGFBRII ECD is operably linked to the human IgG1 Fc region at the C terminal of the TGFBRII ECD. In certain embodiments, the human IgG1 Fc region is encoded by nucleic acid sequence of SEQ ID NO: 10.

The term “operably link” or “operably linked” refers to a juxtaposition, with or without a spacer or linker, of two or more biological sequences of interest in such a way that they are in a relationship permitting them to function in an intended manner. When used with respect to polypeptides, it is intended to mean that the polypeptide sequences are linked in such a way that permits the linked product to have the intended biological function. The term may also be used with respect to polynucleotides. For one instance, when a polynucleotide encoding a polypeptide is operably linked to a regulatory sequence (e.g., promoter, enhancer, silencer sequence, etc. ) , it is intended to mean that the polynucleotide sequences are linked in such a way that permits regulated expression of the polypeptide from the polynucleotide.

Signal peptide

Transport of a protein may be mediated by a signal peptide located at the amino terminus of the protein itself. The signal peptide is comprised of about ten to twenty hydrophobic amino acids which target the nascent protein from the ribosome to a particular membrane bound compartment such as the endoplasmic reticulum (ER) . Proteins targeted to the ER may either proceed through the secretory pathway or remain in any of the secretory organelles such as the ER, Golgi apparatus, or lysosomes. Proteins that transit through the secretory pathway are either secreted into the extracellular space or retained in the plasma membrane. Secreted proteins are often synthesized as inactive precursors that are activated by post-translational processing events during transit through the secretory pathway. Such events include glycosylation, phosphorylation, proteolysis, and removal of the signal peptide by a signal peptidase. Other events that may occur during protein transport include chaperone-dependent unfolding and folding of the nascent protein and interaction of the protein with a receptor or pore complex.

In certain embodiments, the first fusion protein further comprises a signal peptide. In certain embodiments, the signal peptide of the first fusion protein is operably linked to the PD-1 ECD at the C terminal of the signal peptide.

In certain embodiments, the second fusion protein further comprises a signal peptide. In certain embodiments, the signal peptide of the second fusion protein is operably linked to the TGFBRII ECD at the C terminal of the signal peptide.

In certain embodiments, the signal peptide of the first fusion protein is CD33 signal peptide having an amino acid sequence of SEQ ID NO: 4 (MPLLLLLPLLWAGALAM) or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

In certain embodiments, the signal peptide of the second fusion protein is CD33 signal peptide having an amino acid sequence of SEQ ID NO: 4 (MPLLLLLPLLWAGALAM) or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

In certain embodiments, the CD33 signal peptide is encoded by a nucleic acid sequence of SEQ ID NO: 11 (ATGCCACTGCTCCTCCTGCTGCCACTGCTCTGGGCCGGCGCCCTCGCTATG) or SEQ ID NO: 12 (ATGCCTCTGCTGCTGCTGCTGCCTCTGCTGTGGGCCGGCGCCCTGGCCATG) or a homologous sequence thereof having at least 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity.

In certain embodiments, the CD33 signal peptide is operably linked to the TGFBRII ECD at the C terminal of the CD33 signal peptide. In certain embodiments, the CD33 signal peptide is encoded by nucleic acid sequence of SEQ ID NO: 11.

In certain embodiments, the CD33 signal peptide is operably linked to the TGFBRII ECD at the C terminal of the CD33 signal peptide. In certain embodiments, the CD33 signal peptide is encoded by nucleic acid sequence of SEQ ID NO: 12.

Polynucleotide

In certain embodiments, the modified oncolytic virus of the present disclosure comprising a virus genome having a first heterologous polynucleotide encoding a first fusion protein capable of binding to PD-L1 and a second heterologous polynucleotide encoding a second fusion protein capable of binding to TGF-β.

The term “polynucleotide” or “nucleic acid” as used herein refers to ribonucleic acids (RNA) , deoxyribonucleic acids (DNA) , or mixed ribonucleic acids-deoxyribonucleic acids such as DNA-RNA hybrids. The polynucleotide or nucleic acid may be single stranded or double stranded DNA or RNA or DNA-RNA hybrids. The polynucleotide or nucleic acid may be linear or circular. In certain embodiments, wherein the first and the second heterologous polynucleotide are both DNA when the virus is a DNA virus, or the first and the second heterologous polynucleotide are both RNA when the virus is a RNA virus. In certain embodiment, the first heterologous polynucleotide and the second heterologous polynucleotide are both double stranded DNA. The polynucleotides of the present disclosure are double stranded DNA and the nucleic acid sequences are represented with the encoding sequences, such as those shown by SEQ ID NO: 7-19, 22, and 31-40.

The first heterologous polynucleotide and the second heterologous polynucleotide may be introduced into the modified oncolytic virus using conventional methods known in the art, for example by synthesis by polymerase chain reaction (PCR) and ligation with the viral genome having compatible restriction ends. For more details, see, for example, Sambrook et al. Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory, N. Y. (1989) ) , which is incorporated herein by reference in its entirety.

In certain embodiments, the first heterologous polynucleotide and the second heterologous polynucleotide is introduced in the place of the deletion in the ORF. In certain embodiments, the first heterologous polynucleotide is immediately upstream or immediately downstream of the second heterologous polynucleotide. The term “immediately upstream or immediately downstream” as used herein means the first heterologous polynucleotide and the second heterologous polynucleotide are located sufficiently close on the virus genome that they are separated from each other by no more than 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotide (s) . For example, the 3’ end of the upstream polynucleotide is immediately adjacent to the 5’ end of the downstream polynucleotide if the 3’ end of the upstream polynucleotide is separated from the 5’ end of the downstream polynucleotide by no more than 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotide (s) . In certain embodiments, there is no ORF between the first heterologous polynucleotide and the second heterologous polynucleotide. In certain embodiments, there is restriction site between the first heterologous polynucleotide and the second heterologous polynucleotide.

In certain embodiments, the first heterologous polynucleotide encodes the first molecule that is a first fusion protein and the second heterologous polynucleotide encodes the second molecule that is a second fusion protein. In certain embodiments, the first heterologous polynucleotide further comprises a first promoter capable of driving expression of the first fusion protein. In certain embodiments, the second heterologous polynucleotide further comprises a second promoter capable of driving expression of the second fusion protein. In certain embodiments, the first and the second heterologous polynucleotides are arranged in an opposite direction regarding the protein translation. In certain embodiments, the first and the second promoters are in a head-to-head orientation.

The term “head-to-head orientation” as used herein means that two promoters are immediately adjacent to each other on the virus genome and they drive protein expression in opposite directions. An illustrative example is shown in Figures 1 and 4.

