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METHODS AND MATERIALS FOR TREATING CANCER

20240009257 ยท 2024-01-11

    Inventors

    Cpc classification

    International classification

    Abstract

    This document provides methods and materials for treating cancer. For example, methods and materials for using oncolytic viruses (e.g., replication-competent vesicular stomatitis viruses) to treat cancer are provided. Replication-competent oncolytic viruses (e.g., replication-competent oncolytic vesicular stomatitis viruses), nucleic acid molecules encoding a replication-competent oncolytic virus (e.g., replication-competent oncolytic vesicular stomatitis virus), methods for making replication-competent oncolytic viruses (e.g., replication-competent oncolytic vesicular stomatitis viruses), methods for using replication-competent oncolytic viruses (e.g., replication-competent oncolytic vesicular stomatitis viruses) to treat cancer, cancer neoantigens, nucleic acids encoding a cancer neoantigen, and methods for stimulating immune cells (e.g., cytotoxic T lymphocytes) to kill cancer cells also are provided.

    Claims

    1. A method for treating cancer in a mammal, wherein said method comprises administering, to said mammal, (a) a replication-competent oncolytic virus and (b) a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:1 or nucleic acid encoding said polypeptide.

    2. The method of claim 1, wherein said mammal is a human.

    3. The method of any one of claims 1-2, wherein said virus is a vesicular stomatitis virus.

    4. The method of any one of claims 1-3, wherein said polypeptide is a full length CSDE1.sup.P5S polypeptide.

    5. The method of any one of claims 1-3, wherein said polypeptide comprises less than 100 amino acid residues.

    6. The method of any one of claims 1-3, wherein said polypeptide comprises less than 50 amino acid residues.

    7. The method of any one of claims 1-3, wherein said polypeptide comprises less than 25 amino acid residues.

    8. The method of any one of claims 1-3, wherein said polypeptide comprises less than 100 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    9. The method of any one of claims 1-3, wherein said polypeptide comprises less than 50 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    10. The method of any one of claims 1-3, wherein said polypeptide comprises less than 25 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    11. The method of any one of claims 1-10, wherein said polypeptide comprises a cell penetrating amino acid sequence.

    12. The method of claim 11, wherein said cell penetrating amino acid sequence is selected from Table 1.

    13. The method of any one of claims 1-12, wherein said method comprises administering said polypeptide.

    14. The method of any one of claims 1-12, wherein said method comprises administering said nucleic acid.

    15. The method of any one of claims 1-14, wherein said cancer is selected from the group consisting of skin cancer, liver cancer, and kidney cancer.

    16. A replication-competent oncolytic virus comprising nucleic acid encoding a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:1 or a nucleic acid sequence that is a template for said nucleic acid.

    17. The virus of claim 16, wherein said virus is selected from the group consisting of a vesicular stomatitis virus, an adenovirus, and a herpesvirus.

    18. The virus of any one of claims 16-17, wherein said polypeptide is a full length CSDE1.sup.P5S polypeptide.

    19. The virus of any one of claims 16-17, wherein said polypeptide comprises less than 100 amino acid residues.

    20. The virus of any one of claims 16-17, wherein said polypeptide comprises less than 50 amino acid residues.

    21. The virus of any one of claims 16-17, wherein said polypeptide comprises less than 25 amino acid residues.

    22. The virus of any one of claims 16-17, wherein said polypeptide comprises less than 100 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    23. The virus of any one of claims 16-17, wherein said polypeptide comprises less than 50 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    24. The virus of any one of claims 16-17, wherein said polypeptide comprises less than 25 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    25. A substantially pure polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 1.

    26. The polypeptide of claim 25, wherein said polypeptide is a full length CSDE1.sup.P5S polypeptide.

    27. The polypeptide of claim 25, wherein said polypeptide comprises less than 100 amino acid residues.

    28. The polypeptide of claim 25, wherein said polypeptide comprises less than 50 amino acid residues.

    29. The polypeptide of claim 25, wherein said polypeptide comprises less than 25 amino acid residues.

    30. The polypeptide of claim 25, wherein said polypeptide comprises less than 100 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    31. The polypeptide of claim 25, wherein said polypeptide comprises less than 50 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    32. The polypeptide of claim 25, wherein said polypeptide comprises less than 25 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    33. The polypeptide of any one of claims 25-32, wherein said polypeptide comprises a cell penetrating amino acid sequence.

    34. The polypeptide of claim 33, wherein said cell penetrating amino acid sequence is selected from Table 1.

    35. A nucleic acid encoding a polypeptide of any one of claims 25-34.

    36. The nucleic acid of claim 35, wherein said nucleic acid is a plasmid or viral vector.

    37. A composition comprising (a) polypeptide of any one of claims 25-34 and (b) an adjuvant.

    38. The composition of claim 37, wherein said adjuvant is selected from the group consisting of aluminum compound (e.g., amorphous aluminum hydroxyphosphate sulfate (AAHS), aluminum hydroxide, aluminum phosphate, or potassium aluminum sulfate (Alum)), monophosphoryl lipid A (MPL), oil in water emulsion composed of squalene, and cytosine phosphoguanine (CpG).

    39. A replication-competent vesicular stomatitis virus comprising an RNA molecule, wherein said RNA molecule comprises a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV N polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV P polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV M polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV G polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:1, and a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV L polypeptide.

    40. The virus of claim 39, wherein said polypeptide is a full length CSDE1.sup.P5S polypeptide.

    41. The virus of claim 39, wherein said polypeptide comprises less than 100 amino acid residues.

    42. The virus of claim 39, wherein said polypeptide comprises less than 50 amino acid residues.

    43. The virus of claim 39, wherein said polypeptide comprises less than 25 amino acid residues.

    44. The virus of claim 39, wherein said polypeptide comprises less than 100 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    45. The virus of claim 39, wherein said polypeptide comprises less than 50 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    46. The virus of claim 39, wherein said polypeptide comprises less than 25 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    47. The virus of any one of claims 39-46, wherein said RNA molecule comprises a nucleic acid sequence that is a template for a positive sense transcript encoding a interferon- polypeptide.

    48. The virus of claim 47, wherein said interferon- polypeptide is a human interferon- polypeptide.

    49. The virus of any one of claims 39-48, wherein said RNA molecule comprises a nucleic acid sequence that is a template for a positive sense transcript encoding a NIS polypeptide.

    50. The virus of claim 49, wherein said NIS polypeptide is a human NIS polypeptide.

    51. A composition comprising the replication-competent vesicular stomatitis virus of any one of claims 39-50.

    52. A nucleic acid molecule comprising a nucleic acid strand comprising a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV N polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV P polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV M polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV G polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:1, and a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV L polypeptide.

    53. The nucleic acid molecule of claim 52, wherein said polypeptide comprising the amino acid sequence set forth in SEQ ID NO:1 is a full length CSDE1.sup.P5S polypeptide.

    54. The nucleic acid molecule of claim 52, wherein said polypeptide comprising the amino acid sequence set forth in SEQ ID NO:1 comprises less than 100 amino acid residues.

    55. The nucleic acid molecule of claim 52, wherein said polypeptide comprising the amino acid sequence set forth in SEQ ID NO:1 comprises less than 50 amino acid residues.

    56. The nucleic acid molecule of claim 52, wherein said polypeptide comprising the amino acid sequence set forth in SEQ ID NO:1 comprises less than 25 amino acid residues.

    57. The nucleic acid molecule of claim 52, wherein said polypeptide comprising the amino acid sequence set forth in SEQ ID NO:1 comprises less than 100 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    58. The nucleic acid molecule of claim 52, wherein said polypeptide comprising the amino acid sequence set forth in SEQ ID NO:1 comprises less than 50 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    59. The nucleic acid molecule of claim 52, wherein said polypeptide comprising the amino acid sequence set forth in SEQ ID NO:1 comprises less than 25 amino acid residues of a full length CSDE1.sup.P5S polypeptide.

    60. The nucleic acid molecule of any one of claims 52-59, wherein said nucleic acid strand comprises a nucleic acid sequence that is a template for a positive sense transcript encoding a interferon- polypeptide.

    61. The nucleic acid molecule of claim 60, wherein said interferon- polypeptide is a human interferon- polypeptide.

    62. The nucleic acid molecule of any one of claims 52-61, wherein said nucleic acid strand comprises a nucleic acid sequence that is a template for a positive sense transcript encoding a NIS polypeptide.

    63. The nucleic acid molecule of claim 62, wherein said NIS polypeptide is a human NIS polypeptide.

    64. A method for treating cancer, wherein said method comprises administering a virus of any one of claims 16-24 and 39-50 to a mammal comprising cancer cells, wherein the number of cancer cells within said mammal is reduced following said administration.

    65. The method of claim 64, wherein said mammal is a human.

    66. A method for treating cancer, wherein said method comprises administering a polypeptide of any one of claims 25-34 to a mammal comprising cancer cells, wherein the number of cancer cells within said mammal is reduced following said administration.

    67. The method of claim 66, wherein said mammal is a human.

    68. A method for treating cancer, wherein said method comprises administering a nucleic acid of any one of claims 35, 36, and 52-63 to a mammal comprising cancer cells, wherein the number of cancer cells within said mammal is reduced following said administration.

    69. The method of claim 68, wherein said mammal is a human.

    70. A method for treating cancer, wherein said method comprises administering a composition of any one of claims 37, 38, and 51 to a mammal comprising cancer cells, wherein the number of cancer cells within said mammal is reduced following said administration.

    71. The method of claim 70, wherein said mammal is a human.

    72. A method for increasing survival of a mammal having cancer, wherein said method comprises administering a virus of any one of claims 16-24 and 39-50 to said mammal.

    73. The method of claim 72, wherein said mammal is a human.

    74. A method for increasing survival of a mammal having cancer, wherein said method comprises administering a polypeptide of any one of claims 25-34 to said mammal.

    75. The method of claim 74, wherein said mammal is a human.

    76. A method for increasing survival of a mammal having cancer, wherein said method comprises administering a nucleic acid of any one of claims 35, 36, and 52-63 to said mammal.

    77. The method of claim 76, wherein said mammal is a human.

    78. A method for increasing survival of a mammal having cancer, wherein said method comprises administering a composition of any one of claims 37, 38, and 51 to said mammal.

    79. The method of claim 78, wherein said mammal is a human.

    80. A replication-competent oncolytic virus comprising (a) a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:2 or a fragment thereof or (b) nucleic acid encoding said polypeptide or a nucleic acid sequence that is a template for said nucleic acid.

    81. The virus of claim 80, wherein said virus is a vesicular stomatitis virus, an adenovirus, or a herpesvirus.

    82. The virus of any one of claims 80-81, wherein said virus comprises said polypeptide comprising the amino acid sequence set forth in SEQ ID NO:2.

    83. The virus of any one of claims 80-81, wherein said virus comprises said polypeptide comprising said fragment of SEQ ID NO:2.

    84. The virus of claim 83, wherein said fragment of SEQ ID NO:2 comprises at least 750 amino acid residues of SEQ ID NO:2. The virus of claim 83, wherein said fragment of SEQ ID NO:2 comprises at least 700 amino acid residues of SEQ ID NO:2.

    86. The virus of any one of claims 80-85, wherein said virus comprises said nucleic acid.

    87. The virus of any one of claims 80-86, wherein said virus comprises an antigen or nucleic acid encoding said antigen.

    88. The virus of claim 87, wherein said antigen is from a virus or a bacteria.

    89. The virus of claim 87, wherein said antigen is from a SARS-CoV-2 virus, an influenza virus, an EBOLA virus, a yellow fever virus, a dengue virus, a coronavirus, a measles virus, a mumps virus, or a rubella virus.

    90. The virus of claim 87, wherein said antigen is from an Escherichia species, a Salmonella species, a Mycobacterium species, a Clostridium species, a Bacillus species, or a Leptospira species.

    91. The virus of claim 87, wherein said antigen is a SARS-CoV-2 antigen.

    92. The virus of claim 87, wherein said antigen is a SARS-CoV-2 SPIKE protein antigen, a SARS-CoV-2 M protein antigen, a SARS-CoV-2 N protein antigen, an influenza NP protein antigen, an influenza M1 protein antigen, an influenza NS1 protein antigen, an Ebola NP protein antigen, an Ebola GP protein antigen, an Ebola VP35 protein antigen, an Ebola VP40 protein antigen, a yellow fever NS1 protein antigen, a dengue virus NS1 protein antigen, a coronavirus spike protein antigen, a coronavirus M protein antigen, a coronavirus N protein antigen, a measles virus F protein antigen, a measles virus H protein antigen, a mumps nucleocapsid protein antigen, a rubella virus E1 spike protein antigen, a rubella virus E2 spike protein antigen, a rubella virus C protein antigen, an Escherichia coli O antigen, a Mycobacterium tuberculosis glfT2 antigen, a Mycobacterium tuberculosis fas antigen, a Mycobacterium tuberculosis iniB antigen, a Clostridium tatanis tetanus toxoid antigen, a Bacillus anthracis anthrax toxin antigen, a Leptospira species LipL21 antigen, a Leptospira species LipL41 antigen, or a Leptospira species LipL32 antigen.

    93. A nucleic acid encoding said virus of any one of claims 80-92.

    94. The nucleic acid of claim 93, wherein said nucleic acid is a plasmid or viral vector.

    95. A replication-competent vesicular stomatitis virus comprising an RNA molecule, wherein said RNA molecule comprises a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV N polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV P polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV M polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV G polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:2 or a fragment thereof, and a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV L polypeptide.

    96. The virus of claim 95, wherein said RNA molecule comprises said nucleic acid sequence that is a template for a positive sense transcript encoding said polypeptide comprising said amino acid sequence set forth in SEQ ID NO:2.

    97. The virus of any one of claims 95-96, wherein said RNA molecule comprises said nucleic acid sequence that is a template for a positive sense transcript encoding said fragment of SEQ ID NO:2.

    98. The virus of claim 97, wherein said fragment of SEQ ID NO:2 comprises at least 750 amino acid residues of SEQ ID NO:2.

    99. The virus of claim 97, wherein said fragment of SEQ ID NO:2 comprises at least 700 amino acid residues of SEQ ID NO:2.

    100. The virus of any one of claims 95-99, wherein said RNA molecule comprises a nucleic acid sequence that is a template for a positive sense transcript encoding an antigen.

    101. The virus of claim 100, wherein said antigen is from a virus or a bacteria.

    102. The virus of claim 100, wherein said antigen is from a SARS-CoV-2 virus, an influenza virus, an EBOLA virus, a yellow fever virus, a dengue virus, a coronavirus, a measles virus, a mumps virus, or a rubella virus.

    103. The virus of claim 100, wherein said antigen is from an Escherichia species, a Salmonella species, a Mycobacterium species, a Clostridium species, a Bacillus species, or a Leptospira species.

