Mycobacterium tuberculosis vaccines and methods of use thereof

Abstract

Described herein are Mycobacterium tuberculosis-derived sequences for use as immunogens and vaccine compositions.

Description

[0001] Attorney Docket No; 29539-0808WO1 / MGH 2024-658 MYCOBACTERIUM TUBERCULOSIS VACCINES AND METHODS OF USE THEREOF CLAIM OF PRIORITY This application claims the benefit of U.S. Provisional Patent Applications Serial Nos. 63 / 600,609, filed on November 17, 2023; 63 / 678,333, filed on August 1, 2024; and 63 / 693,081, filed on September 10, 2024. The entire contents of the foregoing are hereby incorporated by reference. STATEMENT AS TO FEDERALLY FUNDED RESEARCH This invention was made with government support under Grant No. A1022553 awarded by the National Institutes of Health. The government has certain rights in the invention. TECHNICAL FIELD Described herein are methods and compositions for inducing a protective immune response to tuberculosis (TB). BACKGROUND Tuberculosis is the leading cause of infectious disease death with an annual mortality of more than 1 million individuals a year1. Previous public health progress in improving Tuberculosis (TB) drug access and care was negatively impacted by the COVID-19 pandemic2. A transformative solution for TB would be a protective vaccine. Epidemiological models suggest that a 60% effective vaccine would make a major impact on the global disease pandemic; however, a TB vaccine for human use that achieves the target product profile needed to alter the trajectory of the pandemic has yet to be identified3,4. Studies of immune responses in TB demonstrate that T cell responses during Mtb infection are major determinants of TB disease outcomes5–10. Humans develop CD4+ and CD8+ T cell responses to Mtb antigens11-18. These human T cells can recognize Mtb-infected phagocytes and generate inflammatory responses associated with Mtb control19. Depletion of CD4+ and CD8+ T cells in mice and NHP demonstrate a causal role for T cells in control of TB disease5–7,20. The contribution of CD4+ and CD8+ T cells to protection from TB disease in animal models has led to research programs focused on identification of the relevant Mtb- Attorney Docket No; 29539-0808WO1 / MGH 2024-658 derived antigens recognized by T cells from infected animals and humans. In mice, several immunodominant antigens have been identified using peptide libraries; however, the antigenic complexity of Mtb (~4000 proteins) has prevented the study of the entirety of the Mtb peptidome for T cell responses in humans or animals. A comprehensive understanding of the Mtb antigens that are relevant for T cell immunity in diverse human populations is lacking. To harness T cell immunity in TB, the dynamics and complexity of antigen presentation that occur during infection must be understood to exploit those principles in TB vaccine development. A major challenge in harnessing T cell immunity is the diversity of MHC proteins which present pathogen-derived peptides on the surface of Mtb-infected cells21–26. Humans express diverse MHC-I and MHC-II alleles. Distinct MHC alleles have unique biochemical preferences for the peptides that can bind these alleles27,28. Consequently, vaccines that seek to elicit T cell immunity across diverse populations must address this combinatorial complexity. Conventional animal models do not express human MHC alleles. Given the structure- function relationship between MHC proteins and the peptides they present, animal studies may only recapitulate a fraction of the responses relevant for human immunity27. Another major challenge in harnessing T cells effectively for TB vaccines is that only a small fraction of peptides expressed by the pathogen are presented on MHC by infected cells, and it is difficult to predict these peptides a priori using in vitro binding assays or computational tools for antigen prediction29,30. A study of vaccine-induced CD8+ T cells revealed that vaccine induced T cells are capable of recognizing peptides derived from the vaccine antigen; however, these T cells were incapable of recognizing Mtb-infected cells31. These data suggest a gap in our understanding of how to translate antigen identification knowledge into vaccines that generate pMHC complexes capable of eliciting T cells that recognize Mtb- infected cells. SUMMARY A sensitive method for analysis of presentation of Mtb- derived peptides on diverse human MHC-I alleles was utilized to identify antigens that are presented on Mtb-infected cells, how human MHC diversity influences antigen presentation, and how TB vaccines can be Attorney Docket No; 29539-0808WO1 / MGH 2024-658 engineered to generate pMHC complexes containing Mtb-derived peptides identical to those generated during Mtb infection. Antigens meeting these criteria enable greatly improved vaccine development. Provided herein are vectors comprising a multi-epitope immunogen, wherein the vectors comprise a nucleotide sequence or sequences encoding: i) four or more MHC Class I epitopes, wherein the four or more MHC Class I epitopes are selected from SEAYQGVQQKW (SEQ ID NO:53), LQNLARTI (SEQ ID NO:54), NHVNFFQEL (SEQ ID NO:55), RMWASAQNI (SEQ ID NO:56), HQAIVRDV (SEQ ID NO:57), KLADFGLVRA (SEQ ID NO:58), LLDEGKQSL (SEQ ID NO:59), AAWGGSGSEAY (SEQ ID NO:60), QEQASQQIL (SEQ ID NO:61), QTVEDEARRMW (SEQ ID NO:62), VYLTAHNAL (SEQ ID NO:63), EAVQDVARTY (SEQ ID NO:64), AEILRGVSA (SEQ ID NO:65), EVHSAMLNY (SEQ ID NO:66), IHDQFVATL (SEQ ID NO:67), NASPVAQSY (SEQ ID NO:68), VPLEGGGRL (SEQ ID NO:69), TQHDAADALF (SEQ ID NO:70), LPFEDAPLI (SEQ ID NO:71), ELDEISTNIRQAGVQY (SEQ ID NO:72), QAIVRDVL (SEQ ID NO:73), KQKQELDEI (SEQ ID NO:74), GELRSLGATL (SEQ ID NO:75), TLRVVPESL (SEQ ID NO:76), MEDLVRAY (SEQ ID NO:77), QEAGNFERI (SEQ ID NO:78), AEHQAIVRDVL (SEQ ID NO:79), AEMKTDAATL (SEQ ID NO:80), RFMTDPHAMR (SEQ ID NO:81), SLLDEGKQSLTKL (SEQ ID NO:82), AVVRFQEAANK (SEQ ID NO:83), KIYSEADEAWRK (SEQ ID NO:84), EMKTDAATL (SEQ ID NO:85), and LLDAHIPQL (SEQ ID NO:86), and combinations thereof, or epitopes having at least 65% to about 99% homology to MHC Class I epitopes selected from SEAYQGVQQKW (SEQ ID NO:53), LQNLARTI (SEQ ID NO:54), NHVNFFQEL (SEQ ID NO:55), RMWASAQNI (SEQ ID NO:56), HQAIVRDV (SEQ ID NO:57), KLADFGLVRA (SEQ ID NO:58), LLDEGKQSL (SEQ ID NO:59), AAWGGSGSEAY (SEQ ID NO:60), QEQASQQIL (SEQ ID NO:61), QTVEDEARRMW (SEQ ID NO:62), VYLTAHNAL (SEQ ID NO:63), EAVQDVARTY (SEQ ID NO:64), AEILRGVSA (SEQ ID NO:65), EVHSAMLNY (SEQ ID NO:66), IHDQFVATL (SEQ ID NO:67), NASPVAQSY (SEQ ID NO:68), VPLEGGGRL (SEQ ID NO:69), TQHDAADALF (SEQ ID NO:70), LPFEDAPLI (SEQ ID NO:71), ELDEISTNIRQAGVQY (SEQ ID NO:72), QAIVRDVL (SEQ ID NO:73), KQKQELDEI (SEQ ID NO:74), GELRSLGATL (SEQ ID NO:75), TLRVVPESL (SEQ ID NO:76), MEDLVRAY (SEQ ID NO:77), Attorney Docket No; 29539-0808WO1 / MGH 2024-658 QEAGNFERI (SEQ ID NO:78), AEHQAIVRDVL (SEQ ID NO:79), AEMKTDAATL (SEQ ID NO:80), RFMTDPHAMR (SEQ ID NO:81), SLLDEGKQSLTKL (SEQ ID NO:82), AVVRFQEAANK (SEQ ID NO:83), KIYSEADEAWRK (SEQ ID NO:84), EMKTDAATL (SEQ ID NO:85), and LLDAHIPQL (SEQ ID NO:86), and combinations thereof, and ii) two or more MHC Class II epitopes, wherein the two or more MHC Class II epitopes are selected from AEMKTDAATL (SEQ ID NO:80), RADEEQQQAL (SEQ ID NO:81), ISTNIRQAGVQYSRADEE (SEQ ID NO:82), AAVVRFQEAANKQK, AAVVRFQEAANKQKQ (SEQ ID NO:83), GAAGTAAQAAVVR (SEQ ID NO:84), LQGQWRGAAGTAAQAA (SEQ ID NO:85), SLQGQWRGAAGTAAQAA (SEQ ID NO:86), QGQWRGAAGTAAQA (SEQ ID NO:87), ESSAAFQAAHARFVAAA (SEQ ID NO:88), GESSAAFQAAHARFVAAA (SEQ ID NO:89), SAAFQAAHARFVAAA (SEQ ID NO:90), SSAAFQAAHARFVAAA (SEQ ID NO:91), AAGTYVAADAAAAST (SEQ ID NO:92), VGPQVVNINTKLGYNNA (SEQ ID NO:93), VQVAATEVRR (SEQ ID NO:94), SQRVDPSAASGQDSTEARPA (SEQ ID NO:95), PSAASGQDSTEARPA (SEQ ID NO:96), AIPAYEPEPGKPAPA (SEQ ID NO:97), SGASYAARDALAAASY (SEQ ID NO:98), GHDEESPGAQSLT (SEQ ID NO:99), THAATYQTASAKAAVIHE (SEQ ID NO:100), SGPKVVIDGKDQNVTG (SEQ ID NO:101), DVVDDPAFVLHGNHPVR (SEQ ID NO:102), DAGGTYQPHPAEAVVEK (SEQ ID NO:103), DAGGTYQPHPAEAVVE (SEQ ID NO:104), RQPEPEVDTA (SEQ ID NO:105), LPPPVVAANRIQL (SEQ ID NO:106), PEAVIVSTARSPIG (SEQ ID NO:107), ASAAVEALTARLAAAH (SEQ ID NO:108), IGTTMNAQNAAAAAPT (SEQ ID NO:109), and GTTMNAQNAAAAAPT (SEQ ID NO:110), and combinations thereof, or epitopes having at least 65% to about 99% homology to MHC Class II epitopes selected from AEMKTDAATL (SEQ ID NO:80), RADEEQQQAL (SEQ ID NO:81), ISTNIRQAGVQYSRADEE (SEQ ID NO:82), AAVVRFQEAANKQK, AAVVRFQEAANKQKQ (SEQ ID NO:83), GAAGTAAQAAVVR (SEQ ID NO:84), LQGQWRGAAGTAAQAA (SEQ ID NO:85), SLQGQWRGAAGTAAQAA (SEQ ID NO:86), QGQWRGAAGTAAQA (SEQ ID NO:87), ESSAAFQAAHARFVAAA (SEQ ID NO:88), GESSAAFQAAHARFVAAA (SEQ ID NO:89), SAAFQAAHARFVAAA (SEQ ID NO:90), SSAAFQAAHARFVAAA (SEQ ID NO:91), AAGTYVAADAAAAST (SEQ ID NO:92), VGPQVVNINTKLGYNNA (SEQ ID Attorney Docket No; 29539-0808WO1 / MGH 2024-658 NO:93), VQVAATEVRR (SEQ ID NO:94), SQRVDPSAASGQDSTEARPA (SEQ ID NO:95), PSAASGQDSTEARPA (SEQ ID NO:96), AIPAYEPEPGKPAPA (SEQ ID NO:97), SGASYAARDALAAASY (SEQ ID NO:98), GHDEESPGAQSLT (SEQ ID NO:99), THAATYQTASAKAAVIHE (SEQ ID NO:100), SGPKVVIDGKDQNVTG (SEQ ID NO:101), DVVDDPAFVLHGNHPVR (SEQ ID NO:102), DAGGTYQPHPAEAVVEK (SEQ ID NO:103), DAGGTYQPHPAEAVVE (SEQ ID NO:104), RQPEPEVDTA (SEQ ID NO:105), LPPPVVAANRIQL (SEQ ID NO:106), PEAVIVSTARSPIG (SEQ ID NO:107), ASAAVEALTARLAAAH (SEQ ID NO:108), IGTTMNAQNAAAAAPT (SEQ ID NO:109), and GTTMNAQNAAAAAPT (SEQ ID NO:110), and combinations thereof. As an alternative to nucleic acids, the epitopes can be provided in a composition as peptides or proteins, and can be delivered to a subject as peptides or proteins. In some embodiments, the epitopes comprise sequences of at least 8, e.g., at last 9, 10, or 11 consecutive amino acids from MHC Class I epitope sequences set forth herein (e.g., as listed above), or at least 12, e.g., at least 13, 14, 15, 16, 17, 18, 19, or 20 consecutive amino acids from MHC Class II epitope sequences set forth herein (e.g., as listed above), optionally with 1, 2, or 3 additional amino acids from the full length protein sequence (e.g., as shown in Table 1 or 2) on each end. In some embodiments, the four or more MHC Class I epitopes are selected from LQNLARTI (SEQ ID NO:54), NHVNFFQEL (SEQ ID NO:55), RMWASAQNI (SEQ ID NO:56), HQAIVRDV (SEQ ID NO:57), KLADFGLVRA (SEQ ID NO:58), QAIVRDVL (SEQ ID NO:73), KQKQELDEI (SEQ ID NO:74), GELRSLGATL (SEQ ID