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US-12616746-B2 - Infectious disease antigens and vaccines

US12616746B2US 12616746 B2US12616746 B2US 12616746B2US-12616746-B2

Abstract

Disclosed herein are compositions that include antigen-encoding nucleic acid sequences and/or antigen peptides. Also disclosed are nucleotides, cells, and methods associated with the compositions including their use as vaccines, including vectors and methods for a heterologous prime/boost vaccination strategy.

Inventors

  • Andrew Ferguson
  • Christine Denise Palmer
  • Raphael Rousseau
  • Roman Yelensky
  • James Xin Sun
  • Matthew Joseph Davis
  • Karin Jooss
  • Amy Rachel RAPPAPORT
  • Ciaran Daniel Scallan
  • Leonid Gitlin

Assignees

  • GRITSTONE BIO, INC.

Dates

Publication Date
20260505
Application Date
20221003

Claims (18)

  1. 1 . A composition for delivery of a self-replicating alphavirus-based expression system, wherein the composition for delivery of the self-replicating alphavirus-based expression system comprises: (A) the self-replicating alphavirus-based expression system, wherein the self-replicating alphavirus-based expression system comprises one or more vectors, wherein the one or more vectors comprises: (a) an RNA alphavirus backbone, wherein the RNA alphavirus backbone comprises: (i) at least one promoter nucleotide sequence, and (ii) at least one polyadenylation (poly(A)) sequence; and (b) a cassette, wherein the cassette comprises: (i) at least one antigen-encoding nucleic acid sequence comprising: a. a nucleic acid sequence encoding an infectious disease organism peptide selected from the group consisting of: a pathogen-derived peptide, a virus-derived peptide, a bacteria-derived peptide, a fungus-derived peptide, and a parasite-derived peptide, b. optionally a 5′ linker sequence, and c. optionally a 3′ linker sequence; (ii) optionally, a second promoter nucleotide sequence operably linked to the at least one antigen-encoding nucleic acid sequence; and (iii) optionally, at least one second poly(A) sequence, wherein the second poly(A) sequence is a native poly(A) sequence or an exogenous poly(A) sequence to the alphavirus, wherein an ordered sequence of each element of the cassette in the composition for delivery of the self-replicating alphavirus-based expression system is described in the formula, from 5′ to 3′, comprising: P a -(L5 b -N c -L3 d ) X -(G5 e -U f ) Y -G3 g wherein P comprises the second promoter nucleotide sequence, where a=0 or 1, N comprises one of the epitope-encoding nucleic acid sequences, wherein the epitope-encoding nucleic acid sequence comprises an MHC class I epitope-encoding nucleic acid sequence, where c=1, L5 comprises the 5′ linker sequence, where b=0 or 1, L3 comprises the 3′ linker sequence, where d=0 or 1, G5 comprises one of the at least one nucleic acid sequences encoding a GPGPG amino acid linker, where e=0 or 1, G3 comprises one of the at least one nucleic acid sequences encoding a GPGPG amino acid linker, where g=0 or 1, U comprises one of the at least one MHC class II epitope-encoding nucleic acid sequence, where f=1, X=1 to 400, where for each X the corresponding N c is an MHC class I epitope-encoding nucleic acid sequence, and Y=0, 1, or 2, where for each Y the corresponding U f is an MHC class II epitope-encoding nucleic acid sequence optionally wherein: (a) for each X the corresponding N c is a distinct MHC class I epitope encoding nucleic acid sequence; and/or (b) for each Y the corresponding U f is a distinct MHC class II antigen-encoding nucleic acid sequence; and/or (c) wherein: a=0, b=1, d=1, e=1, g=1, h=1, X=20, Y=2, the at least one promoter nucleotide sequence is a single 26S promoter nucleotide sequence provided by the backbone, the at least one polyadenylation poly(A) sequence is a poly(A) sequence of at least 100 consecutive A nucleotides provided by the backbone, each N encodes a MHC class I epitope 7-15 amino acids in length, L5 is a native 5′ linker sequence that encodes a native N-terminal amino acid sequence of the MHC I epitope, and wherein the 5′ linker sequence encodes a peptide that is at least 2 amino acids in length, L3 is a native 3′ linker sequence that encodes a native C-terminal acid sequence of the MHC I epitope, and wherein the 3′ linker sequence encodes a peptide that is at least 2 amino acids in length, U is each of a PADRE class II sequence and a Tetanus toxoid MHC class II sequence, wherein the alphavirus vector is a Venezuelan equine encephalitis virus vector, each of the MHC class I antigen-encoding nucleic acid sequences encodes a polypeptide that is between 13 and 25 amino acids in length, and optionally wherein at least two of the antigen-encoding nucleic acid sequences encode polypeptide sequences or portions thereof that are presented by MHC class I on the tumor cell surface, and (B) a lipid-nanoparticle (LNP), wherein the LNP encapsulates the self-replicating alphavirus-based expression system.