    104. The virus of claim 100, wherein said antigen is a SARS-CoV-2 antigen.

    105. The virus of claim 100, wherein said antigen is a SARS-CoV-2 SPIKE protein antigen, a SARS-CoV-2 M protein antigen, a SARS-CoV-2 N protein antigen, an influenza NP protein antigen, an influenza M1 protein antigen, an influenza NS1 protein antigen, an Ebola NP protein antigen, an Ebola GP protein antigen, an Ebola VP35 protein antigen, an Ebola VP40 protein antigen, a yellow fever NS1 protein antigen, a dengue virus NS1 protein antigen, a coronavirus spike protein antigen, a coronavirus M protein antigen, a coronavirus N protein antigen, a measles virus F protein antigen, a measles virus H protein antigen, a mumps nucleocapsid protein antigen, a rubella virus E1 spike protein antigen, a rubella virus E2 spike protein antigen, a rubella virus C protein antigen, an Escherichia coli O antigen, a Mycobacterium tuberculosis glfT2 antigen, a Mycobacterium tuberculosis fas antigen, a Mycobacterium tuberculosis iniB antigen, a Clostridium tatanis tetanus toxoid antigen, a Bacillus anthracis anthrax toxin antigen, a Leptospira species LipL21 antigen, a Leptospira species LipL41 antigen, or a Leptospira species LipL32 antigen.

    106. A nucleic acid molecule comprising a nucleic acid strand comprising a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV N polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV P polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV M polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV G polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:2 or a fragment thereof, and a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV L polypeptide.

    107. The nucleic acid molecule of claim 106, wherein said nucleic acid strand comprises said nucleic acid sequence that is a template for a positive sense transcript encoding a polypeptide comprising said amino acid sequence set forth in SEQ ID NO:2.

    108. The nucleic acid molecule of claim 106, wherein said nucleic acid strand comprises said nucleic acid sequence that is a template for a positive sense transcript encoding a polypeptide comprising said fragment of SEQ ID NO:2.

    109. The nucleic acid molecule of claim 108, wherein said fragment of SEQ ID NO:2 comprises at least 750 amino acid residues of SEQ ID NO:2.

    110. The nucleic acid molecule of claim 108, wherein said fragment of SEQ ID NO:2 comprises at least 700 amino acid residues of SEQ ID NO:2.

    111. The nucleic acid molecule of any one of claims 106-110, wherein said nucleic acid strand comprises a nucleic acid sequence that is a template for a positive sense transcript encoding a interferon- polypeptide.

    112. The nucleic acid molecule of claim 111, wherein said interferon- polypeptide is a human interferon- polypeptide.

    113. The nucleic acid molecule of any one of claims 106-112, wherein said nucleic acid strand comprises a nucleic acid sequence that is a template for a positive sense transcript encoding a NIS polypeptide.

    114. The nucleic acid molecule of claim 113, wherein said NIS polypeptide is a human NIS polypeptide.

    115. A composition comprising the replication-competent oncolytic virus of any one of claims 80-92, the nucleic acid of any one of claims 93-94, the replication-competent vesicular stomatitis virus of any one of claims 95-105, or the nucleic acid molecule of any one of claims 106-114.

    116. A method for treating cancer in a mammal, wherein said method comprises administering, to said mammal, (a) a replication-competent oncolytic virus and (b) a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:2 or a fragment thereof, or nucleic acid encoding said polypeptide or said fragment thereof

    117. The method of claim 116, wherein said mammal is a human.

    118. The method of any one of claims 116-117, wherein said virus is a vesicular stomatitis virus.

    119. The method of any one of claims 116-118, wherein said virus comprises said polypeptide comprising the amino acid sequence set forth in SEQ ID NO:2.

    120. The method of any one of claims 116-118, wherein said virus comprises said polypeptide comprising said fragment of SEQ ID NO:2.

    121. The method of claim 120, wherein said fragment of SEQ ID NO:2 comprises at least 750 amino acid residues of SEQ ID NO:2.

    122. The method of claim 120, wherein said fragment of SEQ ID NO:2 comprises at least 700 amino acid residues of SEQ ID NO:2.

    123. The method of any one of claims 116-122, wherein said polypeptide comprises a cell penetrating amino acid sequence.

    124. The method of claim 123, wherein said cell penetrating amino acid sequence is selected from Table 1.

    125. The method of any one of claims 116-124, wherein said method comprises administering said polypeptide.

    126. The method of any one of claims 116-124, wherein said method comprises administering said nucleic acid.

    127. The method of any one of claims 116-126, wherein said cancer is selected from the group consisting of skin cancer, liver cancer, and kidney cancer.

    128. A method for treating cancer, wherein said method comprises administering a virus of any one of claims 80-86 and 95-99 to a mammal comprising cancer cells, wherein the number of cancer cells within said mammal is reduced following said administration.

    129. The method of claim 128, wherein said mammal is a human.

    130. A method for treating cancer, wherein said method comprises administering a nucleic acid of any one of claims 93, 94, and 106-114 to a mammal comprising cancer cells, wherein the number of cancer cells within said mammal is reduced following said administration.

    131. The method of claim 130, wherein said mammal is a human.

    132. A method for treating cancer, wherein said method comprises administering a composition of claim 115 to a mammal comprising cancer cells, wherein the number of cancer cells within said mammal is reduced following said administration.

    133. The method of claim 132, wherein said mammal is a human.

    134. A method for increasing survival of a mammal having cancer, wherein said method comprises administering a virus of any one of claims 80-86 and 95-99 to said mammal.

    135. The method of claim 134, wherein said mammal is a human

    136. A method for increasing survival of a mammal having cancer, wherein said method comprises administering a nucleic acid of any one of claims 93, 94, and 106-114 to said mammal.

    137. The method of claim 136, wherein said mammal is a human.

    138. A method for increasing survival of a mammal having cancer, wherein said method comprises administering a composition of claim 115 to said mammal.

    139. The method of claim 138, wherein said mammal is a human.

    140. A method for inducing an immune response in a mammal, wherein said method comprises administering a virus of any one of claims 87-91 and 100-105 to said mammal.

    141. The method of claim 140, wherein said mammal is a human.

    142. A method for inducing an immune response in a mammal, wherein said method comprises administering a nucleic acid encoding said virus of any one of claims 87-92 and 100-105 to said mammal.

    143. The method of claim 142, wherein said mammal is a human.

    144. A method for inducing an immune response in a mammal, wherein said method comprises administering to said mammal (i) a composition comprising said virus of any one of claims 87-91 and 100-105, or (ii) a composition comprising a nucleic acid encoding said virus of any one of claims 87-91 and 100-105.

    145. The method of claim 138, wherein said mammal is a human.

    Description

    DESCRIPTION OF DRAWINGS

    [0079] FIGS. 1A-1J. Escape from VSV-IFN- selects for the CSDE1.sup.C-T mutation. B16 murine melanoma or Hep3B human HCC cells were infected (MOI 0.01) for 21 days. Surviving cells were pooled, and genomic DNA prepared. Sanger sequencing of CSDE1 is shown for: (FIG. 1A) Parental, uninfected B16 showing a homogenous population of wild type CSDE1 sequence; (FIG. 1B) B16-VSV-GFP-ESC showing a mixed population of escape cells with either wild type ATCC or mutated ATTC sequence; (FIG. 1C) B16 cells stably expressing the HSVtk suicide gene and selected in GCV for 21 days; (FIG. 1D) B16-VSV-IFN--ESC showing a nearly homogenous population of escape cells with mutated ATTC sequence; (FIGS. 1E and 1F) B16 cells stably expressing shRNA against APOBEC3 selected for escape from VSV-GFP (FIG. 1E) or VSV-IFN (FIG. 1F); (FIG. 1G) Parental, uninfected Hep3B; (FIG. 1H) Hep3B-VSV-GFP-ESC; and (FIG. 1I) Hep3B-VSV-IFN-ESC. (FIG. 1J) Mice bearing s.c. Mel888 human melanoma tumors treated with i.t. VSV-hIFN were excised upon escape from treatment, genomic DNA prepared, and Sanger sequencing used to characterize the CSDE1 gene as shown. Four of four excised, VSV-hIFN-escaped tumors had mixed populations of CSDE1.sup.WT and CSDE1.sup.C-T tumor cells at ratios close to 1:1. Results were representative of multiple (>5) separate experiments (FIGS. 1A-1D); three separate experiments (FIGS. 1E and 1F) and (FIGS. 1G-1I); and four separate escape tumors (FIG. 1J).

    [0080] FIGS. 2A-2G. CSDE1 is a positive modulator of VSV replication (FIG. 2A) Hep3B cells were transfected with no siRNA, Negative control siRNA or with [s15373+15374 siRNA] (2 CSDE1-specific siRNA) and levels of CSDE1 assayed by Western Blot 24 or 48 hours later. (FIGS. 2B-2D) 48 hours following transfection with siRNA as in (FIG. 2A), Hep3B cells were infected with VSV-GFP (MOI 0.1). 48 hours (FIG. 2B) or 96 hours (FIG. 2C) later, viral titers were determined by plaque assay, and (FIG. 2D) the number of surviving cells was counted at 96 hours post infection. Representative of two separate experiments. (FIG. 2E) B16, B16-CSDE1.sup.C-T or B16-CSDE1.sup.WT over-expressing cells were infected with VSV-IFN- at a MOI of 0.1. 24, 48, and 72 hours later, viral titers were measured on BHK cells by plaque assay. Representative of multiple experiments. (FIG. 2F) Parental Hep3B cells, or pooled populations of Hep3B over-expressing wild type CSDE1.sup.WT, or mutant CSDE1.sup.C-T, were infected with VSV-IFN- (MOI 0.1) (3 wells/group). 48 hours later, (Passage 1) supernatants were assayed for infectious titers on the same cells on which the virus was passaged. Virus was recovered every 48 hours (Passages 2-5), and the titer similarly determined. Representative of three separate experiments. (FIG. 2G) Stock VSV-IFN- virus, or VSV-IFN- that had been passaged 5 times through Hep3B parental or Hep3B-CSDE1.sup.C-T cells as in (FIG. 2F) had their titers determined on either Hep3B parental cells or on Hep3B-CSDE1.sup.C-T cells. Representative of two separate experiments. MeansSD of 3 technical replicates are shown. P-values were determined using a one way (FIGS. 2B, 2C, and 2D) or two-way (FIGS. 2E, 2G, and 2F) ANOVA with a Tukey multiple comparisons post-test on log transformed data. Statistical significance set at p<0.05, ns>0.05.

    [0081] FIGS. 3A-3D. CSDE1 expressed from the virus enhances replication. (FIG. 3A) Viruses expressing CSDE1.sup.WT and CSDE1.sup.C-T were constructed and validated by Western Blot for expression of CSDE1. Stars indicate clones that were used in subsequent experiments. (FIG. 3B) BHK (hamster), B16 (mouse), Hep3B and Mel888 (human) cell lines were infected with VSV-GFP, VSV-hIFN-, VSV-CSDE1.sup.WT or VSV-CSDE1.sup.C-T at an MOI of 3 (triplicate wells per cell line). 48 hours later, the titer was determined on BHK cells by plaque assay. Representative of multiple experiments. (FIG. 3C) Murine B16 or human Hep3B cells were infected (MOI 0.01) with VSV-IFN, VSV-IFN--CSDE1.sup.WT or with VSV-IFN--CSDE1.sup.C-T viruses (using species matched IFN genes) for 21 days. Surviving cells were pooled and counted. (FIG. 3D) Hep3B cells were infected (MOI 0.01) with the VSV-hIFN--CSDE1.sup.WT virus for 21 days. Surviving cells were pooled, and genomic DNA prepared. Sanger sequencing of CSDE1 is shown for two independent experiments. In these experiments, as well as in two other experiments, a mixed population of mutated and un-mutated cells were selected. MeansSD of 3 technical replicates are shown. P-values were determined using a two way (FIG. 3B) or one-way (FIG. 3C) ANOVA with a Tukey multiple comparisons post-test on log transformed data. Statistical significance set at p<0.05, ns>0.05.

    [0082] FIGS. 4A-4G. Virotherapy trap and immunotherapy ambush. (FIG. 4A) C57Bl/6 mice bearing 10-day B16 tumors were injected i.t. with PBS, VSV-mIFN, VSV-mIFN-CSDE1.sup.WT or VSV-mIFN-CSDE1.sup.C-T. (FIG. 4B) Splenocytes harvested at day 30 were re-stimulated with VSV-N-specific immunodominant peptide (N.sub.52-59), SIINFEKL (SEQ ID NO:14) peptide from OVA, or with B16 cells over-expressing CSDE1.sup.WT or CSDE1.sup.C-T, or with B16 or B16ova cells (E:T 10:1) for 72 hours. Supernatants were assayed for IFN-. Representative of two separate experiments. (FIGS. 4C and 4D) Mice were injected with viruses as in (FIG. 4A) with added groups (3 mice/group) which received no ICB, or anti-PD-1 antibody i.p. at days 10, 12, and 14 or at days 14, 17, and 21. 24 hours after the last injection of virus (day 22), or earlier if tumor>1.0 cm diameter (PBS groups), tumors were dissociated and assayed for (FIG. 4C) IL-12 or (FIG. 4D) TNF- by ELISA (normalized by protein concentration in whole tumor lysates as pg/mL protein). (FIG. 4E) C57Bl/6 mice with 10-day B16 tumors were injected i.t. with PBS, VSV-mIFN, VSV-mIFN-CSDE1.sup.WT or with VSV-mIFN-CSDE1.sup.C-T (10.sup.7 pfu/injection) followed by anti-PD-1 antibody (n=8/group). (FIG. 4F) Kaplan-Meier survival for groups in (FIG. 4E). P-values were determined using the Log-rank Mantel Cox test. For multiple comparisons using the Bonferroni correction, overall statistical significance threshold was set at =0.05 (3 comparisons at p<0.0125 (4 comparisons)). Representative of two separate experiments. (FIG. 4G) C57Bl6 mice with 10-day B16 tumors were injected i.t. with (column 1) PBS, (2) VSV-mIFN, (3) VSV-mIFN-CSDE1.sup.WT or (4) VSV-mIFN-CSDE1.sup.C-T (10.sup.7 pfu/injection) on days 10, 11, and 12. On day 13, tumors were excised, and virus measured by plaque assay on BHK cells. Representative of two separate experiments. Each symbol in (FIG. 4B), (FIG. 4C), (FIG. 4D), and (FIG. 4G) represents a mouse (n=3/group). MeansSD are shown. ND, not detected (below limit of detection). P-values were determined using a two-way (FIG. 4B) or one-way ANOVA (FIGS. 4C, 4D, and 4G) with a Tukey multiple comparisons post-test. Statistical testing was performed on log transformed data in (FIG. 4G). Statistical significance set at p<0.05 for (FIG. 4B), (FIG. 4C), (FIG. 4D), and (FIG. 4G).

