Compositions and methods of use of oncolytic virus like vesicles
The present invention relates to high-titer hybrid vims vectors which produce virus-like vesicle (VLVs) and compositions and methods thereof for targeting a malignancy or infectious disease. VLVs are a capsid-free, self-replicating artificial virus platform carrying positive-strand capped and polyadenylated RNA encoding an in vitro evolved Semliki Forest vims (SFV) RNA-dependent RNA replicase and the vesicular stomatitis virus (VSV) glycoprotein. The VLVs of the present invention and pharmaceutical compositions thereof encode for polynucleotide and/or polypeptide therapeutic agents useful in methods for the treatment, prophylaxis, and prevention of malignancies and infectious diseases.
1 . A high-titer hybrid virus vector for treatment, prophylaxis, or prevention of malignancy or infectious disease comprising the following operably linked sequence elements:
a) a first DNA sequence comprising a DNA promoter sequence;
b) a second DNA sequence encoding alphavirus non-structural protein polynucleotide sequences;
c) a third DNA sequence encoding an alphavirus subgenomic RNA promoter;
d) a fourth DNA sequence comprising:
(i) a sequence domain encoding an IL-12 polypeptide,
(ii) a sequence domain encoding an IL-17RA-DN polypeptide, and
(iii) a sequence domain encoding a PD-L1-short hairpin RNA (shRNA),
wherein each of the sequence domains (i)-(iii) are optionally preceded by a sequence independently selected from the group consisting of one or more subgenomic promoters, a sequence encoding a 2A peptide sequence, or combinations thereof; and
e) a fifth DNA sequence encoding a vesiculovirus glycoprotein;
wherein the titer of the high-titer hybrid virus vector is at least about 1×10 7 plaque forming units (pfu) per mL of virus like vesicles (VLVs), or is at least about 5×10 7 plaque forming units (pfu) per mL of virus like vesicles (VLVs), or is at least about 1×10 8 plaque forming units (pfu) per mL of virus like vesicles (VLVs).
2 . The high-titer hybrid virus vector of claim 1 , wherein the DNA promoter sequence of the first DNA sequence comprises a constitutive promoter for RNA-dependent RNA polymerases.
3 . The high-titer hybrid virus vector of claim 1 , wherein the alphavirus non-structural protein polynucleotide sequences of the second DNA sequence are Semliki Forest virus (SFV) non-structural protein polynucleotide sequences.
4 . The high-titer hybrid virus vector of claim 3 , wherein the SFV non-structural protein polypeptide sequences comprise SEQ ID NO. 13.
5 . The high-titer hybrid virus vector of claim 1 , wherein the alphavirus non-structural protein polynucleotide sequences of the second DNA sequence comprise alphavirus RNA-dependent polymerase.
6 . The high-titer hybrid virus vector of claim 5 , wherein the alphavirus RNA-dependent polymerase is a Semliki Forest virus (SFV) RNA-dependent polymerase.
7 . The high-titer hybrid virus vector of claim 1 , wherein the alphavirus subgenomic RNA promoter of the third DNA sequence is a Semliki Forest virus (SFV) subgenomic RNA promoter.
8 . The high-titer hybrid virus vector of claim 1 , wherein the fourth DNA sequence further comprises at least one sequence domain encoding a cytokine agonist or antagonist polypeptide each independently selected from the group consisting of IL-2, IL-7, IL-15, IL-18, IL-19, IL-35, IL-21, GM-CSF, IL-17, Flt3L, and combinations thereof.
9 . The high-titer hybrid virus vector of claim 1 , wherein the fourth DNA sequence further comprises at least one sequence domain encoding an shRNA polynucleotide checkpoint inhibitor each independently selected from the group consisting of PD-L2, CTLA-4, LAG-3, TIM-3, TIGIT, CD90, BTLA, CD160, PD-1, and combinations thereof.
10 . The high-titer hybrid virus vector of claim 1 , wherein the fourth DNA sequence comprises:
a) a sequence domain comprising SEQ ID NO. 6,
b) a sequence domain comprising SEQ ID NO. 8, and
c) a sequence domain comprising SEQ ID NO. 10,
wherein each of the sequence domains a)-c) are optionally preceded by a sequence independently selected from the group consisting of one or more subgenomic promoters, a sequence encoding a 2A peptide sequence, or combinations thereof.