  2. 2 . The composition of claim 1 , wherein the nucleic acid sequence encoding the peptide comprises encoding a peptide selected from: an epitope, a full-length protein, a protein subunit, a protein domain, and combinations thereof of the protein expressed in the infectious disease organism.
  3. 3 . The composition of claim 1 , wherein the nucleic acid sequence encoding the peptide comprises two or more distinct epitope-encoding nucleic acid sequences, between 1-10, between 1-20, between 1-30, between 1-40, between 1-50, between 1-100, between 1-200, between 1-300, between 1-400, between 1-500, between 2-10, between 2-20, between 2-30, between 2-40, between 2-50, between 2-100, between 2-200, between 2-300, between 2-400, or between 2-500 distinct epitope-encoding nucleic acid sequences distinct epitope-encoding nucleic acid sequences.
  4. 4 . The composition of claim 1 , wherein the encoded peptide or peptides is capable of stimulating an immune response, a T cell response, a B cell response, and/or a T cell response and a B cell response.
  5. 5 . The composition of claim 1 , wherein the infectious disease organism is selected from the group consisting of: Severe acute respiratory syndrome-related coronavirus (SARS), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Ebola, HIV, Hepatitis B virus (HBV), influenza, Hepatitis C virus (HCV), Human papillomavirus (HPV), Cytomegalovirus (CMV), Chikungunya virus, Respiratory syncytial virus (RSV), Dengue virus, a orthymyxoviridae family virus, and tuberculosis.
  6. 6 . The composition of claim 1 , wherein the LNP comprises a lipid selected from the group consisting of: an ionizable amino lipid, a phosphatidylcholine, cholesterol, a PEG-based coat lipid, or a combination thereof; or the LNP comprises an ionizable amino lipid, a phosphatidylcholine, cholesterol, and a PEG-based coat lipid; and optionally wherein the ionizable amino lipids comprise MC3-like (dilinoleylmethyl-4-dimethylaminobutyrate) molecules; and/or the LNP-encapsulated expression system has a diameter of about 100 nm.
  7. 7 . The composition of claim 1 , wherein the RNA alphavirus backbone comprises at least one nucleotide sequence of an Aura virus, a Fort Morgan virus, a Venezuelan equine encephalitis virus, a Ross River virus, a Semliki Forest virus, a Sindbis virus, or a Mayaro virus, optionally wherein a. the RNA alphavirus backbone comprises at least sequences for nonstructural protein-mediated amplification, a 26S promoter sequence, a poly(A) sequence, a nonstructural protein 1 (nsP1) gene, a nsP2 gene, a nsP3 gene, and a nsP4 gene encoded by the nucleotide sequence of the Aura virus, the Fort Morgan virus, the Venezuelan equine encephalitis virus, the Ross River virus, the Semliki Forest virus, the Sindbis virus, or the Mayaro virus, or b. the RNA alphavirus backbone comprises at least sequences for nonstructural protein-mediated amplification, a 26S promoter sequence, and a poly(A) sequence encoded by the nucleotide sequence of the Aura virus, the Fort Morgan virus, the Venezuelan equine encephalitis virus, the Ross River virus, the Semliki Forest virus, the Sindbis virus, or the Mayaro virus; optionally wherein sequences for nonstructural protein-mediated amplification are selected from the group consisting of: an alphavirus 5′ UTR, a 51-nt CSE, a 24-nt CSE, a 26S subgenomic promoter sequence, a 19-nt CSE, an alphavirus 3′ UTR, or combinations thereof; and/or the RNA alphavirus backbone comprises does not encode structural virion proteins capsid, E2 and E1, optionally wherein the antigen cassette is inserted in place of structural virion proteins within the nucleotide sequence of the Aura virus, the Fort Morgan