    [0083] FIGS. 5A-5D. DC-CSDE1.sup.C-T vaccination. (FIG. 5A) In vitro IL-4/GM-CSF matured murine DC were transfected with nothing, CSDE1.sup.WT or CSDE1.sup.C-T expression plasmids and 48 hours later administered as vaccines with i.t. treatments with VSV-mIFN- and anti-PD1. (FIG. 5B) On day 40, spleens and LN were assayed for IFN- following in vitro re-stimulation with live B16 cells or with live B16 cells stably expressing CSDE1.sup.C-T. WT: DC vaccines expressing wild type CSDE1; * DC vaccine expressing mutated CSDE1.sup.C-T. (FIG. 5C) C57Bl/6 mice with 10-day B16 tumors were injected i.t. with PBS or with VSV-mIFN-, (10.sup.7 pfu/injection) and i.p. with unloaded DC (DC), DC vaccine expressing wild type CSDE1 (DC-CSDE1.sup.WT) or with DC vaccine expressing mutated CSDE1.sup.C-T (CSDE1.sup.C-T) followed by anti-PD-1 (n=8/group) as shown in (FIG. 5A). Kaplan-Meier survival for groups is shown. Representative of two separate experiments. P-values were determined using the Log-rank Mantel Cox test. For multiple comparisons using the Bonferroni correction, overall statistical significance threshold was set at =0.05 (3 comparisons at p<0.0167). (FIG. 5D) Mice were injected as in (FIG. 5A) (3 mice/grp). 24 hours after the last injection of virus (day 22), or earlier if tumor size exceeded 1.0 cm diameter in the PBS groups, tumors were excised and assayed for IL-12 or TNF- by ELISA (normalized by protein concentration in whole tumor cell lysates and expressed as pg/mL protein). Representative of two separate experiments. Each symbol in (FIG. 5B) and (FIG. 5D) represents a mouse (n=2 or 3/group). MeansSD are shown. ND, not detected (below limit of detection). P-values were determined using a two-way ANOVA (FIG. 5B) with a Tukey multiple comparisons post-test. Statistical significance set at p<0.05 for (FIG. 5B).

    [0084] FIGS. 6A-6E. Escape from VSV-hIFN is immunogenic. (FIG. 6A) Human CD3+ T cells activated in vitro with anti-CD3 and anti-CD28 antibodies and co-cultured with CD14.sup.+-matured DC (same donor PBMC) were cultured with different Hep3B cell lysates. Lysates were re-added on days 3 and 5. On day 7, CD3+ T cells were isolated and co-cultured with autologous DC and the same Hep3B cell lysates (E:T 10:1). (FIG. 6B) 72 hours later, supernatants were assayed for IFN-. MeansSD of 3 technical replicates from 3 donors. (FIG. 6C) 10.sup.4 target cells (Hep3BP parental or Hep3B-VSV-hIFN-21d ESC) were treated for 24 hours with hIFN-y before being co-cultured with 10.sup.5 T cells primed/expanded on either Hep3BP or Hep3B-VSV-hIFN-21d-ESC cells as in (FIG. 6A). A further 10.sup.5 T cells were added after 48 hours. At 120 hours post co-culture, wells were washed 3 with PBS, and surviving adherent cells counted. (FIG. 6D) NetMHC4.0% Rank of the predicted affinity of the un-mutated CSDE1.sup.WT 9-mer, MSFDPNLLH (SEQ ID NO:17), and its CSDE1.sup.C-T mutated counterpart 9-mer, MSFDSNLLH (SEQ ID NO:18), compared to 400,000 random natural peptides for HLA subtypes. Strong binders defined as % rank<0.5, and weak binders with % rank<2 (http://www.cbs.dtu.dk/services/NetMHC/). (FIG. 6E) Human CD3+ T cells activated in vitro and co-cultured with autologous DC were cultured with Hep3BP or Hep3B-VSV-hIFN-ESC lysates, or with DC transfected 48 hours previously with 10 g pcDNA3.1-CSDE1.sup.WT or pcDNA3.1-CSDE1.sup.C-T plasmids. Lysates, or transfected DC, were re-added on day 5. On day 7, isolated CD3+ T cells were co-cultured with DC and the same Hep3B cell lysates or with similarly transfected DC (E:T 10:1). 72 hours later, supernatants were assayed for IFN-y. MeansSD of 3 technical replicates from two donors. ND, not detected (below limit of detection). P-values were determined using a one-way (FIG. 6B) or two-way (FIG. 6C) ANOVA with a Tukey multiple comparisons post-test. Statistical testing was performed on log transformed data in (FIG. 6C). Statistical significance set at p<0.05, ns>0.05.

    [0085] FIG. 7 is an amino acid sequence listing for a human CSDE1 polypeptide (SEQ ID NO:2).

    [0086] FIG. 8 is a nucleic acid sequence listing that encodes a wild-type mouse CSDE1 polypeptide (SEQ ID NO:3). The C at position 13 (bold, underlined, enlarged) is a wild-type nucleotide that can be mutated to a T in cancer cells escaping treatment.

    [0087] FIG. 9. Parental Hep3B cells, or pooled populations of Hep3B over-expressing mutant CSDE1.sup.C-T were infected with stock VSV-IFN (MOI 0.1) (3 wells/grp). 48 hours later, (Passage 1) supernatants were assayed for infectious titers on the same cells. Virus was recovered every 48 hours (P 2-5) and titered on Hep3B or on Hep3B-CSDE1.sup.C-T cells. *P0.05; ****P0.001.

    [0088] FIGS. 10A-10E. VSV-IFN was passaged 5 times through Hep3B or Hep3B-CSDE1.sup.C-T cells. Sanger sequence was obtained for the IGR between the P and M genes (FIG. 10A) from virus populations passaged through: (FIG. 10B) Hep3B (a homogenous population of wt sequence), (FIG. 10C) Hep3B-CSDE1.sup.C-T cells, or (FIG. 10D) Hep3B-VSV-IFN-21d-ESC cells (largely homogenous for point mutation C-U); and (FIG. 10E) virus population from a Hep3B tumor in a SCID mouse that escaped VSV-IFN (a heterogenous population of wt and mutant IGR P/M viruses).

    [0089] FIGS. 11A-11I. CSDE1 regulates viral M RNA. HepB3, HepB3-CSDE1.sup.C-T, B16, or B16-CSDE1.sup.C-T cells were infected with VSV viruses (VSV-IFN or VSV-IFN-IGR P/M.sup.C-U) (MOI 3). Lanes: 1. Hep3BNSV-hIFN; 2: Hep3BNSV-hIFN-IGR P/M.sup.C-U; 3: Hep3B-CSDE1.sup.C-T/VSV-hIFN; 4. Hep3B-CSDE1.sup.C-T/VSV-hIFN-IGR P/M.sup.C-U; 5. B16/VSV-mIFN; 6: B16NSV-mIFN-IGR P/M.sup.C-U; 7: B16-CSDE1.sup.C-T/VSV-mIFN; 8. B16-CSDE1.sup.C-T/VSV-mIFN-IGR P/M.sup.C-U. Six (6) hours later, qrtPCR was used to assess levels of (FIG. 11B) viral P RNA (primers P1 and P2); (FIG. 11C) viral M RNA (M1 and M2); or (FIG. 11D) viral P-M RNA (P/M IGR-M specific primers IGR1 and M2). Primer locations are indicated in FIG. 11A. Data plotted are representative of 3 experiments. Levels of G, L, and G-L RNA also were measured using primers G1 and G2 (FIG. 11F), L1 and L2 (FIG. 11G), and G1 and L2 (FIG. 11H); primer locations are indicated in FIG. 11E. RNA levels were normalized to expression in Hep3B or B16 infected with VSV-hIFN. (FIG. 11I) Hep3B parental cells (Hep3B) (lanes 1-3), or Hep3B cells engineered to overexpress CSDE1.sup.wt (Hep3B-CSDE1.sup.wt) (lanes 4 and 5) or mutated CSDE1.sup.P5S (Hep3B-CSDE1.sup.C-T) (lanes 6 and 8) proteins, or Hep3B selected in vitro for resistance to VSV-IFN oncolysis for 21 days (Hep3B-VSV-IFN-ESC) (lanes 7 and 9), were infected with VSV-IFN (lanes 2, 5, 6, and 7), or VSV-IFN-IGR P/M.sup.C-U (lanes 3, 4, 8, and 9) (MOI 3). Cells were harvested at 6 or 18 hours post infection, and viral M protein was measured by Western Blot.

    [0090] FIGS. 12A-12D. Evolution of the IGR P/M.sup.C-U mutation in VSV in response to cellular escape from VSV replication is dependent upon APOBEC3B. Hep3B cells engineered to express siRNA to APOBEC3B (FIG. 12B), the dominant negative mutant CSDE1.sup.P5S (FIG. 12C), both (FIG. 12D), or neither (FIG. 12A) were infected with VSV-IFN on day 0 (MOI 0.01) in triplicate wells. On days 1, 14, and 21, virus was harvested and viral genomes were analyzed by deep sequencing. Relative reads for the sequences of the wild type IGR between the P and M genes, compared to the mutated IGR P/M.sup.C-U, are shown. *P0.05; **P0.01.

    [0091] FIG. 13. VSV infection is associated with concentration of CSDE1 in cytoplasmic compartments. Immunofluorescence of CSDE1 in uninfected B16 cells (left) and in B16 cells infected with VSV 8 hours previously at an MOT 0.1 (right). Arrows indicate possible areas of cytoplasmic concentration of CSDE1 that were only observed in infected cells, which may represent cytoplasmic compartments associated with VSV synthesis.

    [0092] FIGS. 14A-14C. CSDE1 expressed from the virus enhances replication. (FIG. 14A) BHK, B16, Hep3B and Mel888 cell lines were infected with VSV-GFP, VSV-hIFN, VSV-CSDE1.sup.WT or VSV-CSDE1.sup.P5S (MOI 3) (triplicate wells). After 48 hours, virus was titered on BHK cells by plaque assay. *P0.05; **P0.01; ***P0.001. (FIG. 14B) B16 or Hep3B cells were infected (MOI 0.01) with VSV-IFN, VSV-IFN-CSDE1.sup.WT, or VSV-IFN-CSDE1.sup.P5S (species matched IFN) for 21 days. Surviving cells were counted. (FIG. 14C) Hep3B cells were infected (MOI 0.01) with VSV-hIFN-CSDE1.sup.WT for 21 days. Sanger sequencing of CSDE1 from surviving cells is shown (2 independent experiments; meanSD of 3 technical replicates). P-values were determined using a two way (FIG. 14A) or one-way (FIG. 14B) ANOVA with a Tukey multiple comparisons post-test (log transformed data). Statistical significance p<0.05, ns>0.05.

    [0093] FIGS. 15A and 15B. CSDE1-expressing VSV generate higher frequency T cell responses. (FIG. 15A) ACEII transgenic mice were vaccinated (3 mice/group) with PBS, VSV-GFP, VSV-CSDE1, VSV-SPIKE, VSV-CSDE1-SPIKE, VSV-IFN, VSV-SPIKE-IFN, or VSV-CSDE1 (CSDE1 between the N and P genes; SPIKE between the M and G genes; IFN between the G and L genes) (10.sup.7 pfu, IM). After 10 days, 10.sup.6 splenocytes were re-stimulated in vitro in IFN ELISPOT wells with 10 g total of 2 combined pools of peptides, consisting of 15-mer sequences with an 11 amino acid (aa) overlap, covering aa 689-895 (PEPTIVATOR SARS-CoV-2 Prot_S+, Miltenyi) and the N-terminal S1 domain (PEPTIVATOR SARS-CoV-2 Prot_S1, Miltenyi) of the Spike glycoprotein. The number of spots per well was plotted, using biological triplicates. (FIG. 15B) C57Bl/6 mice were vaccinated (3 mice/group) as described for FIG. 15A with vectors expressing the hgp100 cDNA (10.sup.7 pfu, IM) and splenocytes were re-stimulated with the H-2Db-restricted human gp10025-33 (KVPRNQDWL hgp100 peptide). *P0.05; **P0.01; ***P0.001.

    [0094] FIG. 16 is a nucleic acid sequence listing for a VSV-CSDE1.sup.WT construct (SEQ ID NO:16) containing the full VSV genome sequence; the underlined sequence encodes mouse CSDE1. The bolded C in the CSDE1 coding sequence is the position that can be mutated to a T in cancer cells escaping treatment.

    DETAILED DESCRIPTION

    [0095] This document provides methods and materials for treating cancer. For example, this document provides oncolytic viruses (e.g., replication-competent vesicular stomatitis viruses), nucleic acid molecules encoding a replication-competent oncolytic virus (e.g., replication-competent oncolytic vesicular stomatitis virus), methods for making replication-competent oncolytic viruses (e.g., replication-competent oncolytic vesicular stomatitis viruses), and methods for using replication-competent oncolytic viruses (e.g., replication-competent oncolytic vesicular stomatitis viruses) to treat cancer.

    [0096] As described herein, a replication-competent oncolytic virus can be designed to deliver nucleic acid encoding a CSDE1 polypeptide (e.g., a wild-type or mutant version of a CSDE1 polypeptide (or a fragment thereof)) to cells (e.g., cancer cells and/or healthy cells within a tumor microenvironment) within a mammal. In some cases, expression of a wild-type version of a CSDE1 polypeptide (or a fragment thereof) can promote replication of an oncolytic virus. In some cases, expression of a mutant version of a CSDE1 polypeptide such as a CSDE1.sup.P5S polypeptide (or a fragment thereof that includes P5S) can promote an immune response against cancer cells within the mammal. Such immune responses can include T cell immune responses such as CTL immune responses that can kill cancer cells.

    [0097] Any appropriate mammal having a cancer or having had cancer can be treated as described herein. Examples of mammals having a cancer or having had cancer that can be treated as described herein include, without limitation, humans, non-human primates (e.g., monkeys), dogs, cats, horses, cows, pigs, sheep, mice, and rats. In some cases, a human having a cancer or having had cancer can be treated as described herein.

    [0098] When treating a mammal (e.g., a human) having a cancer or having had cancer as described herein, the cancer can be any type of cancer. In some cases, a cancer can be a blood cancer. In some cases, a cancer can include one or more solid tumors. Examples of cancers that can be treated as described herein include, without limitation, prostate cancers (e.g., prostate adenocarcinoma), breast cancers (e.g., breast invasive carcinomas and TNBCs), bladder cancers (e.g., bladder urothelial carcinomas), lung cancers (e.g., lung adenocarcinomas, lung squamous cell carcinomas, and mesotheliomas), liver cancers (e.g., liver hepatocellular carcinomas), cervical cancers (e.g., cervical squamous cell carcinomas and endocervical adenocarcinomas), bile duct cancers (e.g., cholangiocarcinomas), colon cancers (colon adenocarcinomas), rectal cancers (e.g., rectum adenocarcinomas), pancreatic cancers (e.g., pancreatic adenocarcinomas), uterine cancers (e.g., uterine corpus endometrial carcinomas and uterine carcinosarcomas), head and neck cancers (e.g., head and neck squamous cell carcinomas), testicular cancers (e.g., testicular germ cell tumors), ovarian cancers (e.g., ovarian serous cystadenocarcinoma), thyroid cancers (e.g., thyroid carcinomas), bone cancers (e.g., sarcomas), skin cancers (e.g., skin cutaneous melanoma), adrenal gland cancers (e.g., adrenocortical carcinomas, pheochromocytoma, and paraganglioma), kidney cancers (e.g., kidney renal clear cell carcinoma, kidney renal papillary cell carcinoma, and kidney chromophobes), lymphomas (e.g., lymphoid neoplasm diffuse large B-cell lymphoma), thymus cancers (e.g., thymoma), brain cancers (e.g., brain lower grade glioma and glioblastoma multiforme), leukemias (acute myeloid leukemia), and cancers of the eye (e.g., uveal melanoma).

    [0099] In some cases, the methods described herein can include identifying a mammal (e.g., a human) as having a cancer. Any appropriate method can be used to identify a mammal as having a cancer. For example, imaging techniques and/or biopsy techniques can be used to identify mammals (e.g., humans) having cancer.