The term “promoter” as used herein refers to a polynucleotide sequence that can control transcription of an encoding sequence. The promoter sequence includes specific sequences that are sufficient for RNA polymerase recognition, binding and transcription initiation. In addition, the promoter sequence may include sequences that modulate this recognition, binding and transcription initiation activity of RNA polymerases. The promoter may affect the transcription of a gene located on the same nucleic acid molecule as itself or a gene located on a different nucleic acid molecule as itself. Functions of the promoter sequences, depending upon the nature of the regulation, may be constitutive or inducible by a stimulus. A “constitutive” promoter as used herein refers to a promoter that functions to continually activate gene expression in host cells. An “inducible” promoter as used herein refers to a promoter that activates gene expression in host cells in the presence of certain stimulus or stimuli.

In certain embodiments, the promoters of the present disclosure are eukaryotic promoters such as the promoters from CMV (e.g., the CMV immediate early promoter (CMV promoter) ) , epstein barr virus (EBV) promoter, human immunodeficiency virus (HIV) promoter (e.g., the HIV long terminal repeat (LTR) promoter) , moloney virus promoter, mouse mammary tumor virus (MMTV) promoter, rous sarcoma virus (RSV) promoter, SV40 early promoter, promoters from human genes such as human myosin promoter, human hemoglobin promoter, human muscle creatine promoter, human metalothionein beta-actin promoter, human ubiquitin C promoter (UBC) , mouse phosphoglycerate kinase 1 promoter (PGK) , human thymidine kinase promoter (TK) , human elongation factor 1 alpha promoter (EF1A) , cauliflower mosaic virus (CaMV) 35S promoter, E2F-1 promoter (promoter of E2F1 transcription factor 1) , promoter of alpha-fetoprotein, promoter of cholecystokinin, promoter of carcinoembryonic antigen, promoter of C-erbB2/neu oncogene, promoter of cyclooxygenase, promoter of CXC-Chemokine receptor 4 (CXCR4) , promoter of human epididymis protein 4 (HE4) , promoter of hexokinase type II, promoter of L-plastin, promoter of mucin-like glycoprotein (MUC1) , promoter of prostate specific antigen (PSA) , promoter of survivin, promoter of tyrosinase related protein (TRP1) , and promoter of tyrosinase.

In certain embodiments, the promoters of the present disclosure may be tumor specific promoters. The term “tumor specific promoter” as used herein refers to a promoter that functions to activate gene expression preferentially or exclusively in tumor cells, and has no activity or reduced activity in non-tumor cells or non-tumor cells. Illustrative examples of tumor specific promoters include, without limitation, E2F-1 promoter, promoter of alpha-fetoprotein, promoter of cholecystokinin, promoter of carcinoembryonic antigen, promoter of C-erbB2/neu oncogene, promoter of cyclooxygenase, promoter of CXCR4, promoter of HE4, promoter of hexokinase type II, promoter of L-plastin, promoter of MUC1, promoter of PSA, promoter of survivin, promoter of TRP1, and promoter of tyrosinase.

In certain embodiments, the first and the second promoters are the same or different. In certain embodiments, the first and the second promoters are both early and late promoter. In certain embodiments, the early and late promoter is pSE/L. In certain embodiments, the pSE/L promoter has a nucleic acid sequence of SEQ ID NO: 15 (AAAAATTGAAATTTTATTTTTTTTTTTTGGAATATAAATAAG) .

In certain embodiments, the first heterologous polynucleotide further comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a first promoter –a polynucleotide encoding the first fusion protein –a first stop codon. The second heterologous polynucleotide further comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a second promoter –a polynucleotide encoding the second fusion protein –a second stop codon. In certain embodiments, the first heterologous polynucleotide is immediately upstream or immediately downstream of the second heterologous polynucleotide.

In certain embodiments, the first and second stop codons are the same or different. In certain embodiments, the first and second stop codons have a nucleic acid sequence of SEQ ID NO: 16 (TTTTTNT, wherein N is A, T, C or G) .

In certain embodiments, the first fusion protein expressed from the first heterologous polynucleotide and the second fusion protein expressed from the second heterologous polynucleotide are expressed as separate proteins. In other words, they are not expressed as a fusion protein, and are not connected with each other either (whether covalently or through a linker) .

In certain embodiments, the first heterologous polynucleotide and the second heterologous polynucleotide are configured such that they are expressed in the same or different stages of replicative cycle of the modified oncolytic virus. For example, the two polynucleotides may be both driven by early promoters which are induced at an early stage of virus replication, or alternatively both driven by late promoters which are induced at a late stage of virus replication, or alternatively one is driven by an early promoter, and the other is driven by a late promoter.

In certain embodiments, the modified oncolytic virus does not include any other protein encoding heterologous polynucleotides except for the first heterologous polynucleotide and the second heterologous polynucleotide.

In certain embodiments, the first heterologous polynucleotide encodes the first molecule that is an anti-PD-1 antibody and the second heterologous polynucleotide encodes the second molecule that is a second fusion protein. In certain embodiments, the first heterologous polynucleotide further comprises a third heterologous polynucleotide and a fourth heterologous polynucleotide. In certain embodiments, the third heterologous polynucleotide further comprises a third promoter capable of driving expression of the anti-PD-1 antibody heavy chain. In certain embodiments, the fourth heterologous polynucleotide further comprises a fourth promoter capable of driving expression of the anti-PD-1 antibody light chain.

In certain embodiments, the third heterologous polynucleotide further comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a third promoter –a polynucleotide encoding the anti-PD-1 antibody heavy chain –a third stop codon. In certain embodiments, the fourth heterologous polynucleotide further comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a fourth promoter –a polynucleotide encoding the anti-PD-1 antibody light chain –a fourth stop codon. In certain embodiments, the third and the fourth promoters are in a head-to-head orientation.

In certain embodiments, the second heterologous polynucleotide further comprises a second promoter capable of driving expression of the second fusion protein. In certain embodiments, the second heterologous polynucleotide comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a second promoter –a polynucleotide encoding the second fusion protein –a second stop codon.

In certain embodiments, wherein the first heterologous polynucleotide that comprises the third and fourth heterologous polynucleotides is immediately upstream or immediately downstream of the second heterologous polynucleotide. In certain embodiments, the third heterologous polynucleotide is immediately upstream or immediately downstream of the fourth heterologous polynucleotide.

In certain embodiments, the second, the third and the fourth promoters are the same or different. In certain embodiments, the second, the third and the fourth promoters are both early and late promoter. In certain embodiments, the early and late promoter is pSE/L. In certain embodiments, the pSE/L promoter has a nucleic acid sequence of SEQ ID NO: 15.

In certain embodiments, the second, the third and the fourth stop codons are the same or different. In certain embodiments, the second, the third and the fourth stop codons have a nucleic acid sequence of SEQ ID NO: 16.