virus, the Venezuelan equine encephalitis virus, the Ross River virus, the Semliki Forest virus, the Sindbis virus, or the Mayaro virus; and/or the insertion of the antigen cassette provides for transcription of a polycistronic RNA comprising the nsP1-4 genes and the at least one antigen-encoding nucleic acid sequence, wherein the nsP1-4 genes and the at least one antigen-encoding nucleic acid sequence are in separate open reading frames; and optionally wherein the Venezuelan equine encephalitis virus comprises: the sequence of SEQ ID NO:3 or SEQ ID NO:5, optionally further comprising a deletion between base pair 7544 and 11175, or the sequence set forth in SEQ ID NO:6 or SEQ ID NO:7, optionally wherein the antigen cassette is inserted at position 7544 to replace the deletion between base pairs 7544 and 11175 as set forth in the sequence of SEQ ID NO:3 or SEQ ID NO:5.
  8. 8 . The composition of claim 1 , wherein the at least one promoter nucleotide sequence is: the native 26S promoter nucleotide sequence encoded by the RNA alphavirus backbone or wherein the at least one promoter nucleotide sequence is an exogenous RNA promoter; and/or wherein the second promoter nucleotide sequence is a 26S promoter nucleotide sequence, or comprises multiple 26S promoter nucleotide sequences, wherein each 26S promoter nucleotide sequence provides for transcription of one or more of the separate open reading frames; and/or the at least one promoter nucleotide sequence or the second promoter nucleotide sequence is inducible or non-inducible; and/or the at least one poly(A) sequence comprises a poly(A) sequence native to the backbone or exogenous to the backbone; and/or the at least one poly(A) sequence is operably linked to at least one of the at least one antigen-encoding nucleic acid sequences; and/or the at least one poly(A) sequence is at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, or at least 90 consecutive A nucleotides or at least 100 consecutive A nucleotides.
  9. 9 . The composition of claim 1 , wherein the epitope-encoding nucleic acid sequence comprises a MHC class I epitope-encoding nucleic acid sequence, and wherein the MHC class I epitope-encoding nucleic acid sequence is selected by performing the steps of: (a) obtaining at least one of exome, transcriptome, or whole genome nucleotide sequencing data from the infectious disease organism, wherein the infectious disease organism nucleotide sequencing data is used to obtain data representing peptide sequences of each of a set of epitopes; (b) inputting the peptide sequence of each epitope into a presentation model to generate a set of numerical likelihoods that each of the epitopes is presented by one or more of the MHC alleles on the infected cell surface, the set of numerical likelihoods having been identified at least based on received mass spectrometry data; and (c) selecting a subset of the set of epitopes based on the set of numerical likelihoods to generate a set of selected epitopes which are used to generate the MHC class I epitope-encoding nucleic acid sequence optionally wherein each of the MHC class I epitope-encoding nucleic acid sequences is selected by performing the above steps (a)-(c); and/or a number of the set of selected epitopes is 2-20; and/or the presentation model represents dependence between: (a) presence of a pair of a particular one of the MHC alleles and a particular amino acid at a particular position of a peptide sequence, and (b) likelihood of presentation on the tumor cell surface, by the particular one of the MHC alleles of the pair, of such a peptide sequence comprising the particular amino acid at the particular position; and/or selecting the set of selected epitopes comprises selecting epitopes that have an increased likelihood of being presented on the tumor cell surface relative to unselected epitopes based on the presentation model; and/or selecting the set of selected epitopes comprises selecting epitopes that have an increased likelihood of being capable of inducing a tumor-specific immune response in the subject relative to unselected epitopes based on the presentation model; and/or selecting the set of selected epitopes comprises selecting epitopes that have an increased likelihood of being capable of being presented to naïve T cells by professional antigen presenting