    [0100] Once identified as having cancer or as having had cancer, the mammal can be administered a replication-competent oncolytic virus designed to deliver nucleic acid encoding a CSDE1 polypeptide (e.g., a wild-type or mutant version of a CSDE1 polypeptide, or a fragment thereof) to cells. Examples of replication-competent oncolytic viruses that can be designed to deliver nucleic acid encoding a CSDE1 polypeptide (e.g., a wild-type or mutant version of a CSDE1 polypeptide, or a fragment thereof) to cells include, without limitation, replication-competent oncolytic vesicular stomatitis viruses, replication-competent adenoviruses viruses, replication-competent herpes viruses, replication-competent pox viruses, replication-competent retroviruses, replication-competent lentiviruses, replication-competent measles viruses, and replication-competent polioviruses.

    [0101] As described herein, a replication-competent vesicular stomatitis virus can be designed to have a nucleic acid molecule that encodes a VSV N polypeptide, a VSV P polypeptide, a VSV M polypeptide, an optional interferon- polypeptide (e.g., a human interferon- polypeptide), a VSV G polypeptide, a CSDE1 polypeptide (e.g., a wild-type or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue), and a VSV L polypeptide. It will be appreciated that the sequences described herein with respect to a vesicular stomatitis virus are incorporated into a plasmid coding for the positive sense cDNA of the viral genome allowing generation of the negative sense genome of vesicular stomatitis viruses. Thus, it will be appreciated that a nucleic acid sequence that encodes a VSV polypeptide, for example, can refer to an RNA sequence that is the template for the positive sense transcript that encodes (e.g., via direct translation) that polypeptide.

    [0102] In some cases, a replication-competent vesicular stomatitis virus can be designed to have a nucleic acid molecule that encodes a VSV N polypeptide, a VSV P polypeptide, a VSV M polypeptide, an interferon- polypeptide (e.g., a human interferon- polypeptide), a VSV G polypeptide, a CSDE1 polypeptide (e.g., a wild-type or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue), and a VSV L polypeptide. In some cases, a vesicular stomatitis virus provided herein can be designed to have a nucleic acid molecule that encodes a VSV N polypeptide, a VSV P polypeptide, a VSV M polypeptide, an interferon- polypeptide (e.g., a human interferon- polypeptide), a VSV G polypeptide, a CSDE1 polypeptide (e.g., a wild-type or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue), and a VSV L polypeptide with the nucleic acid sequence encoding the interferon- polypeptide being located between the sequences encoding the VSV M polypeptide and the VSV G polypeptide and with the nucleic acid sequence encoding the CSDE1 polypeptide being located between the sequences encoding the VSV G polypeptide and the VSV L polypeptide.

    [0103] The nucleic acid encoding a CSDE1 polypeptide (e.g., a wild-type or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue) can be positioned at any location within the VSV genome. In some cases, the nucleic acid encoding a CSDE1 polypeptide (e.g., a wild-type or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue) can be positioned downstream of the nucleic acid encoding the VSV M polypeptide. For example, nucleic acid encoding a CSDE1 polypeptide (e.g., a wild-type or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue) can be positioned between nucleic acid encoding a VSV M polypeptide and nucleic acid encoding a VSV G polypeptide or between nucleic acid encoding a VSV G polypeptide and nucleic acid encoding a VSV L polypeptide.

    [0104] In some cases, a vesicular stomatitis virus provided herein can have a nucleic acid molecule that includes a sequence encoding an interferon (IFN) polypeptide (e.g., a human IFN- polypeptide), a sodium iodide symporter (NIS) polypeptide (e.g., a human NIS polypeptide), a fluorescent polypeptide (e.g., a GFP polypeptide), any appropriate therapeutic transgene (e.g., HSV-TK or cytosine deaminase), a polypeptide that antagonizes host immunity (e.g., influenza NS1, HSV34.5, or SOCS1), or a tumor antigen (e.g., cancer vaccine components). The nucleic acid encoding the IFN polypeptide can be positioned between the nucleic acid encoding the VSV M polypeptide and the nucleic acid encoding the VSV G polypeptide. Such a position can allow the viruses to express an amount of the IFN polypeptide that is effective to activate anti-viral innate immune responses in non-cancerous tissues, and thus alleviate potential viral toxicity, without impeding efficient viral replication in cancer cells. The nucleic acid encoding the NIS polypeptide can be positioned between the nucleic acid encoding the VSV M polypeptide and the VSV G polypeptide. Such a position of can allow the viruses to express an amount of the NIS polypeptide that (a) is effective to allow selective accumulation of iodide in infected cells, thereby allowing both imaging of viral distribution using radioisotopes and radiotherapy targeted to infected cancer cells, and (b) is not so high as to be toxic to infected cells. Positioning the nucleic acid encoding an IFN polypeptide between the nucleic acid encoding the VSV M polypeptide and the nucleic acid encoding the VSV G polypeptide and positioning the nucleic acid encoding a NIS polypeptide between the nucleic acid encoding the VSV M polypeptide and the nucleic acid encoding the VSV G polypeptide within the genome of a vesicular stomatitis virus can result in vesicular stomatitis viruses that are viable, that have the ability to replicate and spread, that express appropriate levels of functional IFN polypeptides, and that express appropriate levels of functional NIS polypeptides to take up radio-iodine for both imaging and radio-virotherapy.

    [0105] Any appropriate nucleic acid encoding a CSDE1 polypeptide (e.g., a wild-type version or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue) can be inserted into the genome of an oncolytic virus such as a vesicular stomatitis virus. For example, nucleic acid encoding a wild-type human CSDE1 polypeptide can be inserted into the genome of an oncolytic virus such as a vesicular stomatitis virus. Examples of nucleic acid encoding CSDE1 polypeptides that can be inserted into the genome of an oncolytic virus such as a vesicular stomatitis virus include, without limitation, nucleic acid encoding a CSDE1 polypeptide set forth in GENBANK Accession No. NM_007158.6, nucleic acid encoding a CSDE1 polypeptide having the amino acid sequence set forth in FIG. 7 (SEQ ID NO:2), the nucleic acid as set forth in FIG. 8 (SEQ ID NO:3), nucleic acid encoding a CSDE1 polypeptide set forth in GENBANK Accession No. NM_007158.6 provided that position 5 contains a serine instead of a proline, nucleic acid encoding a CSDE1 polypeptide having the amino acid sequence set forth in FIG. 7 provided that position 5 contains a serine instead of a proline, and the nucleic acid as set forth in FIG. 8 provided that position 13 contains a T instead of a C. In some cases, the CSDE1 amino acid sequence of a CSDE1 fragment can be amino acid residues 1 to 100, 1 to 75, 1-50, 1-25, 1-13, 1-12, 1-11, 1-10, 1-9, 1-8, 2-100, 2-75, 2-50, 2-25, 2-14, 2-13, 2-12, 2-11, 2-10, 2-9, 3-100, 3-75, 3-50, 3-25, 3-15, 3-14, 3-13, 3-12, 3-11, 3-10, 4-100, 4-75, 4-50, 4-25, 4-16, 4-15, 4-14, 4-13, 4-12, 4-11, 5-100, 5-75, 5-50, 5-25, 5-17, 5-16, 5-15, 5-14, 5-13, or 5-12 of a CSDE1 polypeptide provided that position 5 is a serine instead of a proline. In some cases, the CSDE1 amino acid sequence of a CSDE1 fragment can be at least 700, at least 725, at least 750, or at least 760 amino acids in length. For example, a CSDE1 fragment can have an amino acid sequence with at least 700 (e.g., at least 725, at least 750, or at least 760) consecutive amino acids from SEQ ID NO:2. In some cases, a CSDE1 fragment can lack from 1 to 5 (e.g., 1, 2, 3, 4, or 5) consecutive amino acid residues as compared to SEQ ID NO:2. For example, a CSDE1 fragment can have the sequence of SEQ ID NO:2, except that the fragment lacks from 1 to 5 (e.g., 1, 2, 3, 4, or 5) amino acid residues at the N-terminus of SEQ ID NO:2, or lacks from 1 to 5 (e.g., 1, 2, 3, 4, or 5) amino acid residues at the C-terminus of SEQ ID NO:2.

    [0106] Any appropriate nucleic acid encoding an IFN polypeptide can be inserted into the genome of an oncolytic virus such as a vesicular stomatitis virus provided herein. For example, nucleic acid encoding an IFN beta polypeptide can be inserted into the genome of a vesicular stomatitis virus. Examples of nucleic acid encoding IFN beta polypeptides that can be inserted into the genome of an oncolytic virus such as a vesicular stomatitis virus include, without limitation, nucleic acid encoding a human IFN beta polypeptide of the nucleic acid sequence set forth in GENBANK Accession No. NM_002176.2 (GI No. 50593016), nucleic acid encoding a mouse IFN beta polypeptide of the nucleic acid sequence set forth in GENBANK Accession No. NM_010510.1 (GI No. 6754303), BC119395.1 (GI No. 111601321), or BC119397.1 (GI No. 111601034), and nucleic acid encoding a rat IFN beta polypeptide of the nucleic acid sequence set forth in GENBANK Accession No. NM_019127.1 (GI No. 9506800).

    [0107] Any appropriate nucleic acid encoding a NIS polypeptide can be inserted into the genome of an oncolytic virus such as a vesicular stomatitis virus. For example, nucleic acid encoding a human NIS polypeptide can be inserted into the genome of a vesicular stomatitis virus. Examples of nucleic acid encoding NIS polypeptides that can be inserted into the genome of an oncolytic virus such as a vesicular stomatitis virus include, without limitation, nucleic acid encoding a human NIS polypeptide of the nucleic acid sequence set forth in GENBANK Accession No. NM_000453.2 (GI No.164663746), BC105049.1 (GI No. 85397913), or BC105047.1 (GI No. 85397519), nucleic acid encoding a mouse NIS polypeptide of the nucleic acid sequence set forth in GENBANK Accession No. NM_053248.2 (GI No. 162138896), AF380353.1 (GI No. 14290144), or AF235001.1 (GI No. 12642413), nucleic acid encoding a chimpanzee NIS polypeptide of the nucleic acid sequence set forth in GENBANK Accession No. XM_524154 (GI No. 114676080), nucleic acid encoding a dog NIS polypeptide of the nucleic acid sequence set forth in GENBANK Accession No. XM_541946 (GI No. 73986161), nucleic acid encoding a cow NIS polypeptide of the nucleic acid sequence set forth in GENBANK Accession No. XM_581578 (GI No. 297466916), nucleic acid encoding a pig NIS polypeptide of the nucleic acid sequence set forth in GENBANK Accession No. NM_214410 (GI No. 47523871), and nucleic acid encoding a rat NIS polypeptide of the nucleic acid sequence set forth in GENBANK Accession No. NM_052983 (GI No. 158138504).

    [0108] In some cases, a replication-competent virus (e.g., a vesicular stomatitis virus) can be designed to have a nucleic acid molecule that encodes (or is a template for a nucleic acid that encodes) a VSV N polypeptide, a VSV P polypeptide, a VSV M polypeptide, an interferon- polypeptide (e.g., a human interferon- polypeptide), a VSV G polypeptide, a CSDE1 polypeptide (e.g., a wild-type CSDE1 polypeptide or a fragment thereof), an antigen (e.g., an antigen from an infectious agent, such as a SARS-CoV-2 antigen), and a VSV L polypeptide. In some cases, a virus (e.g., a vesicular stomatitis virus) provided herein can be designed to have a nucleic acid molecule that encodes a VSV N polypeptide, a VSV P polypeptide, a VSV M polypeptide, an interferon- polypeptide (e.g., a human interferon- polypeptide), a VSV G polypeptide, a CSDE1 polypeptide (e.g., a wild-type CSDE1 polypeptide or a fragment thereof), an antigen (e.g., a virus antigen), and a VSV L polypeptide, with the nucleic acid sequence encoding the CSDE1 polypeptide and the nucleic acid encoding the antigen being located between the sequences encoding the VSV N polypeptide and the VSV L polypeptide. Such viruses can be used, for example, to induce an immune response in a mammal, and are referred to as immunogenic viruses.

    [0109] The nucleic acid encoding a CSDE1 polypeptide (e.g., a wild-type CSDE1 polypeptide or a fragment thereof), the nucleic acid encoding an interferon- polypeptide (e.g., human interferon-), and the nucleic acid encoding the antigen can be positioned at any location within the virus (e.g., VSV) genome. In some cases, the nucleic acid encoding a CSDE1 polypeptide (e.g., a wild-type CSDE1 polypeptide or a fragment thereof can be positioned downstream of the nucleic acid encoding the VSV N polypeptide. In some cases, for example, nucleic acid encoding a CSDE1 polypeptide (e.g., a wild-type CSDE1 polypeptide or a fragment thereof) can be positioned between nucleic acid encoding a VSV N polypeptide and nucleic acid encoding a VSV P polypeptide, nucleic acid encoding an antigen (e.g., a virus antigen) can be positioned between nucleic acid encoding a VSV M polypeptide and nucleic acid encoding a VSV G polypeptide, and nucleic acid encoding an interferon- polypeptide (e.g., a human interferon- polypeptide) can be positioned between nucleic acid encoding a VSV G polypeptide and nucleic acid encoding a VSV L polypeptide.

    [0110] Any appropriate antigen can be encoded by a nucleic acid or virus provided herein. In some cases, for example, an antigen can be from an infectious agent, such as a virus (e.g., a SARS-CoV-2 virus, an influenza virus, an EBOLA virus, a yellow fever virus, a dengue virus, a coronavirus, a measles virus, a mumps virus, or a rubella virus) or a bacteria (e.g., an Escherichia species, a Salmonella species, a Mycobacterium species, a Clostridium species, a Bacillus species, or a Leptospira species). Examples of antigens include, without limitation, the spike protein of SARS-CoV-2, the M protein of SARS-CoV-2, the N protein of SARS-CoV-2, the NP protein of influenza, the M1 protein of influenza, the NS1 protein of influenza, the NP protein of Ebola, the GP protein of Ebola, the VP35 protein of Ebola, the VP40 protein of Ebola, the NS1 protein of yellow fever, the NS1 protein of dengue virus, the spike protein of a coronavirus, the M protein of a coronavirus, the N protein of a coronavirus, the F protein from measles virus, the H protein from measles virus, a nucleocapsid protein from mumps, the E1 spike protein from rubella virus, the E2 spike protein from rubella virus, the C protein of rubella virus, the O antigen of Escherichia coli, glfT2 of Mycobacterium tuberculosis, fas of Mycobacterium tuberculosis, iniB of Mycobacterium tuberculosis, tetanus toxoid from Clostridium tatanis, anthrax toxin from Bacillus anthracis, LipL21 from Leptospira species, LipL41 from Leptospira species, LipL32 from Leptospira species, and fragments of any of these proteins.

    [0111] The nucleic acid sequences of a vesicular stomatitis virus provided herein that encode a VSV N polypeptide, a VSV P polypeptide, a VSV M polypeptide, a VSV G polypeptide, and a VSV L polypeptide can be from a VSV Indiana strain as set forth in GENBANK Accession No. NC_001560 (GI No. 9627229) or can be from a VSV New Jersey strain.