11 . The high-titer hybrid virus vector of claim 1 , wherein the high-titer hybrid virus vector is trivalent; and wherein the fourth DNA sequence consists of three sequence domains.
12 . The high-titer hybrid virus vector of claim 1 , wherein the fourth DNA sequence further comprises a sequence domain encoding a polynucleotide or polypeptide inhibitor of an immunosuppressive regulator selected from the group consisting of tryptophan-2,3-dioxygenase (TDO), indoleamine 2, 3-dioxygenase 1 (IDO1), indoleamine 2, 3-dioxygenase 2 (IDO2), and combinations thereof.
13 . The high-titer hybrid virus vector of claim 1 further comprising a sixth DNA sequence comprising an expression cassette expressing single or multiple specific antigens of the malignancy or infectious disease.
14 . The high-titer hybrid virus vector of claim 13 , wherein the expression cassette expresses specific antigens of a tumor or infectious agent to induce humoral and/or cellular immune responses to the antigens.
15 . The high-titer hybrid virus vector of claim 1 , wherein the vesiculovirus glycoprotein of the fifth DNA sequence comprises envelope glycoprotein of vesicular stomatitis Indiana virus, vesicular stomatitis New Jersey virus, Chandipura virus or structurally related vesiculoviruses.
16 . A high-titer hybrid virus vector for generating oncolytic virus-like vesicles (VLVs) comprising the following operably linked sequence elements:
a) a first DNA sequence comprising a DNA promoter sequence;
b) a second DNA sequence encoding alphavirus non-structural protein polynucleotide sequences;
c) a third DNA sequence encoding an alphavirus subgenomic RNA promoter;
d) a fourth DNA sequence comprising:
(i) a sequence domain encoding an IL-12 polypeptide,
(ii) a sequence domain encoding an IL-17RA-DN polypeptide, and
(iii) a sequence domain encoding a PD-L1-short hairpin RNA (shRNA),
wherein each of the sequence domains (i)-(iii) are optionally preceded by a sequence independently selected from the group consisting of one or more subgenomic promoters, a sequence encoding a 2A peptide sequence, or combinations thereof; and
e) a fifth DNA sequence encoding a vesiculovirus glycoprotein;
wherein the titer of the high-titer hybrid virus vector is at least about 1×10 7 plaque forming units (pfu) per mL of virus like vesicles (VLVs), or is at least about 5×10 7 plaque forming units (pfu) per mL of virus like vesicles (VLVs), or is at least about 1×10 8 plaque forming units (pfu) per mL of virus like vesicles (VLVs).
17 . Virus-like vesicles (VLVs) containing replicon RNA generated by the high-titer hybrid-virus vector of claim 1 .
18 . The VLVs of claim 17 , wherein the replicon RNA is positive-strand capped and polyadenylated.
19 . The VLVs of claim 17 , wherein the VLVs are selected from the group consisting of self-replicating VLVs, oncolytic VLVs, or capsid-free VLVs.
20 . A composition comprising virus-like vesicles (VL Vs) produced by the high-titer hybrid virus vector of claim 1 .
21 . A high-titer hybrid virus vector for treatment, prophylaxis, or prevention of malignancy or infectious disease comprising the following operably linked sequence elements:
a) a first DNA sequence comprising a DNA promoter sequence;
b) a second DNA sequence encoding alphavirus non-structural protein polynucleotide sequences;
c) a third DNA sequence encoding an alphavirus subgenomic RNA promoter;
d) a fourth DNA sequence comprising:
(i) a sequence domain comprising SEQ ID NO. 6,
(ii) a sequence domain comprising SEQ ID NO. 8, and
(iii) a sequence domain comprising SEQ ID NO. 10,
wherein each of the sequence domains (i)-(iii) are optionally preceded by a sequence independently selected from the group consisting of one or more subgenomic promoters, a sequence encoding a 2 A peptide sequence, or combinations thereof; and
e) a fifth DNA sequence encoding a vesiculovirus glycoprotein;
wherein the titer of the high-titer hybrid virus vector is at least about 1×10 7 plaque forming units (pfu) per mL of virus like vesicles (VLVs), or is at least about 5×10 7 plaque forming units (pfu) per mL of virus like vesicles (VLVs), or is at least about 1×10 8 plaque forming units (pfu) per mL of virus like vesicles (VLVs).