NO:75), TLRVVPESL (SEQ ID NO:76), MEDLVRAY (SEQ ID NO:77), and LLDAHIPQL (SEQ ID NO:86), and combinations thereof, or epitopes having at least 65% to about 99% homology to MHC Class I epitopes selected from, LQNLARTI (SEQ ID NO:54), NHVNFFQEL (SEQ ID NO:55), RMWASAQNI (SEQ ID NO:56), HQAIVRDV (SEQ ID NO:57), KLADFGLVRA (SEQ ID NO:58), QAIVRDVL (SEQ ID NO:73), KQKQELDEI (SEQ ID NO:74), GELRSLGATL (SEQ ID NO:75), TLRVVPESL (SEQ ID NO:76), MEDLVRAY (SEQ ID NO:77), and LLDAHIPQL (SEQ ID NO:86), and combinations thereof. In some embodiments, the two or more MHC Class II epitopes are SLQGQWRGAAGTAAQAA (SEQ ID NO:86) and LQGQWRGAAGTAAQAA (SEQ ID Attorney Docket No; 29539-0808WO1 / MGH 2024-658 NO:85)or epitopes having at least 65% to about 99% homology to SLQGQWRGAAGTAAQAA (SEQ ID NO:86) and LQGQWRGAAGTAAQAA (SEQ ID NO:85). In some embodiments, the vector further comprises a compartment targeting signal peptide selected from mitochondrial import receptor subunit TOM20 homolog (TOM20), Human immunoglobulin (Ig) light chain, lysosome associated membrane protein 1 (LAMP1), LAMP2, LAMP3, MHC-I trafficking domain (MITD), and nuclear export signal (NES). In some embodiments, e.g., for lamp proteins, the signal sequence is present on the N terminus and a transmembrane domain (e.g., as listed in Table 4) is present on the C terminus. In some embodiments, two or more of the epitopes in the vector are separated by non- immunogenic linkers (GGS) or a self-cleaving P2A peptide sequence. In some embodiments, the nucleotide sequence of the vector comprises an RNA sequence. In some embodiments, the nucleotide sequence of the vector comprises a DNA sequence. In some embodiments, the vector is an RNA vector. In some embodiments, the RNA vector is replicon RNA or self-amplifying RNA. In some embodiments, the vector is a DNA vector. In some embodiments, the DNA vector is a replication-deficient adenoviral vector selected from the group consisting of human adenovirus, rhesus adenovirus, simian adenovirus and gorilla adenovirus viral vectors. Also provided herein are vectors comprising a multi-epitope immunogen, wherein the vectors comprise a nucleotide sequence encoding at least one MHC Class I (Table 1) or MHC Class II (Table 2) heterodimeric pair, or combinations thereof, or nucleotide sequences having at least 65% to about 99% homology to at least one MHC Class I (Table 1) or MHC Class II (Table 2) heterodimeric pair, wherein the MHC Class I heterodimeric pairs are selected from: i) EsxA (MTEQQWNFAGIEAAASAIQGNVTSIHSLLDEGKQSLTKLAAAWGGSGSEAYQGVQQK WDATATELNNALQNLARTISEAGQAMASTEGNVTGMFA, SEQ ID NO:1) and EsxB (MAEMKTDAATLAQEAGNFERISGDLKTQIDQVESTAGSLQGQWRGAAGTAAQAAVVR FQEAANKQKQELDEISTNIRQAGVQYSRADEEQQQALSSQMGF, SEQ ID NO:2) Attorney Docket No; 29539-0808WO1 / MGH 2024-658 ii) EsxG (MSLLDAHIPQLVASQSAFAAKAGLMRHTIGQAEQAAMSAQAFHQGESSAAFQAAHARF VAAAAKVNTLLDVAQANLGEAAGTYVAADAAAASTYTGF, SEQ ID NO:3) and EsxH (MSQIMYNPAMLGHAGDMAGYAGTLQSLGAEIAVEQAALQSAWQGDTGITYQAWQAQ WNQAMEDLVRAYHAMSSTHEANTMAMMARDTAEAAKWGG, SEQ ID NO:9) iii) PE35 (MEKMSHDPIAADIGTQVSDNALHGVTAGSTALTSVTGLVPAGADEVSAQAATAFTSEGI QLLASNASAQDQLHRAGEAVQDVARTYSQIDDGAAGVFAE, SEQ ID NO:10) and PPE68 (MLWHAMPPELNTARLMAGAGPAPMLAAAAGWQTLSAALDAQAVELTARLNSLGEA WTGGGSDKALAAATPMVVWLQTASTQAKTRAMQATAQAAAYTQAMATTPSLPEIAAN HITQAVLTATNFFGINTIPIALTEMDYFIRMWNQAALAMEVYQAETAVNTLFEKLEPMAS ILDPGASQSTTNPIFGMPSPGSSTPVGQLPPAATQTLGQLGEMSGPMQQLTQPLQQVTSLF SQVGGTGGGNPADEEAAQMGLLGTSPLSNHPLAGGSGPSAGAGLLRAESLPGAGGSLTR TPLMSQLIEKPVAPSVMPAAAAGSSATGGAAPVGAGAMGQGAQSGGSTRPGLVAPAPL AQEREEDDEDDWDEEDDW, SEQ ID NO:25) iv) PPE20 (MTEPWIAFPPEVHSAMLNYGAGVGPMLISATQNGELSAQYAEAASEVEELLGVVASEG WQGQAAEAFVAAYMPFLAWLIQASADCVEMAAQQHVVIEAYTAAVELMPTQVELAAN QIKLAVLVATNFFGINTIPIAINEAEYVEMWVRAATTMATYSTVSRSALSAMPHTSPPPLI LKSDELLPDTGEDSDEDGHNHGGHSHGGHARMIDNFFAEILRGVSAGRIVWDPVNGTLN GLDYDDYVYPGHAIWWLARGLEFFQDGEQFGELLFTNPTGAFQFLLYVVVVDLPTHIAQ IATWLGQYPQLLSAALTGVIAHLGAITGLAGLSGLSAIPSAAIPAVVPELTPVAAAPPMLA VAGVGPAVAAPGMLPASAPAPAAAAGATAAGPTPPATGFGGFPPYLVGGGGPGIGFGSG QSAHAKAAASDSAAAESAAQASARAQARAARRGRSAAKARGHRDEFVTMDMGFDAA APAPEHQPGARASDCGAGPIGFAGTVRKEAVVKAAGLTTLAGDDFGGGPTMPMMPGT WTHDQGVFDEHR, SEQ ID NO:11) and PE15 (VTLRVVPESLAGASAAIEAVTARLAAAHAAAAPFIAAVIPPGSDSVSVCNAVEFSVHGS QHVAMAAQGVEELGRSGVGVAESGASYAARDALAAASYLSGGL, SEQ ID NO:23) Attorney Docket No; 29539-0808WO1 / MGH 2024-658 v) PPE51 (MDFALLPPEVNSARMYTGPGAGSLLAAAGGWDSLAAELATTAEAYGSVLSGLAALHW RGPAAESMAVTAAPYIGWLYTTAEKTQQTAIQARAAALAFEQAYAMTLPPPVVAANRI QLLALIATNFFGQNTAAIAATEAQYAEMWAQDAAAMYGYATASAAAALLTPFSPPRQT TNPAGLTAQAAAVSQATDPLSLLIETVTQALQALTIPSFIPEDFTFLDAIFAGYATVGVTQ DVESFVAGTIGAESNLGLLNVGDENPAEVTPGDFGIGELVSATSPGGGVSASGAGGAASV GNTVLASVGRANSIGQLSVPPSWAAPSTRPVSALSPAGLTTLPGTDVAEHGMPGVPGVP VAAGRASGVLPRYGVRLTVMAHPPAAG, SEQ ID NO:15) and PE19 (MSFVTTQPEALAAAAANLQGIGTTMNAQNAAAAAPTTGVVPAAADEVSALTAAQFAA HAQMYQTVSAQAAAIHEMFVNTLVASSGSYAATEAANAAAAG, SEQ ID NO:27) vi) PPE60 (VVDFGALPPEINSARMYAGPGSASLVAAAKMWDSVASDLFSAASAFQSVVWGLTVGS WIGSSAGLMAAAASPYVAWMSVTAGQAQLTAAQVRVAAAAYETAYRLTVPPPVIAEN RTELMTLTATNLLGQNTPAIEANQAAYSQMWGQDAEAMYGYAATAATATEALLPFED APLITNPGGLLEQAVAVEEAIDTAAANQLMNNVPQALQQLAQPAQGVVPSSKLGGLWT AVSPHLSPLSNVSSIANNHMSMMGTGVSMTNTLHSMLKGLAPAAAQAVETAAENGVW AMSSLGSQLGSSLGSSGLGAGVAANLGRAASVGSLSVPPAWAAANQAVTPAARALPLT