    [0112] In one aspect, this document provides vesicular stomatitis viruses containing a nucleic acid molecule (e.g., an RNA molecule) having (e.g., in a 3 to 5 direction) a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV N polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV P polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV M polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV G polypeptide, a nucleic acid sequence that is a template for a positive sense transcript encoding a CSDE1 polypeptide (e.g., a wild-type version or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue), and a nucleic acid sequence that is a template for a positive sense transcript encoding a VSV L polypeptide. Such vesicular stomatitis viruses can infect cells (e.g., cancer cells) and be replication-competent.

    [0113] Any appropriate method can be used to insert nucleic acid (e.g., nucleic acid encoding a CSDE1 polypeptide such as a wild-type version or mutant version of a CSDE1 polypeptide or a fragment thereof such as a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue, nucleic acid encoding an IFN polypeptide, and/or nucleic acid encoding a NIS polypeptide) into the genome of an oncolytic virus such as a vesicular stomatitis virus. For example, methods described elsewhere (e.g., in Schnell et. al., PNAS, 93:11359-11365 (1996); Obuchi et al., J. Virol., 77(16):8843-56 (2003)); Goel et al., Blood, 110(7):2342-50 (2007)); and Kelly et al., J. Virol., 84(3):1550-62 (2010)) can be used to insert nucleic acid into the genome of a vesicular stomatitis virus. Any appropriate method can be used to identify oncolytic viruses such as vesicular stomatitis viruses containing a nucleic acid molecule described herein. Such methods include, without limitation, PCR and nucleic acid hybridization techniques such as Northern and Southern analysis. In some cases, immunohistochemistry and biochemical techniques can be used to determine if an oncolytic virus (e.g., a vesicular stomatitis virus) contains a particular nucleic acid molecule by detecting the expression of a polypeptide encoded by that particular nucleic acid molecule.

    [0114] In another aspect, this document provides nucleic acid molecules that encode a VSV N polypeptide, a VSV P polypeptide, a VSV M polypeptide, a VSV G polypeptide, a CSDE1 polypeptide (e.g., a wild-type version or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue), and a VSV L polypeptide. For example, a nucleic acid molecule provided herein can be a single nucleic acid molecule that includes a nucleic acid sequence that encodes a VSV N polypeptide, a nucleic acid sequence that encodes a VSV P polypeptide, a nucleic acid sequence that encodes a VSV M polypeptide, a nucleic acid sequence that encodes a VSV G polypeptide, a nucleic acid sequence that encodes a CSDE1 polypeptide (e.g., a wild-type version or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue), and a nucleic acid sequence that encodes a VSV L polypeptide. As another example, a nucleic acid molecule provided herein can be a single nucleic acid molecule that includes a nucleic acid sequence that encodes a VSV N polypeptide, a nucleic acid sequence that encodes a VSV P polypeptide, a nucleic acid sequence that encodes a VSV M polypeptide, a nucleic acid sequence that encodes an IFN- polypeptide, a nucleic acid sequence that encodes a VSV G polypeptide, a nucleic acid sequence that encodes a CSDE1 polypeptide (e.g., a wild-type version or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue), and a nucleic acid sequence that encodes a VSV L polypeptide.

    [0115] The term nucleic acid as used herein encompasses both RNA (e.g., viral RNA) and DNA, including cDNA, genomic DNA, and synthetic (e.g., chemically synthesized) DNA. A nucleic acid can be double-stranded or single-stranded. A single-stranded nucleic acid can be the sense strand or the antisense strand. In addition, a nucleic acid can be circular or linear.

    [0116] This document also provides method for treating cancer (e.g., to reduce tumor size, inhibit tumor growth, reduce the number of viable tumor cells, or reduce the number of cancer cells escaping an initial cancer treatment) and methods for inducing host immunity against cancer. For example, an oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be administered to a mammal having cancer to reduce tumor size, to inhibit cancer cell or tumor growth, to reduce the number of viable cancer cells within the mammal, and/or to induce host immunogenic responses against a tumor. An oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be propagated in host cells in order to increase the available number of copies of that virus, typically by at least 2-fold (e.g., by 5- to 10-fold, by 50- to 100-fold, by 500- to 1,000-fold, or even by as much as 5,000- to 10,000-fold). In some cases, an oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be expanded until a desired concentration is obtained in standard cell culture media (e.g., DMEM or RPMI-1640 supplemented with 5-10% fetal bovine serum at 37 C. in 5% CO.sub.2). A viral titer typically is assayed by inoculating cells (e.g., Vero cells) in culture.

    [0117] An oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be administered to a cancer patient by, for example, direct injection into a group of cancer cells (e.g., a tumor), direct injection into a tumor microenvironment, or intravenous delivery to cancer cells. An oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be used to treat different types of cancer including, without limitation, myeloma (e.g., multiple myeloma), melanoma, glioma, lymphoma, mesothelioma, and cancers of the lung, brain, stomach, colon, rectum, kidney, prostate, ovary, breast, pancreas, liver, and head and neck.

    [0118] An oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be administered to a patient in a biologically compatible solution or a pharmaceutically acceptable delivery vehicle, by administration either directly into a group of cancer cells (e.g., intratumorally) or systemically (e.g., intravenously). Suitable pharmaceutical formulations depend in part upon the use and the route of entry, e.g., transdermal or by injection. Such forms should not prevent the composition or formulation from reaching a target cell (i.e., a cell to which the virus is desired to be delivered to) or from exerting its effect. For example, pharmacological compositions injected into the blood stream should be soluble.

    [0119] While dosages administered will vary from patient to patient (e.g., depending upon the size of a tumor), an effective dose can be determined by setting as a lower limit the concentration of virus proven to be safe and escalating to higher doses of up to 10.sup.12 pfu, while monitoring for a reduction in cancer cell growth along with the presence of any deleterious side effects. A therapeutically effective dose typically provides at least a 10% reduction in the number of cancer cells or in tumor size. Escalating dose studies can be used to obtain a desired effect for a given viral treatment (see, e.g., Nies and Spielberg, Principles of Therapeutics, In Goodman & Gilman's The Pharmacological Basis of Therapeutics, eds. Hardman, et al., McGraw-Hill, NY, 1996, pp 43-62).

    [0120] An oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be delivered in a dose ranging from, for example, about 10.sup.3 pfu to about 10.sup.12 pfu (e.g., about 10.sup.5 pfu to about 10.sup.12 pfu, about 10.sup.5 pfu to about 10.sup.11 pfu, about 10.sup.6 pfu to about 10.sup.11 pfu, or about 10.sup.6 pfu to about 10.sup.10 pfu). A therapeutically effective dose can be provided in repeated doses. Repeat dosing is appropriate in cases in which observations of clinical symptoms or tumor size or monitoring assays indicate either that a group of cancer cells or tumor has stopped shrinking or that the degree of viral activity is declining while the tumor is still present. Repeat doses can be administered by the same route as initially used or by another route. A therapeutically effective dose can be delivered in several discrete doses (e.g., days or weeks apart) and in one embodiment, one to about twelve doses are provided. Alternatively, a therapeutically effective dose of an oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be delivered by a sustained release formulation. In some cases, an oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be delivered in combination with pharmacological agents that facilitate viral replication and spread within cancer cells or agents that protect non-cancer cells from viral toxicity. Examples of such agents are described elsewhere (Alvarez-Breckenridge et al., Chem. Rev., 109(7):3125-40 (2009)).

    [0121] An oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be administered using a device for providing sustained release. A formulation for sustained release of viruses can include, for example, a polymeric excipient (e.g., a swellable or non-swellable gel, or collagen). A therapeutically effective dose of an oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be provided within a polymeric excipient, wherein the excipient/virus composition is implanted at a site of cancer cells (e.g., in proximity to or within a tumor). The action of body fluids gradually dissolves the excipient and continuously releases the effective dose of virus over a period of time. Alternatively, a sustained release device can contain a series of alternating active and spacer layers. Each active layer of such a device typically contains a dose of virus embedded in excipient, while each spacer layer contains only excipient or low concentrations of virus (i.e., lower than the effective dose). As each successive layer of the device dissolves, pulsed doses of virus are delivered. The size/formulation of the spacer layers determines the time interval between doses and is optimized according to the therapeutic regimen being used.

    [0122] An oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be directly administered. For example, a virus can be injected directly into a tumor (e.g., a breast cancer tumor) that is palpable through the skin. Ultrasound guidance also can be used in such a method. Alternatively, direct administration of a virus can be achieved via a catheter line or other medical access device, and can be used in conjunction with an imaging system to localize a group of cancer cells. By this method, an implantable dosing device typically is placed in proximity to a group of cancer cells using a guidewire inserted into the medical access device. An effective dose of an oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be directly administered to a group of cancer cells that is visible in an exposed surgical field.

    [0123] In some cases, an oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be delivered systemically. For example, systemic delivery can be achieved intravenously via injection or via an intravenous delivery device designed for administration of multiple doses of a medicament. Such devices include, but are not limited to, winged infusion needles, peripheral intravenous catheters, midline catheters, peripherally inserted central catheters, and surgically placed catheters or ports.

    [0124] The course of therapy with an oncolytic virus provided herein such as a vesicular stomatitis virus provided herein can be monitored by evaluating changes in clinical symptoms or by direct monitoring of the number of cancer cells or size of a tumor. For a solid tumor, the effectiveness of virus treatment can be assessed by measuring the size or weight of the tumor before and after treatment. Tumor size can be measured either directly (e.g., using calipers), or by using imaging techniques (e.g., X-ray, magnetic resonance imaging, or computerized tomography) or from the assessment of non-imaging optical data (e.g., spectral data). For a group of cancer cells (e.g., leukemia cells), the effectiveness of viral treatment can be determined by measuring the absolute number of leukemia cells in the circulation of a patient before and after treatment. The effectiveness of viral treatment also can be assessed by monitoring the levels of a cancer specific antigen. Cancer specific antigens include, for example, carcinoembryonic antigen (CEA), prostate specific antigen (PSA), prostatic acid phosphatase (PAP), CA 125, alpha-fetoprotein (AFP), carbohydrate antigen 15-3, and carbohydrate antigen 19-4.

    [0125] In some cases, a mammal having cancer or having had cancer can be treated using a combination of two or more of a chemotherapeutic agent, an oncolytic virus, and a checkpoint inhibitor. For example, a mammal (e.g., a human) having cancer can be treated by administering (a) one or more chemotherapeutic agents, (b) one or more replication-competent oncolytic viruses provided herein, and (c) one or more checkpoint inhibitors. In some cases, a mammal (e.g., a human) having cancer can be treated by administering (a) one or more chemotherapeutic agents and (b) one or more replication-competent oncolytic viruses provided herein. In some cases, a mammal (e.g., a human) having cancer can be treated by administering (a) one or more replication-competent oncolytic viruses provided herein and (b) one or more checkpoint inhibitors. Examples of chemotherapeutic agents that can be used in such combinations include, without limitation, gemcitabine, cyclophosphamide, tamoxifen, and temozolomide. Examples of checkpoint inhibitor that can be used in such combinations include, without limitation, anti-PD1 antibodies, anti-PD-L1 antibodies, anti-CTLA-4 antibodies, anti-TIM3 antibodies, and anti-Lag3 antibodies.

    [0126] As described herein, cancer cells can escape treatments directed against the cancer cells (e.g., oncolytic therapies) by promoting mutagenesis of their genomes. In some cases, a mutation of a CSDE1 nucleic acid can result in cancer cell escape. To target killing those cancer cells attempting to escape treatment, an oncolytic virus designed to express a CSDE1 polypeptide (e.g., a wild-type version or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue) can be administered to the mammal (e.g., a human) to promote immune responses (e.g., T cell immune responses) against the escaping cancer cells as described herein. In some cases, (a) cells such as dendritic cells designed to express a CSDE1 polypeptide (e.g., a wild-type version or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue), (b) a CSDE1 polypeptide (e.g., a wild-type version or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue), (c) nucleic acid encoding a CSDE1 polypeptide (e.g., a wild-type version or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue), or (d) a combination thereof can be administered in addition to or instead of administering an oncolytic virus designed to express a CSDE1 polypeptide (e.g., a wild-type version or mutant version of a CSDE1 polypeptide) or a fragment thereof (e.g., a fragment of a full length wild-type CSDE1 polypeptide, or a fragment of a full length CSDE1 polypeptide that includes a P5S residue) to promote immune responses (e.g., T cell immune responses such as CTL immune responses) against the escaping cancer cells.

    [0127] This document also provides cancer neoantigens (e.g., a CSDE1.sup.P5S polypeptide or fragment thereof that includes P5S), nucleic acids encoding a cancer neoantigen (e.g., a CSDE1.sup.P5S polypeptide or fragment thereof that includes P5S), and methods for stimulating immune cells (e.g., cytotoxic T lymphocytes) to kill cancer cells by administering a cancer neoantigen and/or nucleic acids encoding a cancer neoantigen to a mammal. For example, this document provides full length CSDE1 polypeptides that include a P5 S amino acid substitution or a fragment thereof (e.g., a fragment of a full length CSDE1 polypeptide provided that the fragment includes the P5S residue). In some cases, the CSDE1 amino acid sequence of such a fragment can be amino acid residues 1 to 100, 1 to 75, 1-50, 1-25, 1-13, 1-12, 1-11, 1-10, 1-9, or 1-8 of a CSDE1 polypeptide provided that position 5 is a serine. In some cases, a full length CSDE1 polypeptide that include a P5S amino acid substitution or a fragment thereof (e.g., a fragment of a full length CSDE1 polypeptide provided that the fragment includes the P5S residue) provided herein can include a cell penetrating amino acid sequence. Examples of cell penetrating sequences that can be contiguous with a full length CSDE1 polypeptide that include a P5S amino acid substitution or a fragment thereof (e.g., a fragment of a full length CSDE1 polypeptide provided that the fragment includes the P5S residue) include, without limitation, those cell penetrating amino acid sequences set forth in Table 1.

    TABLE-US-00001 TABLE1 Cellpenetratingaminoacidsequences. Sequence SEQIDNO: GRKKRRQRRRPPQ 4 RQIKIWFQNRRMKWKK 5 LLIILRRRIRKQAHAHSK 6

    [0128] This document also provides method for inducing host immunity against an antigen. For example, an immunogenic virus provided herein such as a vesicular stomatitis virus provided herein can be administered to a mammal to induce a host immunogenic response an antigen (e.g., an antigen contained in the virus or encoded by nucleic acid in the virus). An immunogenic virus provided herein such as a vesicular stomatitis virus provided herein can be propagated in host cells in order to increase the available number of copies of that virus, typically by at least 2-fold (e.g., by 5- to 10-fold, by 50- to 100-fold, by 500- to 1,000-fold, or even by as much as 5,000- to 10,000-fold). In some cases, an immunogenic virus provided herein such as a vesicular stomatitis virus provided herein can be expanded until a desired concentration is obtained in standard cell culture media (e.g., DMEM or RPMI-1640 supplemented with 5-10% fetal bovine serum at 37 C. in 5% CO.sub.2). A viral titer typically is assayed by inoculating cells (e.g., Vero cells) in culture.

