Compositions and methods for inducing immune responses

1. A nucleic acid molecule comprising:

(i) a first polynucleotide encoding one or more viral replication proteins, wherein the first polynucleotide is codon-optimized as compared to a wild-type polynucleotide encoding the one or more viral replication proteins and wherein the first polynucleotide comprises a sequence having at least 80% identity to a sequence of SEQ ID NO:72; and

(ii) a second polynucleotide comprising a first transgene encoding a first antigenic protein or a fragment thereof.

2. The nucleic acid molecule of claim 1 , further comprising a 5′ untranslated region (UTR), wherein the 5′ UTR comprises an alphavirus 5′ UTR sequence.

3. The nucleic acid molecule of claim 2 , wherein the 5′ UTR comprises a sequence of SEQ ID NO:73, SEQ ID NO:74, or SEQ ID NO:75.

4. The nucleic acid molecule of claim 1 , further comprising a 3′ untranslated region (UTR), wherein the 3′ UTR comprises an alphavirus 3′ UTR sequence.

5. The nucleic acid molecule of claim 4 , wherein the 3′ UTR comprises a poly-A sequence.

6. The nucleic acid molecule of claim 4 , wherein the 3′ UTR comprises a sequence of SEQ ID NO:76.

7. The nucleic acid molecule of claim 1 , wherein the first antigenic protein is a viral protein, a bacterial protein, a fungal protein, a protozoan protein, a parasite protein, or a tumor protein.

8. The nucleic acid molecule of claim 7 , wherein the viral protein is an orthomyxovirus protein, a paramyxovirus protein, a picornavirus protein, a flavivirus protein, a filovirus protein, a rhabdovirus protein, a togavirus protein, an arterivirus protein, a bunyavirus protein, an arenavirus protein, a reovirus protein, a bornavirus protein, a retrovirus protein, an adenovirus protein, a herpesvirus protein, a polyomavirus protein, a papillomavirus protein, a poxvirus protein, or a hepadnavirus protein.

9. The nucleic acid molecule of claim 7 , wherein the first antigenic protein is an influenza virus protein, a respiratory syncytial virus (RSV) protein, a human immunodeficiency virus (HIV) protein, a hepatitis C virus (HCV) protein, a cytomegalovirus (CMV) protein, a Lassa Fever Virus (LFV) protein, an Ebola Virus (EBOV) protein, a Mycobacterium protein, a Bacillus protein, a Yersinia protein, a Streptococcus protein, a Pseudomonas protein, a Shigella protein, a Campylobacter protein, a Salmonella protein, a Plasmodium protein, or a Toxoplasma protein.

10. The nucleic acid molecule of claim 7 , wherein the tumor protein is a kidney cancer, renal cancer, urinary bladder cancer, prostate cancer, uterine cancer, breast cancer, cervical cancer, ovarian cancer, lung cancer, liver cancer, stomach cancer, colon cancer, rectal cancer, oral cavity cancer, pharynx cancer, pancreatic cancer, thyroid cancer, melanoma, skin cancer, head and neck cancer, brain cancer, hematopoietic cancer, leukemia, lymphoma, bone cancer, or sarcoma protein.

11. The nucleic acid molecule of claim 1 , wherein the second polynucleotide comprises at least two transgenes.

12. The nucleic acid molecule of claim 11 , wherein a second transgene encodes a second antigenic protein or a fragment thereof, an immunomodulatory protein, or a reporter protein.

13. The nucleic acid molecule of claim 11 , wherein the second polynucleotide further comprises a sequence encoding a 2A peptide, an internal ribosomal entry site (IRES), a subgenomic promoter, or a combination thereof, located between transgenes.

14. The nucleic acid molecule of claim 11 , wherein the first and second transgenes encode viral proteins, bacterial proteins, fungal proteins, protozoan proteins, parasite proteins, tumor proteins, immunomodulatory proteins, reporter proteins, or any combination thereof.

15. The nucleic acid molecule of claim 1 , wherein the first polynucleotide is located 5′ of the second polynucleotide.

16. The nucleic acid molecule of claim 15 , further comprising an intergenic region located between the first polynucleotide and the second polynucleotide.

17. The nucleic acid molecule of claim 16 , wherein the intergenic region comprises a sequence having at least 85% identity to a sequence of SEQ ID NO:77.

18. The nucleic acid molecule of claim 1 , wherein the nucleic acid molecule is

(a) a DNA molecule; or

(b) an RNA molecule, wherein T is substituted with U.

19. The nucleic acid molecule of claim 18 , wherein the DNA molecule further comprises a promoter located 5′ of the 5′ UTR, wherein the promoter is a T7 promoter, a T3 promoter, or an SP6 promoter.

20. The nucleic acid molecule of claim 18 , wherein the RNA molecule is a self-replicating RNA molecule.

21. The nucleic acid molecule of claim 18 , wherein the RNA molecule further comprises a 5′ cap having a Cap 1 structure, a Cap 1 ( m6 A) structure, a Cap 2 structure, or a Cap 0 structure.

22. A nucleic acid molecule comprising

(a) a sequence of SEQ ID NO:78; or

(b) a sequence of SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:76, and SEQ ID NO:77, wherein T is substituted with U.

23. A pharmaceutical composition comprising the nucleic acid molecule of claim 1 and a lipid formulation.

24. The pharmaceutical composition of claim 23 , wherein the lipid formulation comprises an ionizable cationic lipid.

25. The pharmaceutical composition of claim 24 , wherein the ionizable cationic lipid has a structure of Formula I:

or a pharmaceutically acceptable salt thereof,

wherein R 5 and R 6 are each independently selected from the group consisting of a linear or branched C 1 -C 31 alkyl, C 2 -C 31 alkenyl or C 2 -C 31 alkynyl and cholesteryl; L 5 and L 6 are each independently selected from the group consisting of a linear C 1 -C 20 alkyl and C 2 -C 20 alkenyl; X 5 is —C(O)O—, whereby —C(O)O—R 6 is formed or —OC(O)— whereby —OC(O)—R 6 is formed; X 6 is —C(O)O— whereby —C(O)O—R 5 is formed or —OC(O)— whereby —OC(O)—R 5 is formed; X 7 is S or O; L 7 is absent or lower alkyl; R 4 is a linear or branched C 1 -C 6 alkyl; and R 7 and R 8 are each independently selected from the group consisting of a hydrogen and a linear or branched C 1 -C 6 alkyl.

26. A method of inducing an immune response to an antigenic protein in a subject comprising:

administering to the subject an effective amount of a nucleic acid molecule of claim 1 , thereby inducing an immune response to the first antigenic protein.

27. A method of inducing an immune response to an antigenic protein in a subject comprising:

administering to the subject an effective amount of a pharmaceutical composition of claim 23 , thereby inducing an immune response to the first antigenic protein.