Cancer vaccines

1 . A personalized cancer vaccine for treating a cancer in a subject, comprising:

a messenger ribonucleic acid (mRNA) having an open reading frame (ORF) encoding 5-100 peptide epitopes arranged in a head to tail formation, and

a lipid nanoparticle, wherein the lipid nanoparticle comprises 5-25 mol % non-cationic lipid, 25-55 mol % sterol, 0.5-15 mol % polyethylene glycol (PEG)-modified lipid, and 20-60 mol % of a compound of Formula (I):

or a salt thereof, wherein:

R 1 is selected from the group consisting of C 5-30 alkyl, C 5-20 alkenyl, and —R″M′R′;

R 2 and R 3 are independently selected from the group consisting of C 1-14 alkyl and C 2-14 alkenyl;

R 4 is —(CH 2 ) n Q, wherein Q is —OR, and n is selected from 1, 2, 3, 4, and 5;

each R 5 is H;

each R 6 is H;

M and M′ are independently selected from —C(O)O— and —OC(O)—;

R 7 is H;

R is H;

R′ is selected from the group consisting of C 1-18 alkyl and C 2-18 alkenyl;

R″ is selected from the group consisting of C 3-14 alkyl and C 3-14 alkenyl; and

m is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13,

wherein:

(i) at least one of the peptide epitopes is a major histocompatibility complex (MHC) class I epitope and at least one of the peptide epitopes is an MHC class II epitope, and

(ii) the mRNA comprises N1-methylpseudouridine.

2 . The personalized cancer vaccine of claim 1 , wherein at least two of the peptide epitopes are linked directly to one another without a linker.

3 . The personalized cancer vaccine of claim 2 , wherein a first peptide epitope is linked at its N-terminus directly to a C-terminus of a second peptide epitope without a linker, and wherein a junction formed by 2-10 amino acids of the N-terminus of the first peptide epitope linked to 2-10 amino acids of the C-terminus of the second peptide epitope does not form an immunogenic peptide.

4 . The personalized cancer vaccine of claim 1 , wherein the compound of Formula (I) comprises a structure of Formula (IA):

or a salt thereof, wherein 1 is selected from 1, 2, 3, 4, and 5; m is selected from 5, 6, 7, 8, and 9; and M 1 is M′.

5 . The personalized cancer vaccine of claim 1 , wherein the compound of Formula (I) comprises a structure of Formula (II):

or a salt thereof, wherein 1 is selected from 1, 2, 3, 4, and 5; and M 1 is M′.

6 . The personalized cancer vaccine of claim 1 , wherein the compound of Formula (I) comprises a structure of Formula (IIa), (IIb), (IIc), or (IIe):

or a salt thereof.

7 . The personalized cancer vaccine of claim 1 , wherein the non-cationic lipid is selected from the group consisting of disteroylphosphatidyl choline (DSPC), 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC), dipalmitoylphosphatidylcholine (DPPC), dioleoyl phosphatidylethanolamine (DOPE) and sphingomyelin (SM).

8 . The personalized cancer vaccine of claim 1 , wherein the PEG-modified lipid is selected from the group consisting of PEG-c-DOMG (R-3-[(ω-methoxy-poly(ethyleneglycol)2000) carbamoyl)]-1,2-dimyristyloxypropyl-3-amine), PEG-DSG (1,2-distearoyl-sn-glycerol, methoxypolyethylene glycol), PEG-DMG (polyethylene glycol-1,2-dimyristoyl-sn-glycerol), PEG-DPG (1,2-dipalmitoyl-sn-glycerol, methoxypolyethylene glycol), and PEG-CDMA (poly(ethyleneglycol)-carbamoyl-1,2-dimyristyloxypropylamine).

9 . The personalized cancer vaccine of claim 1 , wherein the sterol is cholesterol.

10 . The personalized cancer vaccine of claim 1 , wherein the compound of Formula (I) is

11 . The personalized cancer vaccine of claim 1 , wherein the mRNA further comprises a 5′ untranslated region (5′-UTR), a 3′ untranslated region (3′-UTR), a 5′ cap, and a poly-A tail.

12 . The personalized cancer vaccine of claim 1 , wherein the mRNA further comprises at least one chemical modification selected from the group consisting of pseudouridine, N1-ethylpseudouridine, 2-thiouridine, 4′-thiouridine, 5-methylcytosine, 2-thio-1-methy 1-1-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-methoxyuridine and 2′-O-methyl uridine.

13 . The personalized cancer vaccine of claim 1 , wherein the mRNA is fully modified with N1-methylpseudouridine.

14 . A personalized cancer vaccine for treating a cancer in a subject, comprising:

a messenger ribonucleic acid (mRNA) having an open reading frame (ORF) encoding 5-50 peptide epitopes arranged in a head to tail formation, and

a lipid nanoparticle, wherein the lipid nanoparticle comprises 5-25 mol % non-cationic lipid, 25-55 mol % sterol, 0.5-15 mol % PEG-modified lipid, and 20-60 mol % compound of Formula (I):

or a salt thereof, wherein:

R 1 is selected from the group consisting of C 5-30 alkyl, C 5-20 alkenyl, and —R″M′R′;

R 2 and R 3 are independently selected from the group consisting of C 1-14 alkyl and C 2-14 alkenyl;

R 4 is —(CH 2 ) n Q, wherein Q is —OR, and n is selected from 1, 2, 3, 4, and 5;

each R 5 is H;

each R 6 is H;

M and M′ are independently selected from —C(O)O— and —OC(O)—;

R 7 is H;

R is H;

R′ is selected from the group consisting of C 1-18 alkyl and C 2-18 alkenyl;

R″ is selected from the group consisting of C 3-14 alkyl and C 3-14 alkenyl; and

m is selected from 5, 6, 7, 8, 9, 10, 11, 12, and 13,

wherein:

(i) at least one of the peptide epitopes is an MHC class I epitope and at least one of the peptide epitopes is an MHC class II epitope, and

(ii) the mRNA comprises N1-methylpseudouridine.