In certain embodiments, the anti-PD-1 antibody heavy chain expressed from the third heterologous polynucleotide and the anti-PD-1 antibody light chain expressed from the fourth heterologous polynucleotide are expressed as separate proteins. In other words, they are not expressed as a fusion protein, and are not connected with each other either (whether covalently or through a linker) .

In certain embodiments, the anti-PD-1 antibody expressed from the first heterologous polynucleotide that comprises the third and fourth heterologous polynucleotides, and the second fusion protein expressed from the second heterologous polynucleotide are expressed as separate proteins. In other words, they are not expressed as a fusion protein, and are not connected with each other either (whether covalently or through a linker) .

When the third and fourth heterologous polynucleotides encodes the anti-PD-1 antibody heavy chain and light chain, respectively, the third, the fourth and the second heterologous polynucleotides are in sequential arrangement regarding the protein translation.

In certain embodiments, the third, the fourth and the second heterologous polynucleotides are configured such that they are expressed in the same or different stages of replicative cycle of the modified oncolytic virus. For example, the polynucleotides may be both driven by early promoters which are induced at an early stage of virus replication, or alternatively driven by late promoters which are induced at a late stage of virus replication, or alternatively one is driven by an early promoter, and the other two are driven by a late promoter, or one is driven by a late promoter, and the other two are driven by an early promoter.

In certain embodiments, the modified oncolytic virus does not include any other protein encoding heterologous polynucleotides except for the third, the fourth and the second heterologous polynucleotides.

Pharmaceutical Composition

In another aspect, the present disclosure provides a pharmaceutical composition, comprising the modified oncolytic virus described in the present disclosure and a pharmaceutically acceptable carrier.

The term “pharmaceutically acceptable” as used herein refers to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio. In certain embodiments, compounds, materials, compositions, and/or dosage forms that are pharmaceutically acceptable refer to those approved by a regulatory agency (such as U.S. Food and Drug Administration, China Food and Drug Administration or European Medicines Agency) or listed in generally recognized pharmacopoeia (such as U.S. Pharmacopoeia, China Pharmacopoeia or European Pharmacopoeia) for use in animals, and more particularly in humans.

The pharmaceutically acceptable carriers for use in the pharmaceutical compositions of the present invention may include, but are not limited to, for example, pharmaceutically acceptable liquids, gels, or solid carriers, aqueous vehicles (e.g., sodium chloride injection, Ringer's injection, isotonic glucose injection, sterile water injection, or Ringer's injection of glucose and lactate) , non-aqueous vehicles (e.g., fixed oils of vegetable origin, cottonseed oil, corn oil, sesame oil, or peanut oil) , antimicrobial agents, isotonic agents (such as sodium chloride or dextrose) , buffers (such as phosphate or citrate buffers) , antioxidants (such as sodium bisulfate) , anesthetics (such as procaine hydrochloride) , suspending/dispending agents (such as sodium carboxymethylcellulose, hydroxypropyl methylcellulose, or polyvinylpyrrolidone) , chelating agents (such as EDTA (ethylenediamine tetraacetic acid) or EGTA (ethylene glycol tetraacetic acid) ) , emulsifying agents (such as Polysorbate 80 (Tween-80) ) , diluents, adjuvants, excipients, or non-toxic auxiliary substances, other components known in the art, or various combinations thereof. Suitable components may include, for example, fillers, binders, disintegrants, buffers, preservatives, lubricants, flavorings, thickeners, coloring agents, or emulsifiers.

In certain embodiments, the pharmaceutical composition is an oral formulation. The oral formulations include, but are not limited to, capsules, cachets, pills, tablets, troches (for taste substrates, usually sucrose and acacia or tragacanth) , powders, granules, or aqueous or non-aqueous solutions or suspensions, or water-in-oil or oil-in-water emulsions, or elixirs or syrups, or confectionery lozenges (for inert bases, such as gelatin and glycerin, or sucrose or acacia) and /or mouthwash and its analogs.

In certain embodiments, the pharmaceutical composition may be an injectable formulation, including sterile aqueous solutions or dispersions, suspensions or emulsions. In all cases, the injectable formulation should be sterile and should be liquid to facilitate injections. It should be stable under the conditions of manufacture and storage, and should be resistant to the infection of microorganisms (such as bacteria and fungi) . The carrier may be a solvent or dispersion medium containing, for example, water, ethanol, polyols (e.g., glycerol, propylene glycol, and liquid polyethylene glycols, etc. ) and suitable mixtures and /or vegetable oils thereof. The injectable formulation should maintain proper fluidity, which may be maintained in a variety of ways, for example, using a coating such as lecithin, using a surfactant, etc. Antimicrobial contamination can be achieved by the addition of various antibacterial and antifungal agents (e.g., parabens, chlorobutanol, phenol, sorbic acid, thimerosal, etc. ) .

In certain embodiments, unit-dose parenteral preparations are packaged in an ampoule, a vial or a syringe with a needle. All preparations for parenteral administration should be sterile and not pyretic, as is known and practiced in the art.

Method of Treatment

In another aspect, the present disclosure provides a method of treating a tumor, comprising administering to a subject an effective amount of the modified oncolytic virus of the present disclosure or the pharmaceutical composition of the present disclosure.

The term “subject” as used herein refers to human and non-human animal. Non-human animals include all vertebrates, e.g., mammals and non-mammals. A “subject” may also be a livestock animal (e.g., cow, swine, goat, chicken, rabbit or horse) , or a rodent (e.g., rat or mouse) , or a primate (e.g., gorilla or monkey) , or a domestic animal (e.g., dog or cat) . A “subject” may be a male or a female, and also may be at different ages. In certain embodiments, the subject is a human. A human “subject” may be Caucasian, African, Asian, Sumerian, or other races, or a hybrid of different races. A human “subject” may be elderly, adult, teenager, child or infant.

The term “tumor” as used herein refers to any medical condition mediated by neoplastic or malignant cell growth, proliferation, or metastasis, and includes both solid tumors and non-solid tumors such as leukemia. In the present disclosure, “tumor” is used interchangeably with the terms “cancer” , “malignancy” , “hyperproliferation” and “neoplasm (s) ” . The term “tumor cell (s) ” is interchangeable with the terms “cancer cell (s) ” , “malignant cell (s) ” , “hyperproliferative cell (s) ” , and “neoplastic cell (s) ” unless otherwise explicitly indicated. In certain embodiments, the tumor is selected from the group consisting of head and neck tumor, breast tumor, colorectal tumor, liver tumor, pancreatic adenocarcinoma, gallbladder and bile duct tumor, ovarian tumor, cervical tumor, small cell lung tumor, non-small cell lung tumor, renal cell carcinoma, bladder tumor, prostate tumor, bone tumor, mesothelioma, brain tumor, soft tissue sarcoma, uterine tumor, thyroid tumor, nasopharyngeal carcinoma, and melanoma. In certain embodiments, the tumor is solid tumor. In certain embodiments, the tumor is melanoma, non-small cell lung cancer, renal cell carcinoma, Hodgkin lymphoma, squamous cell carcinoma of the head and neck, bladder cancer, colorectal cancer, triple negative breast cancer, or hepatocellular carcinoma. In certain embodiments, the tumor is pancreatic cancer, ovarian cancer, colon cancer, pharyngeal squamous cell carcinoma, ovarian teratoma In certain embodiments, the tumor has been refractory to prior therapy (e.g., administration of oncolytic virus, immune checkpoint inhibitor and/or immuno activator separately) .