    [0129] An immunogenic virus provided herein such as a vesicular stomatitis virus provided herein can be administered to a mammal by, for example, injection (e.g., intramuscular, intravenous, or subcutaneous injection). An immunogenic virus provided herein such as a vesicular stomatitis virus provided herein can be used to treat, prevent, or reduce the likelihood of infection by different types of infectious agents, such as viruses (e.g., a SARS-CoV-2 virus, an influenza virus, an EBOLA virus, a yellow fever virus, a dengue virus, a coronavirus, a measles virus, a mumps virus, or a rubella virus) and bacteria (e.g., an Escherichia species, a Salmonella species, a Mycobacterium species, a Clostridium species, a Bacillus species, or a Leptospira species).

    [0130] An immunogenic virus provided herein such as a vesicular stomatitis virus provided herein can be administered to a patient in a biologically compatible solution or a pharmaceutically acceptable delivery vehicle, by administration either directly into a particular tissue (e.g., intramuscularly) or systemically (e.g., intravenously). Suitable pharmaceutical formulations depend in part upon the use and the route of entry, e.g., transdermal or by injection. Such forms should not prevent the composition or formulation from reaching a target cell (i.e., a cell to which the virus is desired to be delivered to) or from exerting its effect. For example, pharmacological compositions injected into the blood stream should be soluble.

    [0131] While dosages administered will vary from patient to patient, an effective dose can be determined by setting as a lower limit the concentration of virus proven to be safe and escalating to higher doses of up to 10.sup.12 pfu, while monitoring for an immune response along with the presence of any deleterious side effects. A therapeutically effective dose typically provides an immune response resulting in antibodies against the antigen. Escalating dose studies can be used to obtain a desired effect for a given viral treatment (see, e.g., Nies and Spielberg, Principles of Therapeutics, In Goodman & Gilman's The Pharmacological Basis of Therapeutics, eds. Hardman, et al., McGraw-Hill, NY, 1996, pp 43-62).

    [0132] An immunogenic virus provided herein such as a vesicular stomatitis virus provided herein can be delivered in a dose ranging from, for example, about 10.sup.3 pfu to about 10.sup.12 pfu (e.g., about 10.sup.5 pfu to about 10.sup.12 pfu, about 10.sup.5 pfu to about 10.sup.11 pfu, about 10.sup.6 pfu to about 10.sup.11 pfu, or about 10.sup.6 pfu to about 10.sup.10 pfu). A therapeutically effective dose can be provided in repeated doses. Repeat dosing is appropriate in cases in which observations indicate either that an immune response has not been achieved, or that the degree of immune response has not reached a desired level. Repeat doses can be administered by the same route as initially used or by another route. A therapeutically effective dose can be delivered in several discrete doses (e.g., days or weeks apart) and in one embodiment, one to about twelve doses are provided. Alternatively, a therapeutically effective dose of an of an immune response virus provided herein such as a vesicular stomatitis virus provided herein can be delivered by a sustained release formulation. In some cases, an of an immune response virus provided herein such as a vesicular stomatitis virus provided herein can be delivered in combination with pharmacological agents that facilitate viral replication and spread, or agents that protect cells from viral toxicity. Examples of such agents are described elsewhere (Alvarez-Breckenridge et al., Chem. Rev., 109(7):3125-40 (2009)).

    [0133] The course of therapy with an immunogenic virus provided herein such as a vesicular stomatitis virus provided herein can be monitored by evaluating changes in clinical symptoms of a mammal having a bacterial or viral infection, or by direct monitoring of the number antibodies against the antigen that are detected in a biological sample from the mammal. The effectiveness of viral treatment also can be assessed by monitoring the levels of a bacteria or virus specific antigen after immunization. Bacteria and virus antigens include, for example, the spike protein of SARS-CoV-2, the M protein of SARS-CoV-2, the N protein of SARS-CoV-2, the NP protein of influenza, the M1 protein of influenza, the NS1 protein of influenza, the NP protein of Ebola, the GP protein of Ebola, the VP35 protein of Ebola, the VP40 protein of Ebola, the NS1 protein of yellow fever, the NS1 protein of dengue virus, the spike protein of a coronavirus, the M protein of a coronavirus, the N protein of a coronavirus, the F protein from measles virus, the H protein from measles virus, a nucleocapsid protein from mumps, the E1 spike protein from rubella virus, the E2 spike protein from rubella virus, the C protein of rubella virus, the O antigen of Escherichia coli, glfT2 of Mycobacterium tuberculosis, fas of Mycobacterium tuberculosis, iniB of Mycobacterium tuberculosis, tetanus toxoid from Clostridium tatanis, anthrax toxin from Bacillus anthracis, LipL21 from Leptospira species, LipL41 from Leptospira species, LipL32 from Leptospira species, and fragments of any of these proteins.

    [0134] The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.

    EXAMPLES

    Example 1Cancer Immunotherapy Against Treatment-Driven Neo-Antigenesis

    Experimental Design

    [0135] These experiments were designed to evaluate how reproducible mutations induced in tumor cells escaping oncolytic virotherapy could be exploited for the design of immunotherapies targeting treatment escape. 7-10 mice per group were used for each survival experiment to achieve statistical power to make multiple comparisons. Animals were randomized to treatment groups following tumor implantation using the GraphPad QuickCalcs online tool (https://www.graphpad.com/quickcalcs/randMenu/).

    Cell lines and Viruses

    [0136] B16 murine melanoma, and human Hep3B hepatocellular carcinoma and BHK cells were originally obtained from the ATCC. Human Mel888 melanoma cells were obtained from the Imperial Cancer Research Fund (ICRF) in 1997/1998 and were grown in DMEM (Hyclone, Logan, UT, USA)+10% FBS (Life Technologies). Cell lines were authenticated by morphology, growth characteristics, PCR for tissue specific gene expression (gp100, TYRP-1, and TYRP-2) and biologic behavior, tested mycoplasma-free (MycoAlert Mycoplasma Detection Kit (Lonza)) and frozen. Cells were cultured for less than 3 months after thawing.

    [0137] B16TK cells were derived from a B16.F1 clone transfected with a plasmid expressing the Herpes Simplex Virus thymidine kinase (HSV-1 TK) gene (Evgin et al., Cancer Immunol. Res., 7:828-40 (2019)). Following stable selection in 1.25 g/mL puromycin, these cells were shown to be sensitive to Ganciclovir (Cymevene) at 5 g/mL. B16TK cells were grown in DMEM+10% FBS (Life Technologies)+1.25 g/mL puromycin (Sigma).

    [0138] B16-CSDE1.sup.WT, B16-CSDE1.sup.C-T, Hep3B-CSDE1.sup.WT, Hep3B-CSDE1.sup.C-T or Mel888-CSDE1.sup.WT or Mel88-CSDE1.sup.C-T cell lines were generated by transfection of parental B16, Hep3B or Mel888 cells with pcDNA3.1 expression vectors expressing either the murine (B16) or human (Hep3B, Mel888) CSDE1 wild type (non-mutated) or CSDE1.sup.C-T mutated genes, isolated by PCR from B16 or Hep3B cells which had escaped in vitro oncolysis by VSV-mIFN- (B16) or VSV-hIFN- (Hep3B) in the 21 day selection protocol (Huff et al., Mol. Ther. Oncolytics, 11:1-13 (2018)) described herein. 48 hours after transfection, cells were selected in G418 (5 mg/mL B16, 3 mg/mL Hep3B, 1 mg/mL Mel888) for 2 weeks. Over-expression of the CSDE1 proteins was confirmed in these bulk G418.sup.r populations of cells by Western Blot.

    [0139] VSV expressing murine IFN (VSV-mIFN-, human IFN- (VSV-hIFN-) (Willmon et al., Cancer Res., 69(19):7713-20 (2009)), murine CSDE1.sup.WT, murine CSDE1.sup.C-T, or GFP (VSV-GFP) was rescued from the pXN2 cDNA plasmid using the established reverse genetics system in BHK cells as described elsewhere (Obuchi et al., J. Virol., 77(16):8843-56 (2003); Willmon et al., Cancer Res., 69(19):7713-20 (2009); Diaz et al., Cancer Res., 67:2840-8 (2007); and Pulido et al., Nat. Biotechnol., 30(4):337-43 (2012)). All transgenes were inserted between viral G and L genes using the XhoI and NheI restriction sites. VSV co-expressing murine, or human, IFN- and CSDE1.sup.WT or CSDE1.sup.C-T were also generated by cloning the CSDE1 genes between the viral M and G genes. Virus titers were determined by plaque assay on BHK cells or on the stated cells lines in the text.

    Mice

    [0140] Female C57BL/6 mice were obtained from The Jackson Laboratory at 6-8 weeks of age and maintained in a pathogen-free BSL2 biohazard facility.

    [0141] In Vivo Experiments

    [0142] Mice were challenged subcutaneously with 210.sup.5 B16 melanoma cells, in 100 L PBS (HyClone, Logan, UT, USA). Subcutaneous tumors were treated with doses of 510.sup.7 pfu of VSV delivered intratumorally (IT) in 50 L of PBS. Tumors were measured using calipers 3 times per week, and mice were euthanized when tumors reached 1.0 cm in diameter. For experiments using immune checkpoint blockade, mice received 300 g each of anti-mouse PD1 antibodies (clone RMP1-14), per dose intraperitoneally (IP) (BioXCell). Control mice received 300 g of control rat IgG (Jackson ImmunoRes e arch).

    Immune Cell Activation

    [0143] Spleens and lymph nodes were immediately excised from euthanized C57Bl/6 mice and dissociated in vitro to achieve single-cell suspensions. Red blood cells were lysed with ACK lysis buffer for 2 minutes. Cells were resuspended at 110.sup.6 cells/mL in Iscove's Modified Dulbecco's Medium (IMDM; Gibco) supplemented with 5% FBS, 1% penicillin-streptomycin, 40 mol/L 2-Mercaptoethanol. Cells were co-cultured with target cells at various effector to target ratios or with stimulating peptides. Supernatants were assayed for TNF and IFN by ELISA as directed in the manufacturer's instructions (Mouse TNF or Mouse IFN- ELISA Kit, OptEIA, BD Biosciences, San Diego, CA).

    In Vitro Selection of Virus Resistant Populations

    [0144] B16, Hep3B, or Mel888 cells were infected at an MOI of 0.01 (VSV) for 1 hour, washed with PBS, and then incubated for 7 days. Dead cells were removed every 2 days by washing with PBS. After 7 days, the cells were collected by detachment with trypsin and re-plated. These cells were subjected to two repeated rounds of infection. After 21 days, or three total rounds of infection, the remaining virus escaped cells were collected.

    Sequencing of the CSDE1 Gene

    [0145] The CSDE1 gene was sequenced using the primer 5-TCACGAAGTGCTG-CTGAAGT-3 (SEQ ID NO:15) and aligned with NCBI Reference Sequence: NM_144901.4.

    APOBEC3 Knockdown

    [0146] Four separate mouse unique 29mer shRNA retroviral constructs (Origene Technologies, Rockville, MD) as a combination significantly reduced expression of murine APOBEC3 in B16 cells compared to a single scrambled shRNA encoding retroviral construct (Huff et al., Mol. Ther. Oncolytics, 11:1-13 (2018)). Optimal knockdown for periods of more than two weeks in culture was achieved using all four constructs pre-packaged as retroviral particles in the GP+E86 ecotropic packaging cell line and used to infect B16 cells at an MOI of 10 per retroviral construct. In addition, a single scrambled negative control non-effective shRNA cassette was similarly packaged and used to infect cells to generate B16 (scrambled shRNA) cells.

    [0147] Hep3B cells were infected with a retroviral vector encoding either full length functional APOBEC3B or a mutated, non-functional form of APOBEC3B as a negative control obtained from Reuben Harris (University of Minnesota, MN) (Evgin et al., Cancer Immunol. Res., 7:828-40 (2019); Huff et al., Mol. Ther. Oncolytics, 11:1-13 (2018); and Driscoll et al., Nat. Comm., 11(1):790 (2020)). Infected populations were selected for 7 days in hygromycin to generate Hep3B (APOBEC3B) or Hep3B (APOBEC3B INACTIVE) cell lines and used for experiments as described.

    Protein Expression Analysis

    [0148] Cells were lysed in NP40 lysis buffer containing Pierce Protease inhibitor tablets at a final concentration of 1 (ThermoScientific). Protein lysates were quantified by BCA assay according the manufacturer's instructions (Pierce-ThermoScientific). Whole tumor cell lysates, recovered from mice in vivo, were normalized by protein concentration prior to ELISA determination of IL-12 and TNF- (OptE1A, BD Biosciences, San Diego) to ensure equal amounts of protein were assayed from tumors of different sizes. For Western blot analysis of CSDE1 (89 KD), 20 g protein lysate was run on a 4-15% SDS-PAGE gel, transferred to PVDF membrane, and blotted with a rabbit anti-CSDE1 polyclonal antibody (Bethyl Laboratories, Montgomery TX, product number #A303-160A) at a dilution of 1/500, overnight at 4 C. Membranes were washed with 0.05% Tween-20 PBS and then probed with an anti-rabbit secondary antibody ( 1/50000) in 5% milk. Membranes were developed with chemiluminescent substrate.

    Human T Cell In Vitro Education and Re-Stimulation

    [0149] Peripheral blood mononuclear cells (PBMCs) were isolated from healthy donor apheresis cones. CD3+ T cells were isolated using a magnetic sorting kit (Miltenyi Biotech) and activated using CD3/CD28 beads (ThermoFisher). T cells were co-cultured at a ratio of 10:1 with CD14+ in vitro matured dendritic cells prepared from the same donor pre-loaded with lysates from target tumor cells at a ratio of 1:10 Target cell lysate:DC. On days 3 and 5, tumor cell lysates were re-added to the co-culture. After 7 days of co-culture, CD3+ T cells were re-isolated using a magnetic sorting kit (Miltenyi Biotech), co-cultured with newly-matured monocyte-derived dendritic cells, and loaded with tumor cell lysate at a ratio of 1:10 Target cell lysate:DC. Three days later, supernatant was collected for interferon gamma ELISA (R&D).

    [0150] In separate experiments, CD3+ T cells from donor 3 were treated as above for 7 days, and re-isolated by magnetic sorting. 10.sup.4 target tumor cells (Hep3B parental or Hep3B-VSV-hIFN- 21d ESC) were treated for 24 hours with hIFN- (200 U/mL for 12 hours) and then co-cultured with 10.sup.5 of the previously primed T cells (primed/expanded on either Hep3B parental or Hep3B-VSV-hIFN- 21 d ESC cells) (triplicate wells per treatment). A further 10.sup.5 T cells were added after 48 hours. At 120 hours post co-culture, wells were washed 3 with PBS, and the surviving adherent cells were counted. Autologous monocyte-derived dendritic cells were matured by isolating CD14+ cells by magnetic sorting (Miltenyi Biotech), followed by incubation with human GM-CSF (800 U/mL) and IL-4 (1000 U/mL). On Days 3 and 5, media was replaced with human GM-CSF (1600 U/mL) and IL-4 (1000 U/mL). On Day 7, non-adherent cells were collected, washed with PBS, and resuspended in medium containing GM-CSF (800 U/mL), IL-4 (1000 U/mL), TNF-alpha (1100 U/mL), IL-1beta (1870 U/mL), IL-6 (1000 U/mL), and PGE2 (1 g/mL). Two days later, dendritic cells were harvested for co-incubation with freshly isolated, or pre-activated, T cells at a ratio of 1:10 as described above.

    siRNA Knockdown of CSDE1

    [0151] Target cells were transfected with no siRNA, 600 pmoles of Silence select Negative siRNA or with 600 pmoles of [s15373+15374 siRNA] (2 CSDE1-specific siRNA) (Martinez-Useros et al., J. Clin. Med., 8(4):560 (2019)), and levels of CSDE1 assayed by Western Blot 24 or 48 hours later.