15 . The personalized cancer vaccine of claim 14 , wherein at least two of the peptide epitopes are linked directly to one another without a linker.

16 . The personalized cancer vaccine of claim 15 , wherein a first peptide epitope is linked at its N-terminus directly to a C-terminus of a second peptide epitope without a linker, and wherein a junction is formed between 2-10 amino acids of the N-terminus of the first peptide epitope linked to 2-10 amino acids of the C-terminus of the second peptide epitope does not form an immunogenic peptide.

17 . The personalized cancer vaccine of claim 14 , wherein the compound of Formula (I) comprises a structure of Formula (IA):

or a salt thereof, wherein 1 is selected from 1, 2, 3, 4, and 5; m is selected from 5, 6, 7, 8, and 9; and M 1 is M′.

18 . The personalized cancer vaccine of claim 14 , wherein the compound of Formula (I) comprises a structure of Formula (II):

or a salt thereof, wherein 1 is selected from 1, 2, 3, 4, and 5; and M 1 is M′.

19 . The personalized cancer vaccine of claim 14 , wherein the compound of Formula (I) comprises a structure of Formula (IIa), (IIb), (IIc), or (IIe):

or a salt thereof.

20 . The personalized cancer vaccine of claim 14 , wherein the non-cationic lipid is selected from the group consisting of DSPC, POPC, DPPC, DOPE and SM.

21 . The personalized cancer vaccine of claim 20 , wherein the PEG-modified lipid is selected from the group consisting of PEG-c-DOMG, PEG-DSG, PEG-DMG, PEG-DPG, and PEG-cDMA.

22 . The personalized cancer vaccine of claim 21 , wherein the sterol is cholesterol.

23 . The personalized cancer vaccine of claim 22 , wherein the compound of Formula (I) is

24 . The personalized cancer vaccine of claim 23 , wherein the mRNA further comprises a 5′ untranslated region (5′-UTR), a 3′ untranslated region (3′-UTR), a 5′ cap, and a poly-A tail.

25 . The personalized cancer vaccine of claim 24 , wherein the mRNA further comprises at least one chemical modification selected from the group consisting of pseudouridine, N1-ethylpseudouridine, 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-methoxyuridine and 2′-O-methyl uridine.

26 . The personalized cancer vaccine of claim 24 , wherein the mRNA is fully modified with N1-methylpseudouridine.

27 . A personalized cancer vaccine for treating a cancer in a subject, comprising:

a messenger ribonucleic acid (mRNA) having an open reading frame (ORF) encoding 5-50 cancer antigen peptide epitopes arranged in a head to tail formation, and

a lipid nanoparticle, wherein the lipid nanoparticle comprises (i) 5-25 mol % non-cationic lipid selected from the group consisting of DSPC, POPC, DPPC, DOPE and SM, (ii) 25-55 mol % cholesterol, (iii) 0.5-15 mol % PEG-modified lipid selected from the group consisting of PEG-c-DOMG, PEG-DSG, PEG-DMG, PEG-DPG, and PEG-cDMA, and (iv) 20-60 mol % of Compound 25

wherein:

(i) at least one of the peptide epitopes is an MHC class I epitope and at least one of the peptide epitopes is an MHC class II epitope,

(ii) at least two of the peptide epitopes are linked directly to one another without a linker,

(iii) the mRNA further comprises a 5′ untranslated region (5′-UTR), a 3′ untranslated region (3′-UTR), a 5′ cap, and a poly-A tail, and

(iv) the mRNA comprises N1-methylpseudouridine.

28 . The personalized cancer vaccine of claim 27 , wherein the ORF encodes 40 or fewer peptide epitopes.

29 . The personalized cancer vaccine of claim 27 , wherein the lipid nanoparticle comprises about 5 to 15 mol % of the non-cationic lipid, about 30 to 50 mol % of cholesterol, about 1 to 2 mol % of the PEG-modified lipid and about 40 to 60 mol % of Compound 25.

30 . The personalized cancer vaccine of claim 27 , wherein the non-cationic lipid is DSPC or DOPE.

31 . The personalized cancer vaccine of claim 27 , wherein the PEG-modified lipid is PEG-DSG or PEG-DMG.

32 . The personalized cancer vaccine of claim 27 , wherein each peptide epitope is 9-29 amino acids in length.

33 . The personalized cancer vaccine of claim 27 , wherein the ORF encodes 25-35 peptide epitopes.

34 . The personalized cancer vaccine of claim 27 , wherein at least 30% of the peptide epitopes are MHC class I epitopes.

35 . The personalized cancer vaccine of claim 27 , wherein at least 50% of the peptide epitopes are MHC class I epitopes.

36 . The personalized cancer vaccine of claim 27 , wherein the ratio of the MHC class I epitopes to the MHC class II epitopes is at least 3:1.