SLTSAAQTAPGHMLGGLPLGHSVNAGSGINNALRVPARAYAIPRTPAAG, SEQ ID NO:16) and PE31 (VSFTAQPEMLAAAAGELRSLGATLKASNAAAAVPTTGVVPPAADEVSLLLATQFRTHA ATYQTASAKAAVIHEQFVTTLATSASSYADTEAANAVVTG, SEQ ID NO:24) vii) PE13 (VSFVMAYPEMLAAAADTLQSIGATTVASNAAAAAPTTGVVPPAADEVSALTAAHFAA HAAMYQSVSARAAAIHDQFVATLASSASSYAATEVANAAAAS, SEQ ID NO:18) and PPE18 (MVDFGALPPEINSARMYAGPGSASLVAAAQMWDSVASDLFSAASAFQSVVWGLTVGS WIGSSAGLMVAAASPYVAWMSVTAGQAELTAAQVRVAAAAYETAYGLTVPPPVIAEN RAELMILIATNLLGQNTPAIAVNEAEYGEMWAQDAAAMFGYAAATATATATLLPFEEA PEMTSAGGLLEQAAAVEEASDTAAANQLMNNVPQALQQLAQPTQGTTPSSKLGGLWKT VSPHRSPISNMVSMANNHMSMTNSGVSMTNTLSSMLKGFAPAAAAQAVQTAAQNGVR Attorney Docket No; 29539-0808WO1 / MGH 2024-658 AMSSLGSSLGSSGLGGGVAANLGRAASVGSLSVPQAWAAANQAVTPAARALPLTSLTS AAERGPGQMLGGLPVGQMGARAGGGLSGVLRVPPRPYVMPHSPAAG, SEQ ID NO:26); and wherein MHC Class II heterodimeric pairs are selected from: i) PE15 (VTLRVVPESLAGASAAIEAVTARLAAAHAAAAPFIAAVIPPGSDSVSVCNAVEFSVHGS QHVAMAAQGVEELGRSGVGVAESGASYAARDALAAASYLSGGL, SEQ ID NO:23) and PPE20 (MTEPWIAFPPEVHSAMLNYGAGVGPMLISATQNGELSAQYAEAASEVEELLGVVASEG WQGQAAEAFVAAYMPFLAWLIQASADCVEMAAQQHVVIEAYTAAVELMPTQVELAAN QIKLAVLVATNFFGINTIPIAINEAEYVEMWVRAATTMATYSTVSRSALSAMPHTSPPPLI LKSDELLPDTGEDSDEDGHNHGGHSHGGHARMIDNFFAEILRGVSAGRIVWDPVNGTLN GLDYDDYVYPGHAIWWLARGLEFFQDGEQFGELLFTNPTGAFQFLLYVVVVDLPTHIAQ IATWLGQYPQLLSAALTGVIAHLGAITGLAGLSGLSAIPSAAIPAVVPELTPVAAAPPMLA VAGVGPAVAAPGMLPASAPAPAAAAGATAAGPTPPATGFGGFPPYLVGGGGPGIGFGSG QSAHAKAAASDSAAAESAAQASARAQARAARRGRSAAKARGHRDEFVTMDMGFDAA APAPEHQPGARASDCGAGPIGFAGTVRKEAVVKAAGLTTLAGDDFGGGPTMPMMPGT WTHDQGVFDEHR, SEQ ID NO:11) ii) PE31 (VSFTAQPEMLAAAAGELRSLGATLKASNAAAAVPTTGVVPPAADEVSLLLATQFRTHA ATYQTASAKAAVIHEQFVTTLATSASSYADTEAANAVVTG, SEQ ID NO:24) and PPE60 (VVDFGALPPEINSARMYAGPGSASLVAAAKMWDSVASDLFSAASAFQSVVWGLTVGS WIGSSAGLMAAAASPYVAWMSVTAGQAQLTAAQVRVAAAAYETAYRLTVPPPVIAEN RTELMTLTATNLLGQNTPAIEANQAAYSQMWGQDAEAMYGYAATAATATEALLPFED APLITNPGGLLEQAVAVEEAIDTAAANQLMNNVPQALQQLAQPAQGVVPSSKLGGLWT AVSPHLSPLSNVSSIANNHMSMMGTGVSMTNTLHSMLKGLAPAAAQAVETAAENGVW AMSSLGSQLGSSLGSSGLGAGVAANLGRAASVGSLSVPPAWAAANQAVTPAARALPLT SLTSAAQTAPGHMLGGLPLGHSVNAGSGINNALRVPARAYAIPRTPAAG, SEQ ID NO:16) iii) PPE51 (MDFALLPPEVNSARMYTGPGAGSLLAAAGGWDSLAAELATTAEAYGSVLSGLAALHW RGPAAESMAVTAAPYIGWLYTTAEKTQQTAIQARAAALAFEQAYAMTLPPPVVAANRI QLLALIATNFFGQNTAAIAATEAQYAEMWAQDAAAMYGYATASAAAALLTPFSPPRQT Attorney Docket No; 29539-0808WO1 / MGH 2024-658 TNPAGLTAQAAAVSQATDPLSLLIETVTQALQALTIPSFIPEDFTFLDAIFAGYATVGVTQ DVESFVAGTIGAESNLGLLNVGDENPAEVTPGDFGIGELVSATSPGGGVSASGAGGAASV GNTVLASVGRANSIGQLSVPPSWAAPSTRPVSALSPAGLTTLPGTDVAEHGMPGVPGVP VAAGRASGVLPRYGVRLTVMAHPPAAG, SEQ ID NO:15) and PE19 (MSFVTTQPEALAAAAANLQGIGTTMNAQNAAAAAPTTGVVPAAADEVSALTAAQFAA HAQMYQTVSAQAAAIHEMFVNTLVASSGSYAATEAANAAAAG, SEQ ID NO:27) iv) PE5 (MTLRVVPEGLAAASAAVEALTARLAAAHASAAPVITAVVPPAADPVSLQTAAGFSAQG VEHAVVTAEGVEELGRAGVGVGESGASYLAGDAAAAATYGVVGG, SEQ ID NO:38) and PPE4 (MAAPIWMASPPEVHSALLSNGPGPGSLVAAATAWSQLSAEYASTAAELSGLLGAVPGW AWQGPSAEWYVAAHLPYVAWLTQASADAAGAAAQHEAAAAAYTTALAAMPTLAELA ANHVIHTVLVATNFFGINTIPITLNEADYVRMWLQAAAVMGLYQAASGAALASAPRTVP APTVMNPGGGAASTVGAVNPWQWLLALLQQLWNAYTGFYGWMLQLIWQFLQDPIGN SIKIIIAFLTNPIQALITYGPLLFALGYQIFFNLVGWPTWGMILSSPFLLPAGLGLGLAAIAFL PIVLAPAVIPPASTPLAAAAVAAGSVWPAVSMAVTGAGTAGAATPAAGAAPSAGAAPAP AAPATASFAYAVGGSGDWGPSLGPTVGGRGGIKAPAATVPAAAAAAATRGQSRARRRR RSELRDYGDEFLDMDSDSGFGPSTGDHGAQASERGAGTLGFAGTATKERRVRAVGLTA LAGDEFGNGPRMPMVPGTWEQGSNEPEAPDGSGRGGGDGLPHDSK, SEQ ID NO:40) v) PE29 (VTLRVVPEGLAAASAAVEALTARLAAAHAGAAPAITAVVAPAADPVSLQSAVGFSALG SEHAAIAGEGVEELGRSGVAVGESGIGYAAGDAVAAATYLVSGGSL, SEQ ID NO:39) and PPE48 (VTAPVWLASPPEVHSALLSAGPGPGSLQAAAAGWSALSAEYAAVAQELSVVVAAVG AGVWQGPSAELFVAAYVPYVAWLVQ, SEQ ID NO:41). In some embodiments, the vector further comprises a compartment targeting signal peptide selected from TOM20, Human Ig Light Chain, LAMP1, LAMP2, LAMP3, MITD, and NES. In some embodiments, e.g., for LAMP1 / 2 / 3 targeting to the lysosome, the signal sequence Attorney Docket No; 29539-0808WO1 / MGH 2024-658 is present on the N terminus and a transmembrane domain (e.g., as listed in Table 4) is present on the C terminus. In some embodiments, two or more of the heterodimers in the vector are separated by non-immunogenic linkers (GGS) or a self-cleaving P2A peptide sequence. In some embodiments, the nucleotide sequence of the vector comprises an RNA sequence. In some embodiments, the nucleotide sequence of the vector comprises a DNA sequence. In some embodiments, the vector is an RNA vector. In some embodiments, the RNA vector is replicon RNA or self-amplifying RNA. In some embodiments, the vector is a DNA vector. In some embodiments, the DNA vector is a replication-deficient adenoviral vector selected from the group consisting of human adenovirus, rhesus adenovirus, simian adenovirus, and gorilla adenovirus viral vectors. As an alternative to nucleic acids, the multi-epitope immunogens can be provided in a composition as recombinant proteins, and can be delivered to a subject as recombinant proteins, optionally comprising the compartment targeting signal peptide. In some embodiments, e.g., for LAMP1 / 2 / 3 targeting to the lysosome, a LAMP1 / 2 / 3 signal sequence (e.g., as listed in Table 3) is present on the N terminus and a LAMP1 / 2 / 3 transmembrane domain (e.g., as listed in Table 4) is present on the C terminus. Also provided herein are vectors and compositions as described herein for use in a method of preventing or treating a Mycobacterium tuberculosis infection in a subject, said method comprising administering the vector to the subject. BRIEF DESCRIPTION OF THE DRAWINGS The following Detailed Description, given by way of example, but not intended to limit the invention to specific embodiments described, may be understood in conjunction with the accompanying figures, incorporated herein by reference. FIG.1 depicts a workflow for identifying Mtb-derived peptides on MHC. Macrophages or dendritic cells are infected with Mtb for varying periods of time. After the appropriate experimental time, cells are lysed and an MHC-I or MHC-II immunoprecipitation (IP) is performed. Peptides are isolated and then analyzed by mass spectrometry. Attorney Docket No; 29539-0808WO1 / MGH 2024-658 FIG.2 depicts SureQuant analysis of Mtb-derived peptide presentation on MHC-I or MHC-II. pMHC standards (hipMHCs) are spiked into lysates prior to IP. MHC IPs are performed, and then peptides are eluted. After elution, peptides are isolated and then heavy- isotope coded peptide standards (identical sequences to those Mtb peptides of interest) are added in. Targeted mass spectrometry is conducted to track the heavy-isotope standards, the endogenous biological peptide, and the peptides from the hipMHCs. hipMHC- derived peptides are used to normalize across experimental conditions. FIGs.3A-B show that the presentation of Mtb-derived peptides on MHC-I is TAP- dependent. (A) In the cytosolic pathway of MHC-I presentation, antigens gain access to the cytosol, are digested and then peptides from those antigens are transported into the ER where they bind MHC-I. (B) SureQuant analysis of presentation of an EsxA-derived peptide in THP-1 MF with or without TAP. ****, p<0.0001. FIGs.4A-B depict SureQuant analysis of EsxA-derived peptides on HLA- A*02:01. The presentation of (A) EsxA- and (B) EsxG-derived peptides on MHC-I was compared in mock or Mtb-infected cells. The synthetic standards were successfully detected across all four conditions (bottom row) was successfully detected, but only one EsxA- and one EsxG-derived peptide was detected in the endogenous peptide pool in Mtb-infected cells. Shown are extracted ion chromatograms for multiple fragment ions from these peptides. FIG.5 depicts sequences, source proteins, associated HLA alleles, and donors for each validated Mtb-derived MHC-I peptide. White squares indicate that the peptide was not detected in the donor and black squares indicated that the peptide was detected in the donor. FIG.6 depicts sequences, source proteins, and donors for each validated Mtb-derived MHC-II peptide. White squares indicate that the peptide was not detected in the donor and black squares indicated that the peptide was detected in the donor. FIG.7 depicts mass spectrometry analysis of an EsxB-derived peptide presented on MHC-II in Mtb-infected human monocyte-derived dendritic cells. FIG.8 depicts activation of an EsxJ-specific T cell clone following mRNA vaccine delivery. FIGs.9A-C show SureQuant experiments to track mRNA-encoded Mtb antigens on MHC-II. The light peptide is the endogenous peptide and the heavy peptide is the internal standard peptide used for normalization across experiments. All the peptides being tracked using Attorney Docket No; 29539-0808WO1 / MGH 2024-658 SureQuant were detected as presented on MHC-II by Mtb-infected macrophages. In (A), an EsxG-derived peptide is tracked, in (B) an EsxB-derived peptide and in (C) another ExG-derived peptide. FIG.10 depicts codelivery of EsxA with EsxB and presentation on MHC-II (extracted ion chromatogram (left) quantifying endogenous peptide (light) and isotopic standard (heavy)) and quantification of results on the right. FIGs.11A-C. Mtb-infected hMDCs present peptides derived from T7SS substrates on MHC-I. A) Schematic representation of the Mtb dendritic cell infection model. hMDCs were allowed to phagocytose Mtb at an MOI of 2.5 for 4 hours, and 72 hours later MHC-I peptides were isolated for MS analysis. B) The proportion of Mtb-derived peptides in each initial DDA analysis and follow-up PRM analysis for each of n = 3 donors. C) Mtb peptide sequences detected in DDA analyses, PRM analyses, or both in the PathMHC workflow (right) and their source proteins (left) for each of three donors. Lowercase m = oxidized methionine. * indicates peptides previously reported to be immunogenic in humans with prior Mtb exposure in IEDB.28• indicates source proteins for which epitopes that are immunogenic in human with prior Mtb exposure have previously been reported in IEDB.28FIG.12 depicts sequences, source proteins, and donors for each validated Mtb-derived MHC-I peptide using the PathMHC approach. White squares indicate that the peptide was not detected in the donor and black squares indicated that the peptide was detected in the donor. DETAILED DESCRIPTION DEFINITIONS: All scientific and technical terms used in this application have meanings commonly used in the art unless otherwise specified. The definitions provided