The term “treating” or “treatment” of a condition as used herein includes preventing or alleviating a condition, slowing the onset or rate of development of a condition, reducing the risk of developing a condition, preventing or delaying the development of symptoms associated with a condition, reducing or ending symptoms associated with a condition, generating a complete or partial regression of a condition, curing a condition, or some combination thereof. With regard to tumor, “treating” or “treatment” may refer to inhibiting or slowing neoplastic or malignant cell growth, proliferation, or metastasis, preventing or delaying the development of neoplastic or malignant cell growth, proliferation, or metastasis, or some combination thereof. With regard to a tumor, “treating” or “treatment” includes eradicating all or part of a tumor, inhibiting or slowing tumor growth and metastasis, preventing or delaying the development of a tumor, or some combination thereof.

The modified oncolytic virus and the pharmaceutical composition may be administered via any suitable routes known in the art, including without limitation, parenteral, oral, enteral, buccal, nasal, topical, rectal, vaginal, transmucosal, epidermal, transdermal, dermal, ophthalmic, pulmonary, and subcutaneous administration routes. In certain embodiments, the route of administering is topical. In certain embodiments, the route of administering is intra-tumor injection.

In certain embodiments, the modified oncolytic virus and the pharmaceutical composition is administered at a therapeutically effective dosage. The term “therapeutic effective dosage” as used herein refers to the amount of a drug capable of ameliorating or eliminating a disease or symptom of a subject, or of preventively inhibiting or preventing the occurrence of the disease or symptom. A therapeutically effective amount can be the amount of a drug that ameliorates one or more diseases or symptoms of a subject to certain extent; the amount of a drug capable of restoring one or more physiological or biochemical parameters associated with the cause of a disease or symptom, partly or completely back to normal; and/or the amount of a drug capable of reducing the possibility that a disease or symptom occurs.

The therapeutically effective dosage of the modified oncolytic virus and the pharmaceutical composition is dependent on various factors known in the art, for example, body weight, age, pre-existing medical condition, therapy currently being received, health condition of the subject, and intensity, allergic, superallergic and side effect of drug interaction, and route of administration and the extent to which the disease develops. A skilled artisan (e.g., a physician or veterinarian) may reduce or increase dosage in accordance with these or other conditions or requirement.

In certain embodiments, the modified oncolytic virus and the pharmaceutical composition may be administered at a therapeutically effective dosage of about 10 ⁴ PFU to about 10 ¹⁴ PFU (e.g., about 10 ⁴ PFU, about 2*10 ⁴ PFU, about 5*10 ⁴ PFU, about 10 ⁵ PFU, about 2*10 ⁵ PFU, about 5*10 ⁵ PFU, about 10 ⁶ PFU, about 2*10 ⁶ PFU, about 5*10 ⁶ PFU, about 10 ⁷ PFU, about 2*10 ⁷ PFU, about 5*10 ⁷ PFU, about 10 ⁸ PFU, about 2*10 ⁸ PFU, about 5*10 ⁸ PFU, about 10 ⁹ PFU, about 2*10 ⁹ PFU, about 5*10 ⁹ PFU, about 10 ¹⁰ PFU, about 2*10 ¹⁰ PFU, about 5*10 ¹⁰ PFU, about 10 ¹¹ PFU, about 2*10 ¹¹ PFU, about 5*10 ¹¹ PFU, about 10 ¹² PFU, about 2*10 ¹² PFU, about 5*10 ¹² PFU, about 10 ¹³ PFU, about 2*10 ¹³ PFU, about 5*10 ¹³ PFU, or about 10 ¹⁴ PFU) . In certain of these embodiments, the modified oncolytic virus and the pharmaceutical composition is administered at a dosage of about 10 ¹¹ PFU or less. In certain of these embodiments, the dosage is 5*10 ¹⁰ PFU or less, 2*10 ¹⁰ PFU or less, 5*10 ⁹ PFU or less, 4*10 ⁹ PFU or less, 3*10 ⁹ PFU or less, 2*10 ⁹ PFU or less, or 10 ⁹ PFU or less. A particular dosage can be divided and administered multiple times separated by interval, e.g., once every day, twice or more every day, twice or more every month, once every week, once every two weeks, once every three weeks, once a month or once every two months or more. In certain embodiments, the administered dosage may vary over the course of treatment. For example, in certain embodiments, the initially administered dosage can be higher than subsequently administered dosages. In certain embodiments, the administered dosages are adjusted in the course of treatment depending on the response of the administration subject.

The term “PFU” as used herein refers to plaque-forming unit, which is a measure of the number of particles capable of forming plaques.

Dosage regimens may be adjusted to provide the optimum desired response (e.g., a therapeutic response) . For example, a single dose may be administered, or several divided doses may be administered over time.

Combination

In certain embodiments, the pharmaceutical compositions may be used in combination with one or more other drugs. In certain embodiments, the composition comprises at least one other drug.

In certain embodiments, the other drugs are anti-tumor agent. Any agents known to be active against tumor may be used as anti-tumor agent. In certain embodiments, the anti-tumor agent is selected from the group consisting of a chemical agent, a polynucleotide, a peptide, a protein, or any combination thereof.

In certain embodiments, the anti-tumor agent is a chemical agent. Illustrative examples of anti-tumor chemical agent include, without limitation, Mitomycin C, Daunorubicin, Doxorubicin, Etoposide, Tamoxifen, Paclitaxel, Vincristine, and Rapamycin.

In certain embodiments, the anti-tumor agent is a polynucleotide. Illustrative examples of anti-tumor polynucleotide include, without limitation, anti-sense oligonucleotides such as bcl-2 antisense oligonucleotides, clusterin antisense oligonucleotides, and c-myc antisense oligonucleotides; and RNAs capable of RNA interference (including small interfering RNA (siRNA) , short hairpin RNA (shRNAs) , and micro interfering RNAs (miRNA) ) , such as anti-VEGF siRNA, shRNA, or miRNA, anti-bcl-2 siRNA, shRNA, or miRNA, and anti-claudin-3 siRNA, shRNA, or miRNA.