cells (APCs) relative to unselected epitopes based on the presentation model, optionally wherein the APC is a dendritic cell (DC); and/or selecting the set of selected epitopes comprises selecting epitopes that have a decreased likelihood of being subject to inhibition via central or peripheral tolerance relative to unselected epitopes based on the presentation model; and/or the set of selected epitopes comprises selecting epitopes that have a decreased likelihood of being capable of inducing an autoimmune response to normal tissue in the subject relative to unselected epitopes based on the presentation model; and/or exome or transcriptome nucleotide sequencing data is obtained by performing sequencing on the tumor tissue, optionally wherein the sequencing is next generation sequencing (NGS) or any massively parallel sequencing approach.
  10. 10 . The composition of claim 1 , wherein: the cassette comprises junctional epitope sequences formed by adjacent sequences in the cassette, optionally wherein at least one or each junctional epitope sequence has an affinity of greater than 500 nM for MHC and/or wherein each junctional epitope sequence is non-self; and/or the cassette does not encode a non-therapeutic MHC class I or class II epitope nucleic acid sequence comprising a translated, wild-type nucleic acid sequence, wherein the non-therapeutic epitope is predicted to be displayed on an MHC allele of the subject, optionally wherein the non-therapeutic predicted MHC class I or class II epitope sequence is a junctional epitope sequence formed by adjacent sequences in the cassette; and/or the prediction is based on presentation likelihoods generated by inputting sequences of the non-therapeutic epitopes into a presentation model; and/or an order of the antigen-encoding nucleic acid sequences in the cassette is determined by a series of steps comprising: (a) generating a set of candidate cassette sequences corresponding to different orders of the antigen-encoding nucleic acid sequences; (b) determining, for each candidate cassette sequence, a presentation score based on presentation of non-therapeutic epitopes in the candidate cassette sequence; and (c) selecting a candidate cassette sequence associated with a presentation score below a predetermined threshold as the cassette sequence for a vaccine.
  11. 11 . The composition of claim 1 , wherein the epitope-encoding nucleic acid sequences comprises at least one MHC class I epitope-encoding nucleic acid sequence, and wherein each antigen-encoding nucleic acid sequence encodes a polypeptide sequence between 8 and 35 amino acids in length, optionally 9-17, 9-25, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 amino acids in length.
  12. 12 . The composition of claim 1 , wherein: one or more of the epitope-encoding nucleic acid sequences are derived from an infection in or an infected cell of a subject; or each of the epitope-encoding nucleic acid sequences are derived from an infection in or an infected cell of a subject; or one or more of the epitope-encoding nucleic acid sequences are not derived from an infection in or an infected cell of a subject; or each of the epitope-encoding nucleic acid sequences are not derived from an infection in or an infected cell of a subject.
  13. 13 . A method for stimulating an immune response in a subject, the method comprising administering to the subject the composition for delivery of the self-replicating alphavirus-based expression system of claim 1 , and optionally administering to the subject a composition for delivery of a chimpanzee adenovirus (ChAdV)-based expression system, and, optionally wherein the composition for delivery of the ChAdV-based expression system is administered as a priming dose and either the composition for delivery of the ChAdV-based expression system or the composition for delivery of the self-replicating alphavirus-based expression system is administered as one or more boosting doses, or the composition for delivery of the self-replicating alphavirus-based expression system is administered as a priming dose either the composition for delivery of the ChAdV-based expression system or the composition for delivery of the self-replicating alphavirus-based expression system is administered as one or more boosting doses; and/or optionally wherein two or more, or 1, 2, 3, 4, 5, 6, 7, or 8 boosting doses are administered; and/or optionally wherein the cassette of the composition for delivery of the ChAdV-based expression system is identical to the cassette of the composition for delivery of the self-replicating alphavirus-based expression system.
  14. 14 . The method of claim 13 , wherein the composition for delivery of the self-replicating alphavirus-based expression system of claim 1 is administered as the priming dose and administered as one or more boosting doses.
  15. 15 . A composition for delivery of a self-replicating alphavirus-based expression system, wherein the composition for delivery of the self-replicating alphavirus-based expression system comprises: (A) the self-replicating alphavirus-based expression system, wherein the self-replicating alphavirus-based expression system comprises one or more vectors, wherein the one or more vectors comprises: (a) an RNA alphavirus backbone, wherein the RNA alphavirus backbone comprises: (i) at least one promoter nucleotide sequence, and (ii) at least one polyadenylation (poly(A)) sequence; and (b) a cassette, wherein the cassette comprises: (i) at least one antigen-encoding nucleic acid sequence comprising: a. a nucleic acid sequence encoding an infectious disease organism peptide selected from the group consisting of: a pathogen-derived peptide, a virus-derived peptide, a bacteria-derived peptide, a fungus-derived peptide, and a parasite-derived peptide, b. optionally a 5′ linker sequence, and c. optionally a 3′ linker sequence; (ii) optionally, a second promoter nucleotide sequence operably linked to the at least one antigen-encoding nucleic acid sequence; and (iii) optionally, at least one second poly(A) sequence, wherein the second poly(A) sequence is a native poly(A) sequence or an exogenous poly(A) sequence to the alphavirus, wherein the at least one promoter nucleotide sequence is: the native 26S promoter nucleotide sequence encoded by the RNA alphavirus backbone or wherein the at least one promoter nucleotide sequence is an exogenous RNA promoter; and/or wherein the second promoter nucleotide sequence is a 26S promoter nucleotide sequence, or comprises multiple 26S promoter nucleotide sequences, wherein each 26S promoter nucleotide sequence provides for transcription of one or more of the separate open reading frames; and/or the at least one promoter nucleotide sequence or the second promoter nucleotide sequence is inducible or non-inducible; and/or the at least one poly(A) sequence comprises a poly(A) sequence native to the backbone or exogenous to the backbone; and/or the at least one poly(A) sequence is operably linked to at least one of the at least one antigen-encoding nucleic acid sequences; and/or the at least one poly(A) sequence is at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, or at least 90 consecutive A nucleotides or at least 100 consecutive A nucleotides, and (B) a lipid-nanoparticle (LNP), wherein the LNP encapsulates the self-replicating alphavirus-based expression system.
  16. 16 . A method for stimulating an immune response in a subject, the method comprising administering to the subject the composition for delivery of the self-replicating alphavirus-based expression system of claim 15 , and optionally administering to the subject a composition for delivery of a chimpanzee adenovirus (ChAdV)-based expression system, and, optionally wherein the composition for delivery of the ChAdV-based expression system is administered as a priming dose and either the composition for delivery of the ChAdV-based expression system or the composition for delivery of the self-replicating alphavirus-based expression system is administered as one or more boosting doses, or the composition for delivery of the self-replicating alphavirus-based expression system is administered as a priming dose either the composition for delivery of the ChAdV-based expression system or the composition for delivery of the self-replicating alphavirus-based expression system is administered as one or more boosting doses; and/or optionally wherein two or more, or 1, 2, 3, 4, 5, 6, 7, or 8 boosting doses are administered; and/or optionally wherein the cassette of the composition for delivery of the ChAdV-based expression system is identical to the cassette of the composition for delivery of the self-replicating alphavirus-based expression system.