    Statistical Analyses

    [0152] All analysis was performed within GraphPad Prism software (GraphPad). Multiple comparisons were analyzed using one-way or two-way ANOVAs with a Tukey's post-hoc multi comparisons test. Survival data was assessed using the Log-Rank test using a Bonferroni correction for multiple comparisons. Data is expressed as group meanSD.

    Escape from VSV-IFN Oncolysis is Associated with High Frequency Mutation in CSDE1

    [0153] B16 populations selected for escape from VSV-GFP (B16-VSV-GFP-ESC) were heterogeneous for both CSDE1.sup.WT and CSDE1.sup.C-T (FIGS. 1A and 1B). B16-HSVtk cells that escaped GCV chemotherapy (Evgin et al., Cancer Immunol. Res., 7:828-40 (2019)) had no mutation in CSDE1 (FIG. 1C). Expression of IFN from the virus increased IFN, APOBEC3, and the number of virus-resistant cells (Huff et al., Mol. Ther. Oncolytics, 11:1-13 (2018)). Whereas CSDE1.sup.C-T was present at 50% in B16-VSV-GFP-ESC cells, over 90% of CSDE1 sequence in B16-VSV-IFN-ESC cells was CSDE1.sup.C-T suggesting mutation at most of the alleles in ESC cells (FIG. 1D). However, when both B16-VSV-GFP-ESC and B16-VSV-IFN-ESC cells were selected from B16 cells expressing shRNA against mAPOBEC3 (Huff et al., Mol. Ther. Oncolytics, 11:1-13 (2018)), only CSDE1.sup.WT was present (FIGS. 1E and 1F). CSDE1.sup.C-T was present at >90% in murine and human VSV-IFN-ESC cells, and always at higher clonality than in VSV-GFP-ESC cells (FIGS. 1G, 1H, and 1I). CSDE1.sup.C-T was present in Mel888 tumors that escaped VSV-hIFN in vivo (Huff et al., Mol. Ther. Oncolytics, 11:1-13 (2018)), but only in 30-50% of the cells (FIG. 1J), probably reflecting less efficient in vivo infection.

    [0154] Taken together, these results are consistent with the CSDE1.sup.C-T mutation, which has a typical mAPOBEC3/APOBEC3B signature (TTCA-TCCA) (Driscoll et al., Nat. Comm., 11(1):790 (2020); Walker et al., Nat. Commun., 6:6997 (2015); and Roberts et al., Nat. Genet., 45(9):970-6 (2013)), being induced through Type I IFN-induction of mAPOBEC3/hAPOBEC3B activity at high clonality in VSV-IFN ESC cells across species and tumor types (FIGS. 1A-J).

    CSDE1 is a Positive Mediator of VSV Replication and Oncolysis

    [0155] These results suggested that CSDE1 may be involved in the replication/oncolytic activity of VSV, that the CSDE1.sup.C-T mutation drives escape, and that co-expression of IFN enhances mutation of this escape-promoting gene. Consistent with this, replication of (FIGS. 2A-C), and oncolysis by (FIG. 2D), VSV-GFP was reduced by >2 orders of magnitude by CSDE1 knock down in human cells.

    CSDE1.SUP.C-T .Inhibits VSV Replication

    [0156] Similarly, VSV-IFN replicated to significantly higher titers in B16 cells over-expressing CSDE1.sup.WT (p<0.0001 at 72 hours) (FIG. 2E), but significantly worse in B16 cells over-expressing CSDE1.sup.C-T (p<0.0001 at 72 hours), compared to parental B16 (FIG. 2E). B16-CSDE1.sup.C-T cells still have both normal alleles of CSDE1 in situ and express endogenous CSDE1.sup.WT, showing that CSDE1.sup.P5S acts as a dominant-negative regulator of VSV replication and exerts a strong selective pressure on the viral genome, across species and histological types. Multiple passage of VSV-IFN through human Hep3B-CSDE1.sup.WT increased replication compared to passage through Hep3BP parental cells (FIG. 2F). In contrast, after just a single passage through Hep3B-CSDE1.sup.C-T cells, titers were significantly lower than with passage through Hep3BP (p<0.0001) (FIG. 2F). By passage 3 through Hep3B-CSDE1.sup.C-T, titers began to recover, and reached almost Hep3BP levels by passage 5 (FIG. 2F). Virus recovered from 5 passages through Hep3BP (from FIG. 2F), replicated well on Hep3BP cells (FIG. 2G) but had orders of magnitude lower titers on Hep3B-CSDE1.sup.C-T cells (FIG. 2G). Conversely, virus from 5 passages through Hep3B-CSDE1.sup.C-T replicated poorly on Hep3BP cells but at near wild-type levels on Hep3B-CSDE1.sup.C-T cells (FIG. 2G). Thus, VSV-IFN can, if given sufficient time, adapt to the emergence of escape cells by complementing the CSDE1.sup.C-T mutation.

    VSV Expressing an Escape Associated Tumor Antigen

    [0157] The APOBEC3B-generated CSDE1.sup.C-T mutation creates a heteroclitic neo-epitope in the B16/C57Bl/6 model (Driscoll et al., Nat. Comm., 11(1):790 (2020)), and is highly selected for in tumors forced to escape VSV-IFN. This treatment-driven neo-antigenesis makes CSDE1.sup.P5S an Escape-Associated Tumor Antigen (EATA) target for immunotherapy against treatment-resistant tumors. Therefore, viruses expressing either CSDE1.sup.WT or the CSDE1.sup.P5S EATA were constructed (FIG. 3A). The nucleic acid sequence of the VSV-CSDE1.sup.WT construct (SEQ ID NO:16) is shown in FIG. 16; the underlined sequence encodes CSDE1. Consistent with FIGS. 2A-G, over-expression of CSDE1.sup.WT from VSV significantly enhanced viral replication on human and murine (but not hamster) cells, compared to VSV-GFP (FIG. 3B). Conversely, viral-driven CSDE1.sup.P5S exerted a significant dominant-negative effect (FIG. 3B). Low MOI infection of Hep3BP or B16 cells with VSV-IFN-CSDE1.sup.WT significantly reduced both escape (FIG. 3C) and the escape-enabling CSDE1.sup.C-T mutation (10-50% in FIG. 3D, compared to >90% in FIG. 11) compared to VSV-IFN.

    Trap and Ambush immunotherapy for Tumor Escape

    [0158] Mice treated intra-tumorally with VSV-mIFN-CSDE1.sup.WT or VSV-mIFN-CSDE1.sup.C-T (FIG. 4A) generated comparable strong anti-viral T cell responses (FIG. 4B). Although VSV-mIFN-CSDE1.sup.WT did not generate anti-CSDE1.sup.WT T cells, VSV-mIFN-CSDE1.sup.C-T induced potent T cell responses against the CSDE1.sup.P5S neoantigen (FIG. 4B), as well as weaker responses against B16-CSDE1.sup.WT, and B16 (expressing endogenous CSDE1), confirming that CSDE1.sup.P5S acts as a heteroclitic neo-epitope in the C57Bl/6 model (Driscoll et al., Nat. Comm., 11(1):790 (2020)). Only VSV-mIFN-CSDE1.sup.C-T induced intra-tumoral IL-12 after 6 i.t. injections (FIG. 4C), which correlated with the anti-tumor T cell response (FIG. 4B). All three viruses induced similar levels of TNF- within injected tumors (FIG. 4D).

    [0159] Immune checkpoint blockade (ICB) with anti-PD-1 antibody (Wei et al., Cancer Discov., 8(9):1069-86 (2018); Shi et al., Front Immunol., 11:683 (2020); Saibil et al., Curr. Oncol., 27(Suppl 2):S98-S105 (2020); and Shim et al., Mol. Ther 25(4):962-75 (2017)) concomitant with i.t. virus, significantly decreased IL-12 in VSV-mIFN-CSDE1.sup.C-T-treated tumors (FIG. 4C). In contrast, anti-PD-1 ICB 4 days after the first viral injection significantly increased IL-12 in VSV-mIFN-CSDE1.sup.C-T-treated tumors (FIG. 4C). Levels of TNF- were not significantly altered from no, or early, ICB (FIG. 4D).

    [0160] To compare the relative therapeutic contributions of increased viral replication/oncolysis (VSV-mIFN-CSDE1.sup.WT) with decreased oncolysis but treatment-driven neo-antigenesis in VSV-IFN-ESC tumors (VSV-mIFN-CSDE1.sup.C-T), mice were treated i.t. with viruses+anti-PD-1 late after induction of T cell responses (FIG. 4E). VSV-mIFN generated therapy, but all tumors eventually escaped (FIG. 4F). VSV-IFN-CSDE1.sup.WT significantly increased median survival compared to VSV-mIFN (FIG. 4F), correlated with enhanced i.t. replication (FIG. 4G) (consistent with FIG. 3). However, expression of the CSDE1.sup.P5S EATA from the virus completely prevented tumor escape (FIG. 4F), despite significantly less replication in tumors compared to either VSV-mIFN or VSV-mIFN-CSDE1.sup.WT (FIGS. 4G and 2).

    Dendritic Cell Vaccination against an Escape Associated Tumor Antigen

    [0161] To separate the conflicting effects of decreased oncolysis (FIGS. 3 and 4G) against neo-antigenesis (FIG. 4F), EATA-targeted immunotherapy was tested using dendritic cells expressing CSDE1.sup.P5S. DC-CSDE1.sup.C-T also generated strong anti-CSDE1.sup.P5S T cell responses (FIGS. 5A and 5B). VSV-IFN+DC-CSDE.sup.C-T+anti-PD-1 significantly enhanced therapy relative to VSV-IFN+DC-CSDE.sup.WT+anti-PD-1 (FIG. 5C), but never achieved the 100% cure rates of VSV-IFN-CSDE1.sup.C-T+anti-PD-1 (FIG. 4F), which correlated with 3-fold lower levels of i.t. IL-12 (FIGS. 5D and 4C).

    Human Tumor Cells that Escape VSV-IFN are Immunogenic

    [0162] The following was performed to determine whether CSDE1.sup.P5S, and other undefined EATA, would be immunogenic for human T cells. In three separate co-cultures, CD3/CD28-activated human CD3+ T cells had different baseline reactivity against Hep3B targets, reflecting different alloreactivities (Driscoll et al., Nat. Comm., 11(1):790 (2020); Shim et al., Mol. Ther., 25(4):962-75 (2017); Errington et al., Gene Ther., 13:138-49 (2006); Merrick et al., Br. J. Cancer, 92(8):1450-8 (2005); and Ilett et al., Gene Ther., 24(1):21-30 (2017)) (FIGS. 6A and 6B). Nonetheless, both APOBEC3B-mutated Hep3B targets, as well as CSDE1.sup.C-T-expressing Hep3B-VSV-hIFN-ESC cells (FIG. 1I), were significantly more immunogenic than Hep3BP across all three donors (FIG. 6B). Immunogenicity was significantly reduced by knockdown of CSDE1 (Martinez-Useros et al., J. Clin. Med., 8(4):560 (2019)) (FIG. 6B), suggesting that neo-antigenesis of hCSDE1.sup.P5S may serve as an EATA. T cells expanded against Hep3B were unable to kill either Hep3B, or Hep3B-VSV-IFN-ESC, targets (FIG. 6C). In contrast, T cells expanded against Hep3B-VSV-IFN-ESC cells showed significant cytotoxicity against Hep3B-VSV-IFN-ESC targets (FIG. 6C), and some cytotoxicity against Hep3B, suggesting that some T cell responses against EATA may be heteroclitic. Of all possible 8-, 9-, 10-, and 11-mers with the Proline-Serine mutation at amino acid position 5, the 9-mer, MSFDSNLLH (SEQ ID NO:17), was predicted to have weak binding affinity for HLA-A*01:01, HLA-A*03:01, and HLA-B*58:01 (FIG. 6D), which, for HLA-A*01:01 and HLA-B*58:01, was predicted to be stronger than the wild-type epitope MSFDPNLLH (SEQ ID NO:18). T cells from one additional donor could be primed by CSDE1.sup.C-T-transfected DC, but not by CSDE1.sup.WT-transfected DC, to recognize the CSDE1.sup.P5S EATA. However, T cells from a second donor did not recognize either wild-type, or mutated, CSDE1 (FIG. 6E). Both donors 4 and 5 exhibited high level T cell priming against Hep3B-VSV-IFN-ESC cells compared to Hep3B (FIGS. 6E and 6B). Thus, escape from VSV-hIFN generated cells that were consistently more immunogenic than parental in both human and murine contexts.

    Discussion

    [0163] The results provided herein demonstrate that neo-antigenesis resulting from high mutational plasticity of tumors, which also facilitates treatment escape, can be exploited to impose a powerful immunotherapy against escape tumors as they are forced to evolve in response to frontline treatment. By targeting a predictable and reproducible mutation induced with high clonality within treatment escape tumors, the efficacy of VSV-IFN viro-immunotherapy can be significantly improved over that obtained with the virotherapy alone.

    [0164] Escape from treatments such as oncolytic virotherapy can occur for multiple reasons, involving not only tumor cell mutational plasticity but also other mechanisms including a simple lack of efficient infection, HLA incompatibility with EATA, immune suppression, and anti-viral tumor microenvironments. However, mutational pathways, such as APOBEC3B, induced by frontline treatment with a clinical agent VSV-IFN were shown to lead to the emergence of escape variants carrying a very specific mutation that is heavily selected for at high frequency (FIG. 1). It was reasoned that such mutations may be in genes/proteins that mediate escape from innate, and adaptive, immune-mediated mechanisms of tumor clearance induced by VSV infection and/or may allow infected cells to down regulate critical steps in viral replication and thereby escape oncolysis.

    [0165] Across species and tumors, knockdown of CSDE1 significantly decreased VSV replication, whilst its overexpression enhanced virus replication (FIGS. 2 and 3). Overexpression of CSDE1.sup.P5S also significantly decreased VSV replication (FIGS. 2 and 3), despite intact endogenous CSDE1.sup.WT protein. CSDE1 expressed from VSV (VSV-IFN-CSDE1.sup.WT) enhanced replication in vitro and in vivo (FIGS. 3B and 4G), reduced escape (FIG. 3C), inhibited evolution of the escape-promoting CSDE1.sup.C-T mutation (FIG. 3D), and was significantly more effective than a current clinical agent VSV-IFN (FIGS. 4E and 4F). Overall, these results demonstrate that CSDE1 is a major positive regulator of VSV replication, and that CSDE1.sup.P5S acts as a dominant negative inhibitor to facilitate escape from oncolysis. These results also demonstrate that VSV-IFN-CSDE1 can be used as a clinical agent beyond VSV-IFN.