In certain embodiments, the anti-tumor agent is a peptide or protein. Illustrative examples of anti-tumor peptide or protein include, without limitation, antibodies such as, Trastuzumab, Rituximab, Edrecolomab, Alemtuzumab, Daclizumab, Nimotuzumab, Gemtuzumab, Ibritumomab, and Edrecolomab, protein theraputics such as, Endostatin, Angiostatin K1-3, Leuprolide, Sex hormone-binding globulin, and Bikunin.

Medical Usage

In another aspect, the present disclosure provides use of the modified oncolytic virus of the present disclosure or the pharmaceutical composition of the present disclosure in the manufacture of a medicament for treating a tumor.

In another aspect, the present disclosure provides the modified oncolytic virus of the present disclosure or the pharmaceutical composition of the present disclosure for use in treating a tumor.

EXAMPLES

The following Examples are set forth to aid in the understanding of the present disclosure, and should not be construed to limit in any way the scope of the invention as defined in the claims which follow thereafter.

Example 1: Virus Construction

The starting Western Reserve (WR) strain of vaccinia virus was obtained from ATCC (www. atcc. org: VR-1354) . Due to multiple genes involved, virus WR-GO-001 (see Figure 1) with genomic sequence of SEQ ID NO: 17 has been built in a step-by-step engineering approach. In brief, in the first step, WR DNA is recombined with a modified pJS1175 vector to insert selection genes into the thymidine kinase (TK) locus. Afterwards, a recombination plasmid with flanking sequences of J1R and J3R and encoding recombinant human PD-1 Fc chimera protein and recombinant human TGF-beta RII Fc chimera protein was transfected into CV-1 cells infected with WR to completely delete TK and insert the chimera protein sequences (see Table 4 below) .

Table 4. WR-GO-001 Plaque Generation and Purification Procedure

The amino acid sequences of the recombinant human PD-1 Fc chimera protein and recombinant human TGF-beta RII Fc chimera protein are shown as SEQ ID NOs: 5 and 6, respectively. The nucleic acid sequence encoding the recombinant human PD-1 Fc chimera protein is set forth as SEQ ID NO: 13 and the recombinant human TGF-beta RII Fc chimera protein is set forth as SEQ ID NO: 14 (see Table 5) .

WR-GO-002 (insertion of a gene encoding recombinant human TGF-beta RII Fc chimera protein is shown in Figures 2, with genomic sequence of SEQ ID NO: 18 shown in Table 5) , WR-GO-003 (insertion of a gene encoding recombinant human PD-1 Fc chimera protein is shown in Figures 3, with genomic sequence of SEQ ID NO: 19 shown in Table 5) and WR-GO-004 (insertion of both gene encoding recombinant human TGF-beta RII Fc chimera protein and anti-human PD-1 heavy chain and light chain with genomic sequence of SEQ ID NO: 22. The amino acid sequence of anti-human PD-1 light chain and heavy chain are shown as SEQ ID NOs: 20 and 21, respectively, and the amino acid sequence of recombinant human TGF-beta RII Fc chimera protein are shown as SEQ ID NO: 6 were manufactured by the same protocol as WR-GO-001 (see Table 5) .

Table 5. Sequences in WR-GO-001, WR-GO-002, WR-GO-003, and WR-GO-004

Example 2: Characterization of WR-GO-001, WR-GO-002, WR-GO-003, and WR-GO-004

During the engineering process of these new viruses, their genomic integrity and protein expression were closely monitored.

PCR and sequencing

Viruses (WR-GO-001, WR-GO-002, WR-GO-003 and WR-GO-004) identity are confirmed by qPCR (TaqMan) . TK deletion is also verified through Sanger sequencing. Alignment of Sanger sequencing of WR-GO-001 viral genome against designed DNA sequences for expressing recombinant human PD-1 Fc chimera protein (rPD-1 Fc) and recombinant human TGF-beta RII Fc chimera protein (rTGF-beta RII Fc) in WR-GO-001 is conducted. The Alignment showed that the viral genome of WR-GO-001 is identical to the designed DNA sequence.

Confirmation of expression of human PD-1 Fc chimera protein, human TGF-beta RII Fc chimera protein and anti-human PD-1 antibody using ELISA

Recombinant human PD-1 Fc chimera protein (rPD-1 Fc) expressed from WR-GO-001 and WR-GO-003, and WR-WT infected Supernatants and Intracellular samples are tested by ELISA (R&D Systems) . Recombinant human TGF-beta RII Fc chimera protein (rTGF-beta RII Fc) expressed from WR-GO-001, WR-GO-002 and WR-GO-004 and WR-WT infected supernatants and intracellular samples are tested by ELISA (R&D Systems) . Anti-human PD-1 antibody expressed from WR-GO-004 infected supernatants and intracellular samples are tested by ELISA (R&D Systems) . Dilute the capture antibody in PBS without carrier protein. Immediately coat a 96-well microplate with 100 μL per well of the diluted capture antibody. Seal the plate and incubate overnight at room temperature. Aspirate each well and wash with wash buffer, repeating the process two times for a total of three washes. Wash by filling each well with wash buffer (400μL) using a squirt bottle, manifold dispenser, or autowasher. Complete removal of liquid at each step is essential for good performance. After the last wash, remove any remaining wash buffer by aspirating or by inverting the plate and blotting it against clean paper towels. Block each well of the microplate. Incubate at room temperature for a minimum of 1 hour. Add 100 μL sample or standards in reagent diluent, or an appropriate diluent to each well and cover the plate with an adhesive strip and incubate 2 hours at room temperature. Repeat the aspiration/wash step as previously described. Add 100 μL Detection Antibody to each well and cover the plate with a new adhesive strip and incubate 2 hours at room temperature. Repeat the aspiration/wash step as previously described. Add 100 μL working dilution of Streptavidin-HRP to each well and cover the plate and incubate for 20 minutes at room temperature. Avoid placing the plate in direct light. Repeat the aspiration/wash step as previously described. Add 100 μL substrate solution to each well and incubate for 20 minutes at room temperature. Avoid placing the plate in direct light. Add 50 μL stop solution to each well. Gently tap the plate to ensure thorough mixing. Determine the optical density of each well immediately using a microplate reader set to 450 nm.

The expression of human PD-1 Fc chimera protein, human TGF-beta Receptor II Fc chimera protein and Anti-human PD-1 antibody in both supernatant and intracellular samples of Hela cells infected by WR-GO-002, WR-GO-003 or WR-GO-004 was measured using ELISA method.