  17. 17 . A composition for delivery of a self-replicating alphavirus-based expression system, wherein the composition for delivery of the self-replicating alphavirus-based expression system comprises: (A) the self-replicating alphavirus-based expression system, wherein the self-replicating alphavirus-based expression system comprises one or more vectors, wherein the one or more vectors comprises: (a) an RNA alphavirus backbone, wherein the RNA alphavirus backbone comprises: (i) at least one promoter nucleotide sequence, and (ii) at least one polyadenylation (poly(A)) sequence; and (b) a cassette, wherein the cassette comprises: (i) at least one antigen-encoding nucleic acid sequence comprising: a. a nucleic acid sequence encoding an infectious disease organism peptide selected from the group consisting of: a pathogen-derived peptide, a virus-derived peptide, a bacteria-derived peptide, a fungus-derived peptide, and a parasite-derived peptide, b. optionally a 5′ linker sequence, and c. optionally a 3′ linker sequence; (ii) optionally, a second promoter nucleotide sequence operably linked to the at least one antigen-encoding nucleic acid sequence; and (iii) optionally, at least one second poly(A) sequence, wherein the second poly(A) sequence is a native poly(A) sequence or an exogenous poly(A) sequence to the alphavirus, wherein the cassette comprises junctional epitope sequences formed by adjacent sequences in the cassette, optionally wherein: at least one or each junctional epitope sequence has an affinity of greater than 500 nM for MHC and/or wherein each junctional epitope sequence is non-self; and/or the cassette does not encode a non-therapeutic MHC class I or class II epitope nucleic acid sequence comprising a translated, wild-type nucleic acid sequence, wherein the non-therapeutic epitope is predicted to be displayed on an MHC allele of the subject, optionally wherein the non-therapeutic predicted MHC class I or class II epitope sequence is a junctional epitope sequence formed by adjacent sequences in the cassette; and/or the prediction is based on presentation likelihoods generated by inputting sequences of the non-therapeutic epitopes into a presentation model; and/or an order of the antigen-encoding nucleic acid sequences in the cassette is determined by a series of steps comprising: (a) generating a set of candidate cassette sequences corresponding to different orders of the antigen-encoding nucleic acid sequences; (b) determining, for each candidate cassette sequence, a presentation score based on presentation of non-therapeutic epitopes in the candidate cassette sequence; and (c) selecting a candidate cassette sequence associated with a presentation score below a predetermined threshold as the cassette sequence for a vaccine, and (B) a lipid-nanoparticle (LNP), wherein the LNP encapsulates the self-replicating alphavirus-based expression system.
  18. 18 . A method for stimulating an immune response in a subject, the method comprising administering to the subject the composition for delivery of the self-replicating alphavirus-based expression system of claim 17 , and optionally administering to the subject a composition for delivery of a chimpanzee adenovirus (ChAdV)-based expression system, and, optionally wherein the composition for delivery of the ChAdV-based expression system is administered as a priming dose and either the composition for delivery of the ChAdV-based expression system or the composition for delivery of the self-replicating alphavirus-based expression system is administered as one or more boosting doses, or the composition for delivery of the self-replicating alphavirus-based expression system is administered as a priming dose either the composition for delivery of the ChAdV-based expression system or the composition for delivery of the self-replicating alphavirus-based expression system is administered as one or more boosting doses; and/or optionally wherein two or more, or 1, 2, 3, 4, 5, 6, 7, or 8 boosting doses are administered; and/or optionally wherein the cassette of the composition for delivery of the ChAdV-based expression system is identical to the cassette of the composition for delivery of the self-replicating alphavirus-based expression system.