    [0166] VSV expressing IFN was developed to increase anti-viral safety and anti-tumor immunogenicity (Willmon et al., Cancer Res., 69(19):7713-20 (2009); and Jenks et al., Human Gene Ther., 21:451-62 (2010)). However, addition of IFN unexpectedly increased escape through increased APOBEC3B, resulting in enhanced clonality of CSDE1.sup.C-T compared to VSV-GFP-ESC cells (FIG. 1). Although this was an unexpected byproduct of inclusion of IFN into the virus, expression of the highly selected CSDE1.sup.C-T mutation in escape cells presented an opportunity that can be exploited as described herein through targeting of this escape-induced mutation. Thus, since CSDE1.sup.C-T encodes a heteroclitic neo-epitope in the C57Bl/6 model (FIG. 4B), it was reasoned that, by forcing evolution of tumors to express CSDE1.sup.C-T through virotherapy (neo-antigenesis), escape variants could be ambushed by T cell responses against this discovered and consistently occurring CSDE1.sup.P5S EATA. VSV is an excellent platform for vaccination against tumor antigens (Diaz et al., Cancer Res., 67:2840-8 (2007); Durham et al., Mol. Ther., 25(8):1917-32 (2017); Pulido et al., Nat. Biotechnol., 30(4):337-43 (2012); Alonso-Camino et al., Mol. Ther., 22(11):1936-48 (2014); Kottke et al., Nature Med., 2011:854-9 (2011); Janette et al., Mol. Ther., 22(6):1198-210 (2014); Bridle et al., Mol. Ther., 17:1814-21 (2009); and Wongthida et al., Human Gene Ther., 22:1343-53 (2011)) and was used as described herein to co-express CSDE1.sup.C-T from VSV-IFN to prime escape-specific T cell responses. VSV-IFN-CSDE1.sup.C-T, replicated significantly less well than VSV-IFN or VSV-IFN-CSDE1.sup.WT (FIGS. 3B and 4G), but induced potent T cell responses against the CSDE1.sup.P5S EATA (FIG. 4B), which completely prevented escape (FIG. 4F). Although VSV-mIFN-CSDE1.sup.WT was a significantly better oncolytic than VSV-IFN (FIGS. 3B, 3C, 4F, and 4G), it did not generate anti-CSDE1.sup.WT, or anti-CSDE1.sup.P5S, T cell responses (FIG. 4B), it suppressed evolution of the CSDE1.sup.P5S immunogen in escaping cells (FIG. 3D), and it was not as effective as VSV-IFN-CSDE1.sup.C-T in achieving tumor treatment/cures (FIG. 4F). Thus, the therapeutic value of T cell control of emerging escape variants outweighed the loss of oncolytic potency of VSV-IFN-CSDE1.sup.C-T (FIG. 4F).

    [0167] VSV-IFN-ESC tumors in vivo rarely contained a completely homogenous population of CSDE1.sup.C-T mutant tumor cells (FIG. 1J). Therefore, the heteroclitic anti-CSDE1.sup.P5S T cell responses (FIG. 4B) probably contributed a significant bystander effect against tumor cells that do not become infected, that escape direct oncolysis or innate immune clearance, or that do not evolve the CSDE1.sup.C-T mutation. Thus, it may be that intra-tumoral IL-12 (FIG. 4C), which correlated with anti-CSDE1.sup.P5S T cell responses (FIG. 4B), reflects T cell killing of both CSDE1.sup.P5S positive tumor cells and CSDE1.sup.WT cells through the generation of heteroclitic T cell responses (FIG. 4F). DC-CSDE1.sup.C-T, with intra-tumoral VSV-IFN+anti-PD-1, was not as effective as when the neo-antigen was expressed using the virus (FIG. 5C) and was associated with lower intra-tumoral IL-12 (FIGS. 4C and 5C). These results are consistent with a model in which intra-tumoral VSV-IFN-CSDE1.sup.C-T provides both high levels of inflammation (TNF- in all VSV-injected tumors, FIGS. 4D and 5D) to enhance trafficking of anti-CSDE1.sup.P5S-specific T cells. Simultaneously, VSV-IFN-CSDE1.sup.C-T also provides high concentrations of target antigen (CSDE1.sup.P5S) (reflected by IL-12 only in VSV-IFN--CSDE1.sup.C-T-injected tumors, FIG. 4C), which are lacking with i.p. DC and intra-tumoral VSV-IFN.

    [0168] Human VSV-hIFN-ESC tumor cells also were significantly more immunogenic than untreated cells (FIG. 6), implying neo-antigenesis of EATA. These could include CSDE1.sup.C-T, which was present at high clonality (FIG. 1I), knockdown of which significantly reduced T cell activation (FIG. 6B). Virotherapy with escape-targeting immunotherapy can include identifying HLA-/patient-specific EATA, such as CSDE1.sup.P5S where HLA compatibility is predicted (FIG. 6D), or the simultaneous targeting of multiple (unidentified) EATAs, for example, using VSV-expressed cDNA libraries derived from treatment-escape tumors.

    [0169] In summary, the genetic plasticity of tumors was exploited by using oncolytic virotherapy to drive them into an escape phenotype so that they could then be ambushed by vaccination against a predictably arising EATA. This approach can be applied across a range of different frontline therapies that are potent enough to drive tumor cell mutation/evolution, thereby inducing neo-antigenesis resulting in a novel immunopeptidome associated with acquired treatment resistance.

    Example 2Loss of Oncolytic Fitness via Mutation of Target Tumor Cell Genome

    Restoration of Oncolytic Fitness through Mutation of VSV

    [0170] Multiple passage of VSV-IFN through cells overexpressing wild type CSDE1.sup.WT (Hep3B or Mel888) significantly increased replication compared to passage through parental cells (FIG. 2F). Virus passaged 5 times through parental Hep3B replicated well on Hep3B but had orders of magnitude lower titers on Hep3B-CSDE1.sup.P5S (FIG. 9). Conversely, virus passaged 5 times through Hep3B-CSDE1.sup.C-T had very poor titers on Hep3B but replicated to near wild type levels on Hep3B-CSDE1.sup.P5S (FIG. 9). Thus, while cells mutate to escape oncolysis (CSDE.sup.WT to CSDE1.sup.P5S ), the virus can, with time, evolve to complement those mutations.

    [0171] VSV-IFN passaged 5 times through Hep3B-CSDE1.sup.P5S (FIG. 9) contained low frequency mutations (<5%) throughout the genome, as determined by RNAseq. However, a single C-U mutation in the intergenic region (IGR) between the VSV P gene and the VSV M gene was present at 100% frequency in the population; this mutation was undetectable in stock VSV-IFN or in VSV-IFN passaged 5 times through Hep3B (FIGS. 10A-10C). The same IGR P/M.sup.C-U mutation was recovered from VSV-IFN passaged 5 times through Mel888-CSDE1.sup.P5S. Similarly, VSV-IFN passaged through Hep3B-21d-ESC cells was almost entirely mutant for IGR P/M.sup.C-U (FIG. 10D). Virus recovered from a Hep3B tumor in vivo which escaped VSV-IFN contained a mixed population of viruses (FIG. 10E).

    CSDE1 Regulates Levels of Viral P and M mRNA

    [0172] CSDE1, an RNA binding protein involved in translational control, binds RNA at a consensus site of 5-(purine)(aagua)-3. The IGR P/M.sup.C-U point mutation C-U on the ye sense strand of the VSV genome corresponds to a G-A mutation on the +ve sense strand (FIG. 10A) precisely within an exact copy of the consensus CSDE1 binding site in the IGR between the P and M genes (FIG. 10A) (5-aaaaa(aaGua)-3 to 5-aaaaa(aaAua)-3). This site in the IGR between the P and M genes is the only perfect CSDE1 consensus binding site in the VSV genome. This consensus site generally is present only in viral +ve sense transcripts, when the +ve sense genomic full-length strand is made during normal replication of the VSV genome (ve to +ve RNA). The consensus site also exists if a sub-genomic, +ve strand P-M mRNA is made when the polymerase reads through the P/M IGR to make a unicistronic P-M mRNA. Such read-through is rare because P and M mRNAs usually are made by disengagement of polymerase at the P-M IGR, followed by re-initiation at the M gene. Thus, P, M, and P-M mRNAs from VSV-IFN or VSV-IFN-IGR P/M.sup.C-U were measured, on infection of B16 and Hep3BP, or B16-CSDE1.sup.P5S and Hep3B-CSDE1.sup.P5S, cells within 6 hours of infection (early stage of replication) (FIGS. 11A-11I). When levels of RNA were normalized to those in cells infected by VSV-IFN, there were no significant changes in levels of P RNA in cells infected with VSV-IFN-IGR P/MC-U (FIG. 11B). In contrast to moderate or no changes in P RNA levels, levels of M RNA were very significantly decreased following infection of Hep3B-CSDE1.sup.P5S cells with VSV-IFN, or upon infection of Hep3BP cells with VSV-IFN-IGR P/M.sup.C-U (FIG. 11C). Infection of B16- or Hep3B-CSDE1.sup.P5S with VSV-IFN-IGR P/M.sup.C-U completely normalized levels of M RNA and protein, demonstrating that the negative effects of CSDE1.sup.P5S on transcription of viral M RNA were compensated by the presence of the IGR P/M.sup.C-U mutation in the viral genome (FIG. 11C). Levels of P-M bicistronic RNA were increased between 20- and 30-fold on infection of cells with VSV-IFN-IGR P/M.sup.C-U, and between 10 and 30-fold in cells over-expressing CSDE1.sup.P5S infected with VSV-IFN (FIG. 11D). Again, infection of CSDE1.sup.P5S cells with VSV-IFN-IGR P/M.sup.C-U showed normalized P-M RNA levels seen (FIG. 11D). Relative levels of viral G and L RNA, as well as G-L RNA, were not significantly changed in cells infected with VSV-IFN-IGR P/M.sup.C-U or in CSDE1.sup.P5S cells infected with VSV-IFN, (FIGS. 11E-11H). These data suggested that CSDE1.sup.P5S interferes with early stage VSV replication, leading to loss of unicistronic M RNA and increased bicistronic P-M RNA. This hypothesis was strongly supported at the protein level as seen by Western Blot analysis for M protein (FIG. 110. For example, while overexpression of CSDE1.sup.P5S highly inhibited levels of M protein from VSV-IFN (FIG. 11I, lanes 2 and 6), it rescued expression of M protein from the VSV-IFN-IGR P/M.sup.C-U virus (FIG. 11I, lane 8).

    [0173] Further studies showed that as cells evolved to escape from VSV replication/lysis by selection of CSDE1.sup.P5S, the proportion of VSV-IFN-IGR P/M.sup.C-U virus, while low, increased progressively (FIG. 12A). However, when target cells expressed reduced levels of APOBEC3B (by siRNA), emergence of VSV-IFN-IGR P/M.sup.C-U was undetectable by Deep Sequencing (FIG. 12B). Conversely, when target cells over-expressed CSDE1.sup.P5S, emergence of VSV-IFN-IGR P/M.sup.C-U was significantly enhanced (FIG. 12C)an effect that was abolished when APOBEC3B was knocked down (FIG. 12D). These data demonstrated that (1) VSV can, if given sufficient time, evolve in response to selective pressures that reduce viral replication/lysis, and (2) the IGR P/M.sup.C-U mutation in VSV that rescues replication in cells expressing CSDE1.sup.P5S is dependent upon APOBEC3B activity in the target cells.

    CSDE1 Localizes to Cytoplasmic Replication Compartments

    [0174] VSV sequesters its replication machinery into specialized non-membrane bound cytoplasmic compartments where RNA synthesis occurs. Experiments using simple immunofluorescence indicated that CSDE1 localizes to these cytoplasmic replication compartments in VSV infected cells (FIG. 13).

    VSV-CSDE1 as an Oncolytic

    [0175] VSV-CSDE1.sup.WT was validated by Western Blot for expression of CSDE1. BHK, B16, Hep3B and Mel888 cell lines were infected with VSV-GFP, VSV-hIFN-, VSV-CSDE1.sup.WT or VSV-CSDE1.sup.5P-S (MOI 3; triplicate wells). After 48 hours, the virus was titered on BHK cells by plaque assay. These studies revealed that over-expression of CSDE1.sup.WT from VSV significantly enhanced replication compared to VSV-GFP, while virus-driven CSDE1.sup.P5S inhibited replication (FIG. 14A).

    [0176] B16 or Hep3B cells were infected (MOI 0.01) with VSV-IFN, VSV-IFN--CSDE1.sup.WT, or VSV-IFN--CSDE1.sup.5P-S (species matched IFN) for 21 days. Surviving cells were counted. In addition, Sanger sequencing of CSDE1 from surviving cells after infection with VSV-hIFN-CSDE1.sup.WT was conducted. These studies showed that infection with VSV-IFN-CSDE1.sup.WT significantly reduced both escape (FIG. 14B), and the escape-enabling CSDE1.sup.C-T mutation (10-50% in FIG. 14C, compared to >90% in FIG. 1), compared to VSV-IFN. These data suggested that VSV-GFP/IFN-CSDE1.sup.WT is a significantly more effective oncolytic than parental VSV.

    Vaccinating Potential of VSV-CSDE1.SUP.WT

    [0177] Enhanced replication of VSV-CSDE1.sup.WT over VSV may significantly enhance immunogenicity of encoded foreign immunogens for vaccination against infectious agents, such as EBOLA or SARS-CoV-2. To test this, VSV expressing SPIKE, M, or N proteins of SARS-CoV-2, +/IFN, were generated to induce T cell responses to support current antibody-based vaccines. The SPIKE of SARS-CoV-2 was codon optimized, truncated by deleting the ER targeting sequence to enhance Spike pseudotype morphogenesis, and cloned into the stable Prefusion conformation (introduction of 2 prolines in S2 with a furin cleavage mutation in the Receptor binding domain (RBD)) with a GFP-luciferase reporter. Spike replaced VSV-G and mediated infection of the Delta-G pseudotyped virus through the ACEII receptor of SARS-CoV-2. ACEII transgenic or C57BL/6 mice that were vaccinated with VSV expressing SARS-CoV-2 SPIKE (infectious agent vaccine) or hgp100 (anti-melanoma vaccine) showed a highly significant (p<0.001) increase in the frequency of anti-immunogen T cells induced by CSDE1.sup.WT-overexpressing VSV compared to non-CSDE1.sup.WT-expressing counterparts (FIGS. 15A and 15B), consistent with the hypothesis that enhanced replicative capacity of VSV expressing CSDE1.sup.WT enhances the immunogenicity of expressed antigens.

    [0178] In summary, the studies described above demonstrated that in multiple cell types, (1) knockdown of CSDE1 decreases viral replication (e.g., VSV replication); (2) overexpression of CSDE1 enhances viral replication (e.g., VSV replication); (3) overexpression of CSDE1.sup.P5S decreases viral replication (e.g., VSV replication); (4) a compensatory C-U mutation in the P/M IGR correlates with forced evolution of VSV to replicate on cells overexpressing CSDE1.sup.P5S; and (5) emergence of VSV-IFN-IGR P/M.sup.C-U in response to selection increases progressively with time, but lags behind cellular mutation of CSDE1.sup.P5S and is dependent upon APOBEC3B. These results demonstrate that CSDE1, not previously associated with VSV replication, is a critical mediator of the replication/oncolytic activity of VSV-IFN, that CSDE1.sup.P5S allows escape from VSV-IFN virotherapy, and that VSV can evolve compensatory mutations to recover its fitness in CSDE1.sup.P5S cells, of which the IGR P/M.sup.C-U mutation is a major driver.

    Other Embodiments

    [0179] It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.