The results of expression levels are shown in Figure 5A, 5B and 5C. Figure 5A shows that WR-GO-001 stably expresses PD-1-Fc protein, which was mainly detected in the WR-GO-003 supernatant. Figure 5B shows that WR-GO-004 stably expresses anti-PD-1-antibody, which was mainly detected in the WR-GO-004 supernatant. Figure 5C shows that all of WR-GO-001, WR-GO-002 and WR-GO-004 stably express TGFBRII-Fc protein, which was mainly detected in the supernatants, respectively.

Example 3: In vitro and in vivo study of WR-GO-001, WR-GO-002, WR-GO-003 and WR-GO-004 recombinant viruses

The following in vitro and in vivo study are conducted to test the selectivity and antitumor effects of the new viral constructs.

Stage 1. Measurement of in vitro killing effect to cancer cell and transgene expression.

1. Manufacture and sucrose cushion purification of sufficient amount of each of the four recombinant viruses to perform the in vitro assay and in vivo experiment.

2. Confirm virus identity by the transgenes using qPCR (TaqMan) and ELISA (R&D Systems) .

3. Perform mycoplasma testing of the gene engineered Vaccinia Virus and the cell lines used above to confirm sterility.

4. Measure cell killing effect of Hepa1-6, 4T1, FaDu , and A549 at four different time points (24 hours, 48 hours, 72 hours, and 96 hours) and three different multiplicity of infection (MOI) using MTS (3- (4, 5-dimethylthiazol-2-yl) -5- (3-carboxymethoxyphenyl) -2- (4-sulfophenyl) -2H-tetrazolium) . Hepa1-6 (ATCC, CRL-1830) and 4T1 (ATCC, CRL-2539) are mouse tumor cell lines, FaDu (ATCC, HTB-43) and A549 (ATCC, CCL-185) are human tumor cell lines.

5. ELISA (R &D Systems) measurement of recombinant PD-1 Fc (rPD-1 Fc) and recombinant TGF-beta RII Fc (rTGF-beta RII Fc) expression in vitro in FaDu human tumor cell line.

6. Formulate the four recombinant viruses separately in buffer compatible with in vivo administration and at 10 ⁸ and 10 ⁷ PFU/ml.

7. Virus replication assay in the above 4 different tumor cell lines is detected by q-RT-PCR (Taqman) .

Stage 2. Test on Safety and bio-distribution of viral vectors.

1.5-week-old BALB/C mice and BALB/C Nude mice are used. BALB/C Mice are distributed across 5 treatment groups (i.e., PBS control, WR-WT Control, low-, medium-and high-dose WR-GO-001 groups) . The BALB/C Nude mice are treated in the same way as BALB/C mice.

2. Oncolytic virus treatment starts when the tumor size in the tumor group reaches 100-300mm ³. Administration with a single injection of the recombinant viruses within the tumor.

3. Monitor the body weight, tumor volume and the wellness of the recombinant virus treated mice.

4. At day 9 after virus injection, mice are sacrificed and tissues from heart, liver, spleen, stomach, kidney, lung and tumor are collected. Vaccinia genomic copies in different tissues are quantified by qPCR.

5. Rechallenge. After tumor regression, the tumor is implanted on the other side of the mouse. Monitor the tumor volume and wellness of the treated mice.

Stage 3. Anti-tumor Activity in Tumor Model

1.5-week-old BALB/C mice were used for 4T1 tumor cell line implantation (day1) . Mice are further distributed across 6 treatment groups, i.e. PBS control, WR-WT control, WR-GO-001, WR-GO-002, WR-GO-003 and WR-GO-004 groups.

Treatment starts when the tumor size reaches 100-300mm ³.

2. The virus (1×10 ⁷ pfu) is injected into individual tumors twice at

day

7 and 10 from the day of tumor implantation, respectively.

3. Monitor the body weight and tumor size of the mice.

4. At day 28, mice are sacrificed and the PBMC cells are collected.

5. Antigen-specific splenocyte responses are assayed by ELISPOT and CTL.

Stage 4. The measurement of tumor-specific cytotoxicity

The cytotoxicity of WR-GO-GO001, WR-GO-GO002, WR-GO-003 and WR-GO-GO004 in two categories of mouse tumor cell lines (CT26 and MC38 ) , three categories of human tumor cell lines (FaDu, PA1 and PANC-1) and one kind of human normal cell line (HUVEC) was measured using CCK-8 method.

The specific cells were infected by WR-GO-001, WR-GO-002, WR-GO-003 and WR-GO-004 at the MOI of 10.0, 1.0 and 0.1, respectively. The cytotoxicity was tested at 24 hours, 48 hours and 72 hours post viral-infection.

2.1 Cell culturing:

200μL of medium containing 2.5×104 of specific cells were seeded in 96-well plates and incubated overnight. Cell counting before viral-infection.

2.2 Viral infection:

Cells in 96 wells plate were infected by WR-GO-001, WR-GO-002, WR-GO-003 and WR-GO-004 at three different MOIs (0.1, 1.0 and 10.0 PFU/cell) , respectively.

2.3 Cell viability assay:

At indicated time points (24, 48 and 72 hours post viral-infection) , 10μL of CCK-8 were added to the testing wells and incubated 2 hours in incubator. Then, the cell viability was measured at 450nm by ultraviolet spectrophotometer (n=3) .

Figures 6A-6H show the obvious cytotoxicity, in vitro, of these recombinant viruses both in MC38 and CT26 cells at 72h post viral-infection, when the MOIs were 10.0 and 1.0.

Figures 7A-7D show the cytotoxicity assay results of WR-GO-003 in human tumor cell lines (FaDu , PA1, PANC-1) and human normal cell line (HUVEC) . The obvious cytotoxicity, in vitro, of WR-GO-003 in human tumor cells was shown, and WR-GO-003 showed more obvious cytotoxicity to FaDu, PANC-1 than PA1. Meanwhile, the cytotoxicity to HUVEC was not obvious, which showed a tumor-specific cytotoxicity of WR-GO-003.

Figures 8A-8D show the cytotoxicity assay results of WR-GO-004 in human tumor cell lines (FaDu, PA1 PANC-1) and human normal cell line (HUVEC) . The obvious cytotoxicity, in vitro, of WR-GO-004 in human tumor cells was shown, and WR-GO-004 showed more obvious cytotoxicity to FaDu, PANC-1 than PA1 at 24h post viral-infection. Meanwhile, the cytotoxicity to HUVEC was not obvious, which showed a tumor-specific cytotoxicity of WR-GO-004.

Stage 5. Viral replication (Viral Particles; VP) curve in FaDu, measured by q-RT-PCR.