Description

CROSS REFERENCE TO RELATED APPLICATIONS This application is continuation of International Application No. PCT/US2021/025828, filed Apr. 5, 2021, which claims the benefit of U.S. Provisional Application No. 63/005,160 filed Apr. 3, 2020, which is hereby incorporated in its entirety by reference for all purposes. SEQUENCE LISTING The instant application contains a Sequence Listing which has been submitted electronically and is hereby incorporated by reference in its entirety. The accompanying sequence listing .XML file name GSO-090WOC1, was created on Oct. 31, 2022, and is 381 kb in size. BACKGROUND One question for antigen vaccine design is which of the many coding mutations present generate the “best” therapeutic antigens, e.g., antigens that can elicit immunity. In addition to the challenges of current antigen prediction methods, certain challenges also exist with the available vector systems that can be used for antigen delivery in humans, many of which are derived from humans. For example, many humans have pre-existing immunity to human viruses as a result of previous natural exposure, and this immunity can be a major obstacle to the use of recombinant human viruses for antigen delivery for vaccination, such as infectious disease vaccines. SUMMARY Disclosed herein is a composition for delivery of a self-replicating alphavirus-based expression system, wherein the composition for delivery of the self-replicating alphavirus-based expression system comprises: (A) the self-replicating alphavirus-based expression system, wherein the self-replicating alphavirus-based expression system comprises one or more vectors, wherein the one or more vectors comprises: (a) an RNA alphavirus backbone, wherein the RNA alphavirus backbone comprises: (i) at least one promoter nucleotide sequence, and (ii) at least one polyadenylation (poly(A)) sequence; and (b) a cassette, wherein the cassette comprises: (i) at least one antigen-encoding nucleic acid sequence comprising: a. a. a nucleic acid sequence encoding an infectious disease organism peptide selected from the group consisting of: a pathogen-derived peptide, a virus-derived peptide, a bacteria-derived peptide, a fungus-derived peptide, and a parasite-derived peptide, b. optionally a 5′ linker sequence, and c. optionally a 3′ linker sequence; (ii) optionally, a second promoter nucleotide sequence operably linked to the at least one antigen-encoding nucleic acid sequence; and (iii) optionally, at least one second poly(A) sequence, wherein the second poly(A) sequence is a native poly(A) sequence or an exogenous poly(A) sequence to the alphavirus, and (B) a lipid-nanoparticle (LNP), wherein the LNP encapsulates the self-replicating alphavirus-based expression system. Also disclosed herein is a composition for delivery of a self-replicating alphavirus-based expression system, wherein the composition for delivery of the self-replicating alphavirus-based expression system comprises: (A) the self-replicating alphavirus-based expression system, wherein the self-replicating alphavirus-based expression system comprises one or more vectors, wherein the one or more vectors comprises: (a) an RNA alphavirus backbone, wherein the RNA alphavirus backbone comprises the nucleic acid sequence set forth in SEQ ID NO:6, wherein the RNA alphavirus backbone sequence comprises a 26S promoter nucleotide sequence and a poly(A) sequence, wherein the 26S promoter sequence is endogenous to the RNA alphavirus backbone, and wherein the poly(A) sequence is endogenous to the RNA alphavirus backbone; and (b) a cassette integrated between the 26S promoter nucleotide sequence and the poly(A) sequence, wherein the cassette is operably linked to the 26S promoter nucleotide sequence, and wherein the cassette comprises at least one antigen-encoding nucleic acid sequence comprising: a. a nucleic acid sequence encoding an infectious disease organism peptide selected from the group consisting of: a pathogen-derived peptide, a virus-derived peptide, a bacteria-derived peptide, a fungus-derived peptide, and a parasite-derived peptide b. optionally a 5′ linker sequence, and c. optionally a 3′ linker sequence; and (B) a lipid-nanoparticle (LNP), wherein the LNP encapsulates the self-replicating alphavirus-based expression system. In some aspects, the nucleic acid sequence encoding the peptide comprises an epitope-encoding nucleic acid sequence. In some aspects, the nucleic acid sequence encoding the peptide comprises two or more distinct epitope-encoding nucleic acid sequences. In some aspects, the nucleic acid sequence encoding the peptide comprises two or more distinct epitope-encoding nucleic acid sequences. In some aspects, the nucleic acid sequence encoding the peptide comprises between 1-10, between 1-20, between 1-30, between 1-40, between 1-50, between 1-100, between 1-200, between 1-300, between 1-400, or between 1-500 distinct epitope-encoding nucleic acid sequences distinct epitope-encoding nucleic acid sequ