Immunomodulatory therapeutic mrna compositions encoding activating oncogene mutation peptides

Abstract

The disclosure features immunomodulatory therapeutic compositions of an mRNA encoding an activating oncogene mutation peptide and an mRNA encoding a polypeptide that enhances immune responses to the activating oncogene mutation peptide, for example an mRNA encoding an immune potentiator. The disclosure also features methods of using the same, for example, to stimulate anti-cancer immune responses.

1 . An immunomodulatory therapeutic composition, comprising:
 an mRNA comprising an open reading frame encoding a concatemer of two or more activating oncogene mutation peptides.   
     
     
         2 . (canceled) 
     
     
         3 . The immunomodulatory therapeutic composition of  claim 1 , wherein at least one of the activating oncogene mutation peptides is a KRAS mutation peptide, optionally wherein the KRAS mutation peptide comprises a G12 mutation and/or a G13 mutation, optionally wherein the G12 KRAS mutation is selected from (i) G12D, G12V, G12S, G12C, G12A, and G12R KRAS mutations; or (ii) G12D, G12V, and G12C KRAS mutations, optionally wherein the G13 KRAS mutation is a G13D KRAS mutation. 
     
     
         4 - 10 . (canceled) 
     
     
         11 . The immunomodulatory therapeutic composition of  claim 3 , wherein the concatemer comprises 3, 4, 5, 6, 7, 8, 9, or 10 activating oncogene mutation peptides, optionally wherein the concatemer comprises 4 activating oncogene mutation peptides. 
     
     
         12 . (canceled) 
     
     
         13 . The immunomodulatory therapeutic composition of  claim 11 , wherein the concatemer comprises activating oncogene mutation peptides comprising, individually, G12D, G12V, G12C, and G13D KRAS mutations. 
     
     
         14 - 16 . (canceled) 
     
     
         17 . The immunomodulatory therapeutic composition of  claim 3 , wherein the activating oncogene mutation peptides comprise, individually, 10-30, 15-25, or 20-25 amino acids in length, or wherein the activating oncogene mutation peptides comprise, individually, 20, 21, 22, 23, 24, or 25 amino acids in length. 
     
     
         18 - 53 . (canceled) 
     
     
         54 . The immunomodulatory therapeutic composition of  claim 3 , wherein the concatemer comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 42-47, 73 and 137, or wherein the mRNA encoding the concatemer comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 129-131, 133, 138 and 169. 
     
     
         55 . (canceled) 
     
     
         56 . The immunomodulatory therapeutic composition of  claim 54 , wherein the mRNA includes at least one chemical modification, optionally wherein the chemical modification is selected from the group consisting of pseudouridine, N1-methylpseudouridine, 2-thiouridine, 4′-thiouridine, 5-methylcytosine, 2-thio-1-methyl-1-deaza-pseudouridine, 2-thio-1-methyl-pseudouridine, 2-thio-5-aza-uridine, 2-thio-dihydropseudouridine, 2-thio-dihydrouridine, 2-thio-pseudouridine, 4-methoxy-2-thio-pseudouridine, 4-methoxy-pseudouridine, 4-thio-1-methyl-pseudouridine, 4-thio-pseudouridine, 5-aza-uridine, dihydropseudouridine, 5-methyluridine, 5-methyluridine, 5-methoxyuridine, and 2′-O-methyl uridine, or wherein the chemical modification is selected from the group consisting of pseudouridine or a pseudouridine analog, or wherein the chemical modification is N1-methylpseudouridine. 
     
     
         57 - 69 . (canceled) 
     
     
         70 . A lipid nanoparticle comprising the immunomodulatory therapeutic composition of  claim 1 , optionally wherein the lipid nanoparticle comprises a molar ratio of about 20-60% ionizable amino lipid:5-25% phospholipid:25-55% sterol, and 0.5-15% PEG-modified lipid, optionally wherein the ionizable amino lipid is a compound of Formula (I), optionally wherein the compound of Formula (I) is Compound 25. 
     
     
         71 - 106 . (canceled) 
     
     
         107 . The lipid nanoparticle of  claim 70 , wherein the lipid nanoparticle comprises a molar ratio of about 50% Compound 25:about 10% DSPC:about 38.5% cholesterol; and about 1.5% PEG-DMG. 
     
     
         108 - 119 . (canceled) 
     
     
         120 . A pharmaceutical composition comprising the immunomodulatory therapeutic composition of  claim 1 , and a pharmaceutically acceptable carrier, optionally wherein the pharmaceutically acceptable carrier comprises a buffer solution. 
     
     
         121 . A pharmaceutical composition comprising the lipid nanoparticle of  claim 70 , and a pharmaceutically acceptable carrier, optionally, wherein the pharmaceutically acceptable carrier comprises a buffer solution. 
     
     
         122 . The pharmaceutical composition of  claim 120 , which is formulated for intramuscular delivery. 
     
     
         123 - 124 . (canceled) 
     
     
         125 . A kit comprising a container comprising the immunomodulatory therapeutic composition of  claim 1 , and an optional pharmaceutically acceptable carrier, and a package insert comprising instructions for administration of the immunomodulatory therapeutic composition, the lipid nanoparticle or pharmaceutical composition, for treating or delaying progression of cancer in an individual. 
     
     
         126 . The kit of  claim 125 , wherein the package insert further comprises instructions for administration of the immunomodulatory therapeutic composition in combination with a composition comprising a checkpoint inhibitor polypeptide, and an optional pharmaceutically acceptable carrier, for treating or delaying progression of cancer in an individual. 
     
     
         127 - 134 . (canceled) 
     
     
         135 . A method of reducing or decreasing a size of a tumor, inhibiting a tumor growth, or inducing an anti-tumor response in a subject in need thereof, comprising administering to the subject the immunomodulatory therapeutic composition of  claim 1 . 
     
     
         136 . The method of  claim 135 , wherein the immunomodulatory therapeutic composition is administered in combination with a cancer therapeutic agent, or wherein the immunomodulatory therapeutic composition is administered in combination with an inhibitory checkpoint polypeptide or polynucleotide encoding the same, optionally wherein the inhibitory checkpoint polypeptide is an antibody or an antigen-binding fragment thereof that specifically binds to a molecule selected from the group consisting of PD-1, PD-L1, TIM-3, VISTA, A2AR, B7-H3, B7-H4, BTLA, CTLA-4, IDO, KIR and LAG3. 
     
     
         137 - 138 . (canceled) 
     
     
         139 . The method of  claim 135 , wherein the cancer is selected from a cancer of the pancreas, peritoneum, large intestine, small intestine, biliary tract, lung, endometrium, ovary, genital tract, gastrointestinal tract, cervix, stomach, urinary tract, colon, rectum, and hematopoietic and lymphoid tissues. 
     
     
         140 - 189 . (canceled) 
     
     
         190 . The pharmaceutical composition of  claim 121 , which is formulated for intramuscular delivery. 
     
     
         191 . The immunomodulatory therapeutic composition of  claim 1 , wherein the concatemer comprises the amino acid sequence of SEQ ID NO: 137. 
     
     
         192 . The immunomodulatory therapeutic composition of  claim 1 , wherein the ORF comprises the nucleotide sequence of SEQ ID NO: 169. 
     
     
         193 . The immunomodulatory therapeutic composition of  claim 1 , wherein the mRNA comprises the nucleotide sequence of SEQ ID NO: 167. 
     
     
         194 . The immunomodulatory therapeutic composition of  claim 193 , wherein the mRNA comprises at least one chemical modification that is N1-methylpseudouridine.