5.0×10 ⁵ tumor cells, inoculated in 6-well plate overnight, were infected with WR-GO-003 or WR-GO-004 at the MOI of 0.1 in serum free medium. At indicated time points (24h, 48h, 72h post viral-infection) , both cell lysate and supernatant were harvested. The genomic DNA was extracted using the tissue and blood DNA extracted kit. The VP were finally evaluated by q-RT-PCR system.

The results are shown in Figures 9A and 9B, which shows both WR-GO-003 and WR-GO-004 were effectively replicated in FaDu cells.

While various aspects and embodiments have been disclosed herein, other aspects and embodiments will be apparent to those skilled in the art. The various aspects and embodiments disclosed herein are for purposes of illustration and are not intended to be limiting, with the true scope and spirit being indicated by the following claims.

Claims

A modified oncolytic virus comprising a virus genome having a first heterologous polynucleotide encoding a first molecule capable of inhibiting the interaction between PD-1 and PD-L1 and a second heterologous polynucleotide encoding a second molecule capable of inhibiting TGF-β signaling.
The modified oncolytic virus of claim 1, wherein the oncolytic virus is selected from the group consisting of vaccinia virus, adenovirus, reovirus, herpes simplex virus, Semliki Forest virus, Venezuelan equine encephalitis, Parvovirus, Chicken Anemia Virus, Measles Virus, Coxsackie Virus, Vesicular Stomatitis Virus, Seneca Valley Virus, Maraba virus, Newcastle disease virus and Myxoma virus.
The modified oncolytic virus of claim 2, wherein the oncolytic virus is vaccinia virus.
The modified oncolytic virus of claim 1, wherein the modified oncolytic virus is attenuated and can replicate in a tumor cell.
The modified oncolytic virus of claim 1, wherein the virus genome comprises at least one deletion or disruption that renders the virus capable of selective replication in a tumor cell.
The modified oncolytic virus of claim 5, wherein the deletion or the disruption is in an Open Reading Frame (ORF) encoding at least a part of an enzyme that is both essential for replication of the virus and preferentially expressed in a tumor cell than in a non-tumor cell.
The modified oncolytic virus of claim 6, wherein the enzyme is a kinase.
The modified oncolytic virus of claim 7, wherein the enzyme is thymidine kinase.
The modified oncolytic virus of claim 2, wherein the oncolytic virus is derived from the Western Reserve strain.
The modified oncolytic virus of claim 4, wherein the first heterologous polynucleotide and the second heterologous polynucleotide is inserted in the place of the deletion.
The modified oncolytic virus of claim 1, wherein the first heterologous polynucleotide and the second heterologous polynucleotide are configured such that they are expressed in the same or different stages of replicative cycle of the modified oncolytic virus.
The modified oncolytic virus of claim 1, wherein the first molecule is a first fusion protein and the second molecule is a second fusion protein.
The modified oncolytic virus of claim 12, wherein the first heterologous polynucleotide comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a first promoter -a polynucleotide encoding the first fusion protein –a first stop codon, and the second heterologous polynucleotide comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a second promoter –a polynucleotide encoding the second fusion protein –a second stop codon.
The modified oncolytic virus of claim 13, wherein the first fusion protein expressed from the first heterologous polynucleotide and the second fusion protein expressed from the second heterologous polynucleotide are expressed as separate proteins.
The modified oncolytic virus of claim 13, wherein the first heterologous polynucleotide is immediately upstream or immediately downstream of the second heterologous polynucleotide.
The modified oncolytic virus of claim 13, wherein the first promoter is capable of driving expression of the first fusion protein, and the second promoter is capable of driving expression of the second fusion protein, wherein the first and the second promoters are in a head-to-head orientation.
The modified oncolytic virus of claim 13, wherein the first and the second promoters are the same or different.
The modified oncolytic virus of claim 17, wherein the first and the second promoters are both early and late promoter.
The modified oncolytic virus of claim 18, wherein the early and late promoter is pSE/L.
The modified oncolytic virus of claim 13, wherein the first and second stop codons are the same or different.
The modified oncolytic virus of claim 12, wherein the first fusion protein comprises PD-1 extracellular domain (PD-1 ECD) .
The modified oncolytic virus of claim 21, wherein the first fusion protein further comprises a first immunoglobulin Fc region.
The modified oncolytic virus of claim 22, wherein the first immunoglobulin Fc region is a first human IgG1 Fc region.
The modified oncolytic virus of claim 23, wherein the PD-1 ECD is operably linked to the first immunoglobulin Fc region at the C terminal of the PD-1 ECD.
The modified oncolytic virus of claim 21, wherein the first fusion protein further comprises a signal peptide.
The modified oncolytic virus of claim 25, wherein the signal peptide is operably linked to the PD-1 ECD at the C terminal of the signal peptide.
The modified oncolytic virus of claim 25, wherein the signal peptide is CD33 signal peptide.
The modified oncolytic virus of claim 21, wherein the PD-1 ECD comprises an amino acid sequence of SEQ ID NO: 1 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 28, wherein the amino acid sequence is encoded by a nucleic acid sequence of SEQ ID NO: 7 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 23, wherein the first human IgG1 Fc region comprises an amino acid sequence of SEQ ID NO: 3 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 30, wherein the amino acid sequence is encoded by a nucleic acid sequence of SEQ ID NO: 9 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 27, wherein the CD33 signal peptide comprises an amino acid sequence of SEQ ID NO: 4 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 32, wherein the amino acid sequence is encoded by a nucleic acid sequence comprising SEQ ID NO: 11 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 12, wherein the first fusion protein comprises an amino acid sequence of SEQ ID NO: 5 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 34, wherein the amino acid sequence is encoded by a nucleic acid sequence comprising SEQ ID NO: 13 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of any of claims 1, wherein the first molecule is an anti-PD-1 antibody and the second molecule is a second fusion protein.
The modified oncolytic virus of claim 36, wherein the anti-PD-1 antibody comprises:

a HCDR1 having an amino acid sequence of SEQ ID NO: 23 or a homologous sequence thereof having at least 80%sequence identity,

a HCDR2 having an amino acid sequence of SEQ ID NO: 24 or a homologous sequence thereof having at least 80%sequence identity,

a HCDR3 having an amino acid sequence of SEQ ID NO: 25 or a homologous sequence thereof having at least 80%sequence identity,

a LCDR1 having an amino acid sequence of SEQ ID NO: 26 or a homologous sequence thereof having at least 80%sequence identity,

a LCDR2 having an amino acid sequence of SEQ ID NO: 27 or a homologous sequence thereof having at least 80%sequence identity, and

a LCDR3 having an amino acid sequence of SEQ ID NO: 28 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 37, wherein

the HCDR1 is encoded by a nucleic acid sequence of SEQ ID NO: 31 or a homologous sequence thereof having at least 80%sequence identity,

the HCDR2 is encoded by a nucleic acid sequence of SEQ ID NO: 32 or a homologous sequence thereof having at least 80%sequence identity,

the HCDR3 is encoded by a nucleic acid sequence of SEQ ID NO: 33 or a homologous sequence thereof having at least 80%sequence identity,

the LCDR1 is encoded by a nucleic acid sequence of SEQ ID NO: 34 or a homologous sequence thereof having at least 80%sequence identity,

the LCDR2 is encoded by a nucleic acid sequence of SEQ ID NO: 35 or a homologous sequence thereof having at least 80%sequence identity, and

the LCDR3 is encoded by a nucleic acid sequence of SEQ ID NO: 36 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 36, wherein the anti-PD-1 antibody comprises a heavy chain variable region having an amino acid sequence of SEQ ID NO: 29 or a homologous sequence thereof having at least 80%sequence identity, and a light chain variable region having an amino acid sequence of SEQ ID NO: 30 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 39, wherein the anti-PD-1 antibody heavy chain variable region is encoded by a nucleic acid sequence of SEQ ID NO: 37 or a homologous sequence thereof having at least 80%sequence identity, and the anti-PD-1 antibody light chain variable region is encoded by a nucleic acid sequence of SEQ ID NO: 38 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 36, wherein the anti-PD-1 antibody comprises a full length heavy chain having an amino acid sequence of SEQ ID NO: 21 or a homologous sequence thereof having at least 80%sequence identity, and a full length light chain having an amino acid sequence of SEQ ID NO: 20 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 41, wherein the anti-PD-1 antibody full length heavy chain is encoded by a nucleic acid sequence of SEQ ID NO: 39 or a homologous sequence thereof having at least 80%sequence identity, and the anti-PD-1 antibody full length light chain is encoded by a nucleic acid sequence of SEQ ID NO: 40 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 36, wherein the first heterologous polynucleotide further comprises a third heterologous polynucleotide and a fourth heterologous polynucleotide, wherein the third heterologous polynucleotide comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a third promoter –a polynucleotide encoding the anti-PD-1 antibody heavy chain –a third stop codon, and wherein the fourth heterologous polynucleotide comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a fourth promoter –a polynucleotide encoding the anti-PD-1 antibody light chain –a fourth stop codon; and the second heterologous polynucleotide further comprises the following elements in frame in an orientation from 5’ to 3’ of the sense strand: a second promoter –a polynucleotide encoding the second fusion protein –a second stop codon.
The modified oncolytic virus of claim 43, wherein the third heterologous polynucleotide is immediately upstream or immediately downstream of the fourth heterologous polynucleotide.
The modified oncolytic virus of claim 44, wherein the third promoter is capable of driving expression of the anti-PD-1 antibody heavy chain, and the fourth promoter is capable of driving expression of the anti-PD-1 antibody light chain, wherein the third and the fourth promoters are in a head-to-head orientation.
The modified oncolytic virus of claim 36, wherein the first heterologous polynucleotide is immediately upstream or immediately downstream of the second heterologous polynucleotide.
The modified oncolytic virus of claims 46, wherein the anti-PD-1 antibody expressed from the first heterologous polynucleotide and the second fusion protein expressed from the second heterologous polynucleotide are expressed as separate proteins.
The modified oncolytic virus of claim 42, wherein the second, the third and the fourth promoters are the same or different.
The modified oncolytic virus of claim 47, wherein the second, the third and the fourth promoters are both early and late promoter.
The modified oncolytic virus of claim 48, wherein the early and late promoter is pSE/L.
The modified oncolytic virus of claim 42, wherein the second, the third and fourth stop codons are the same or different.
The modified oncolytic virus of claim 12 or 36, wherein the second fusion protein comprises TGF-β receptor II extracellular domain (TGFBRII ECD) .
The modified oncolytic virus of claim 52, wherein the second fusion protein further comprises a second immunoglobulin Fc region.
The modified oncolytic virus of claim 53, wherein the immunoglobulin Fc region is a second human IgG1 Fc region.
The modified oncolytic virus of claim 54, wherein the TGFBRII ECD is operably linked to the second immunoglobulin Fc region at the C terminal of the TGFBRII ECD.
The modified oncolytic virus of claim 52, wherein the second fusion protein further comprises a signal peptide.
The modified oncolytic virus of claim 56, wherein the signal peptide is operably linked to the TGFBRII ECD at the C terminal of the signal peptide.
The modified oncolytic virus of claim 56, wherein the signal peptide is CD33 signal peptide.
The modified oncolytic virus of claim 52, wherein the TGFBRII ECD comprises an amino acid sequence of SEQ ID NO: 2 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 59, wherein the amino acid sequence is encoded by a nucleic acid sequence of SEQ ID NO: 8 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 54, wherein the second human IgG1 Fc region comprises an amino acid sequence of SEQ ID NO: 3 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 61, wherein the amino acid sequence is encoded by a nucleic acid sequence of SEQ ID NO: 10 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 58, wherein the CD33 signal peptide comprises an amino acid sequence of SEQ ID NO: 4 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 63, wherein the amino acid sequence is encoded by a nucleic acid sequence comprising SEQ ID NO: 12 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 12 or 36, wherein the second fusion protein comprises an amino acid sequence of SEQ ID NO: 6 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 65, wherein the amino acid sequence is encoded by a nucleic acid sequence comprising SEQ ID NO: 14 or a homologous sequence thereof having at least 80%sequence identity.
The modified oncolytic virus of claim 12, wherein the first fusion protein and the second fusion protein are capable of forming a dimer.
The modified oncolytic virus of claim 67, wherein the dimer is formed via the association of the first immunoglobulin Fc region and the second immunoglobulin Fc region.
The modified oncolytic virus of claim 1 having a nucleic acid sequence of SEQ ID NO: 17 or SEQ ID NO: 22.
A pharmaceutical composition comprising the modified oncolytic virus of any one of claims 1-69 and a pharmaceutically acceptable carrier.
A method of treating a tumor, comprising administering to a subject an effective amount of the modified oncolytic virus of any one of claims 1-69 or the pharmaceutical composition of claim 70.
The method of claim 71, wherein the subject is human.
The method of claim 71, wherein the tumor is a solid tumor.
The method of claim 71, wherein the tumor is melanoma, non-small cell lung cancer, renal cell carcinoma, Hodgkin lymphoma, squamous cell carcinoma of the head and neck, bladder cancer, colorectal cancer, triple negative breast cancer, hepatocellular carcinoma, pancreatic cancer, ovarian cancer, colon cancer, pharyngeal squamous cell carcinoma, or ovarian teratoma.
The method of claim 71, wherein the route of administering is topical.
The method of claim 75, wherein the route of administering is intra-tumor injection.