herein are to facilitate understanding of certain terms used frequently herein and are not meant to limit the scope of the application. The articles "a" and "an" are used herein to refer to one or to more than one (i.e.,to at least one) of the grammatical object of the article. By way of example, "an element" means one element or more than one element. The terms "comprise," "comprising," "include," "including," "have," and "having" are used in the inclusive, open sense, meaning that additional elements may Attorney Docket No; 29539-0808WO1 / MGH 2024-658 be included. The terms "such as", "e.g.", as used herein are non-limiting and are for illustrative purposes only. "Including" and "including but not limited to" are used interchangeably. The term "or" as used herein should be understood to mean "and / or", unless the context clearly indicates otherwise. As used herein, the term "about" or "approximately" (unless otherwise defined) refers to a quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length that varies by plus or minus 15% to a reference quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length. Ranges provided herein are understood to be shorthand for all of the values within the range. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting of 1, 2, 3, 4, 5, 6, 7, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 (as well as fractions thereof unless the context clearly dictates otherwise). As used herein, an “immunogen” is an amino acid sequence comprising an epitope, or multiple epitopes, that elicits a T cell response. Immunogens can be used to form a therapeutic composition, such as a vaccine to treat or prevent Tuberculosis. The term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. Preferred vectors are those capable of one or more of, autonomous replication and expression of nucleic acids to which they are linked. Vectors capable of directing the expression of genes to which they are operatively linked are referred to herein as "expression vectors". Vectors described herein comprise amino acid sequences that are translated into immunogens. Accordingly, a nucleic acid such as DNA, RNA, e.g., mRNA, may encode the immunogen. Accordingly, a transcribable nucleic acid sequence or a transcript thereof may contain an open reading frame (ORF) encoding the immunogen. As used herein, a vector can be viral or non-viral, or can comprise DNA or RNA (e.g., mRNA) encoding the immunogens. As used herein, “polynucleotides” or “nucleic acids” refer to a polymer of nucleotides (nucleotide monomers). Thus, nucleic acids are also referred to as polynucleotides. Nucleic acids may be or may include, for example, deoxyribonucleic acids (DNAs), ribonucleic acids (RNAs), threose nucleic acids (TNAs), glycol nucleic acids (GNAs), peptide nucleic acids (PNAs), locked Attorney Docket No; 29539-0808WO1 / MGH 2024-658 nucleic acids (LNAs, including LNA having a beta-D-ribo configuration, alpha-LNA having an alpha-L-ribo configuration (a diastereomer of LNA), 2'-amino-LNA having a 2'-amino functionalization, and 2'-amino-alpha-LNA having a 2'-amino functionalization), ethylene nucleic acids, cyclohexenyl nucleic acids and / or chimeras and / or combinations thereof. According to the invention, the term “nucleic acid encoding an amino acid sequence” means that the nucleic acid, if present in the appropriate environment, preferably within a cell, can direct the assembly of amino acids to produce the peptide, protein, epitope and / or immunogen during the process of translation. As used herein, “messenger RNA” or “mRNA” is any RNA that encodes a (at least one) protein (e.g., a polypeptide as described herein) and can be translated to produce the encoded protein in vitro, in vivo, in situ, or ex vivo. The skilled artisan will appreciate that, except where otherwise noted, nucleic acid sequences set forth in the instant application may recite "T"s in a representative DNA sequence but where the sequence represents RNA (e.g., mRNA), the "T"s would be substituted for "U"s. Thus, any of the DNAs disclosed and identified by a particular sequence identification number herein also disclose the corresponding RNA (e.g., mRNA) sequence complementary to the DNA, where each "T" of the DNA sequence is substituted with "U." As used herein, an “open reading frame” or “ORF” is a continuous stretch of DNA or RNA beginning with a start codon (e.g., methionine (ATG or AUG)) and ending with a stop codon (e.g., TAA, TAG or TGA, or UAA, UAG or UGA). An ORF typically encodes a protein. It will be understood that the sequences disclosed herein may further include additional elements, e.g., 5' and 3' UTRs, but that those elements, unlike the ORF, need not necessarily be present in an RNA polynucleotide disclosed herein. The term "variant" refers to a single or a grouping of sequences (e.g., in an amino acid sequence) that have undergone changes as referenced against a particular species or sub- populations within a particular species due to mutations, recombination / crossover or genetic drift. Examples of types of variants include, but are not limited to: single nucleotide polymorphisms (SNPs), copy number variations (CNVs), insertions / deletions (indels), single nucleotide variant (SNVs), multiple nucleotide variants (MNVs), inversions, etc. Variants may have homology to native (unmutated) amino acid sequences, including about 65% to about 99% homology to the amino acid sequence, about 75% to about 99% homology to the amino acid Attorney Docket No; 29539-0808WO1 / MGH 2024-658 sequence, about 85% to about 99% homology to the amino acid sequence, about 90% to about 99% homology to the amino acid sequence, or about 95% to about 99% homology to the amino acid sequence. The term “heterodimeric” refers to a protein dimer made up of two similar but not identical subunits. As used herein, the terms “percent (%) identity” or “percent sequence identity” refers to the percentage of amino acid residues of a candidate sequence, e.g., an epitope variant that are identical to the amino acid residues of a reference sequence, e.g., a naturally occurring epitope, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent identity (i.e., gaps can be introduced in one or both of the candidate and reference sequences for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). Alignment for purposes of determining percent identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, ALIGN, or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. In some embodiments, the percent amino acid sequence identity of a given candidate sequence to, with, or against a given reference sequence (which can alternatively be phrased as a given candidate sequence that has or includes a certain percent amino acid sequence identity to, with, or against a given reference sequence) is calculated as follows: 100 x (fraction of A / B) where A is the number of amino acid residues scored as identical in the alignment of the candidate sequence and the reference sequence, and where B is the total number of amino acid residues in the reference sequence. In some embodiments where the length of the candidate sequence does not equal to the length of the reference sequence, the percent amino acid sequence identity of the candidate sequence to the reference sequence would not equal to the percent amino acid sequence identity of the reference sequence to the candidate sequence. As used herein, the terms "treatment," "treating," and the like, refer to obtaining a desired pharmacologic or physiologic effect. The effect may be therapeutic in terms of a partial or complete cure for a disease or an adverse effect attributable to the disease. "Treatment," as used herein, covers any treatment of a disease in a mammal, particularly in a human, and can include Attorney Docket No; 29539-0808WO1 / MGH 2024-658 inhibiting the disease or condition, i.e., arresting its development; and relieving the disease, i.e., causing regression of the disease. "Treatment," as used herein, covers both prophylactic or preventive treatment (that prevents and / or slows the development of a targeted pathologic condition or disorder) and curative, therapeutic or disease-modifying treatment. In some embodiments, the term “treatment” can include inhibiting, attenuating or preventing the development or establishment of a tuberculosis infection in a subject, e.g., by vaccination using a preventative vaccine including antigenic material described herein to stimulate a subject’s immune system to develop adaptive immunity to tuberculosis. A “subject” is a vertebrate, including any member of the class mammalia, including humans, domestic and farm animals, and zoo, sports or pet animals, such as mouse, rabbit, pig, sheep, goat, cattle and higher primates. COMPOSITIONS COMPRISING MULTI-EPITOPE IMMUNOGENS AND METHODS OF USE Multi-epitope immunogens as described herein combine MHC Class I epitopes described herein, preferably two, three, four or more MHC Class I epitopes described herein, together with MHC Class II epitopes described herein, preferably two or more MHC Class II epitopes described herein, selected on the basis of MHC Class I and / or II presentation during TB infection in a human cell. The epitopes can include sequences of at least 8, e.g., at last 9, 10, or 11 consecutive amino acids from the MHC Class I epitope sequences set forth herein, or at least 12, e.g., at least 13, 14, 15, 16, 17, 18, 19, or 20 consecutive amino acids from the MHC Class II epitope sequences set forth herein, optionally with 1, 2, or 3 additional amino acids from the full length protein sequence (e.g., as shown in Table 1 or 2) on each end. In some embodiments, the four or more MHC Class I epitopes are selected from SEAYQGVQQKW (SEQ ID NO:53), LQNLARTI (SEQ ID NO:54), NHVNFFQEL (SEQ ID NO:55), RMWASAQNI (SEQ ID NO:56), HQAIVRDV (SEQ ID NO:57), KLADFGLVRA (SEQ ID NO:58), LLDEGKQSL (SEQ ID NO:59), AAWGGSGSEAY (SEQ ID NO:60), QEQASQQIL (SEQ ID NO:61), QTVEDEARRMW (SEQ ID NO:62), VYLTAHNAL (SEQ ID NO:63), EAVQDVARTY (SEQ ID NO:64), AEILRGVSA (SEQ ID NO:65), EVHSAMLNY (SEQ ID NO:66), IHDQFVATL (SEQ ID NO:67), NASPVAQSY (SEQ ID NO:68), VPLEGGGRL (SEQ ID NO:69), TQHDAADALF (SEQ ID NO:70), LPFEDAPLI (SEQ ID Attorney Docket No; 29539-0808WO1 / MGH 2024-658 NO:71), ELDEISTNIRQAGVQY (SEQ ID NO:72), QAIVRDVL (SEQ ID NO:73), KQKQELDEI (SEQ ID NO:74), GELRSLGATL (SEQ ID NO:75), TLRVVPESL (SEQ ID NO:76), MEDLVRAY (SEQ ID NO:77), QEAGNFERI (SEQ ID NO:78), AEHQAIVRDVL (SEQ ID NO:79), AEMKTDAATL (SEQ ID NO:80), RFMTDPHAMR (SEQ ID NO:81), SLLDEGKQSLTKL (SEQ ID NO:82), AVVRFQEAANK (SEQ ID NO:83), KIYSEADEAWRK (SEQ ID NO:84), EMKTDAATL (SEQ ID NO:85), and LLDAHIPQL (SEQ ID NO:86), and combinations thereof, optionally with 1, 2, or 3 additional amino acids from the full length protein sequence (e.g., as shown in Table 1 or 2) on each end. Four or more refers to any number from 4 to 50 (e.g., 4, 5, 6, 7, 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, 35, 36, 37, 38 ,39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50). In some embodiments, the two or more MHC Class II epitopes are selected from AEMKTDAATL (SEQ ID NO:80), RADEEQQQAL (SEQ ID NO:81), ISTNIRQAGVQYSRADEE (SEQ ID NO:82), AAVVRFQEAANKQK, AAVVRFQEAANKQKQ (SEQ ID NO:83), GAAGTAAQAAVVR (SEQ ID NO:84), LQGQWRGAAGTAAQAA (SEQ ID NO:85), SLQGQWRGAAGTAAQAA (SEQ ID NO:86), QGQWRGAAGTAAQA (SEQ ID NO:87), ESSAAFQAAHARFVAAA (SEQ ID NO:88), GESSAAFQAAHARFVAAA (SEQ ID NO:89), SAAFQAAHARFVAAA (SEQ ID NO:90), SSAAFQAAHARFVAAA (SEQ ID NO:91), AAGTYVAADAAAAST (SEQ ID NO:92), VGPQVVNINTKLGYNNA (SEQ ID NO:93), VQVAATEVRR (SEQ ID NO:94), SQRVDPSAASGQDSTEARPA (SEQ ID NO:95), PSAASGQDSTEARPA (SEQ ID NO:96), AIPAYEPEPGKPAPA (SEQ ID NO:97), SGASYAARDALAAASY (SEQ ID NO:98), GHDEESPGAQSLT (SEQ ID NO:99), THAATYQTASAKAAVIHE (SEQ ID NO:100), SGPKVVIDGKDQNVTG (SEQ ID NO:101), DVVDDPAFVLHGNHPVR (SEQ ID NO:102), DAGGTYQPHPAEAVVEK (SEQ ID NO:103), DAGGTYQPHPAEAVVE (SEQ ID NO:104), RQPEPEVDTA (SEQ ID NO:105), LPPPVVAANRIQL (SEQ ID NO:106), PEAVIVSTARSPIG (SEQ ID NO:107), ASAAVEALTARLAAAH (SEQ ID NO:108), IGTTMNAQNAAAAAPT (SEQ ID NO:109), and GTTMNAQNAAAAAPT (SEQ ID NO:110), optionally with 1, 2, or 3 additional amino acids from the full length protein sequence (e.g., as shown in Table 1 or 2) on each end, and combinations thereof. Two or more refers to any number from 2 to 50 (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, Attorney Docket No; 29539-0808WO1 / MGH 2024-658 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38 ,39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50). Immunogens useful in the present methods and compositions can include variants having at least 65% to about 99% homology (e.g., at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% homology) to the amino acid sequence of the epitopes described herein. In some embodiments, multi-epitope immunogens combine four or more MHC Class I epitopes selected from the following proteins: EsxA, EsxB, EsxG, EsxJ, EsxK, EsxP, EsxW, PE35, PPE20, PPE51, PPE60, PPE19, PE13, TB8.4, Rv1211, Rv3196A, EspC, EspA, EsxN, EsxO, PknL, PE31, PE15, PPE68, PPE18 or PE19 and combinations thereof, and variants having at least 65% to about 99% homology (e.g., at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% homology) to the amino acid sequence of the proteins described herein. TABLE 1. SEQ Mycobacterium tuberculosis MHC I ID : Attorney Docket No; 29539-0808WO1 / MGH 2024-658 SEQ Mycobacterium tuberculosis MHC I ID NO: Attorney Docket No; 29539-0808WO1 / MGH 2024-658 SEQ Mycobacterium tuberculosis MHC I ID NO: Attorney Docket No; 29539-0808WO1 / MGH 2024-658 SEQ Mycobacterium tuberculosis MHC I ID NO: e mu t -ep tope mmunogens can comb ne two or more C C ass ep topes se ected from the following proteins: EccC5, EsxG, PE15, PE19, FadA3, LpqH, Rv0308, SodC, TatA, Wag31, Rv1683, PE5, FadB, PE29, PE31, PepA, EsxB, PPE51, PPE4, PPE48, PE15, PPE20 or PPE60 and combinations thereof, and variants having at least 65% to about 99% homology (e.g., at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% homology) to the amino acid sequence of the proteins described herein.

[0002] Attorney Docket No; 29539-0808WO1 / MGH 2024-658 TABLE 2. Mycobacterium tuberculosis MHC II SEQ ID NO: E C5 MKRGFARPTPEKPPVIKPENIVLSTPLSIPPPEGKPWWLIVVGVVVVGLL 28. . Attorney Docket No; 29539-0808WO1 / MGH 2024-658 Mycobacterium tuberculosis MHC II SEQ ID NO: H37Rv / VGSLSPWHWAILAVVVIVLFGAKKLPDAARSLGKSLRIFKSEVRELQNE 30. . . . . . Attorney Docket No; 29539-0808WO1 / MGH 2024-658 Mycobacterium tuberculosis MHC II SEQ ID NO: AGIAYVSAKAGYEVVLKDVSLEAAAKGKGYSEKLEAKALERGRTTQE . . . . . . . . Attorney Docket No; 29539-0808WO1 / MGH 2024-658 Mycobacterium tuberculosis MHC II SEQ ID NO: FLTNPIQALITYGPLLFALGYQIFFNLVGWPTWGMILSSPFLLPAGLGLG . . . , t one set of heterodimeric pairs in a vector. More specifically, the vector comprises a nucleotide sequence encoding at least one MHC Class I (Table 1) or MHC Class II (Table 2) heterodimeric pair, or combinations thereof, or nucleotide sequences having at least 65% to about 99% homology to at least one MHC Class I (Table 1) or MHC Class II (Table 2) heterodimeric pair, optionally wherein the MHC Class I heterodimeric pairs are selected from: i) EsxA (MTEQQWNFAGIEAAASAIQGNVTSIHSLLDEGKQSLTKLAAAWGGSGSEAYQGVQQK WDATATELNNALQNLARTISEAGQAMASTEGNVTGMFA, SEQ ID NO:1) and Attorney Docket No; 29539-0808WO1 / MGH 2024-658 EsxB (MAEMKTDAATLAQEAGNFERISGDLKTQIDQVESTAGSLQGQWRGAAGTAAQAAVVR FQEAANKQKQELDEISTNIRQAGVQYSRADEEQQQALSSQMGF, SEQ ID NO:2) ii) EsxG (MSLLDAHIPQLVASQSAFAAKAGLMRHTIGQAEQAAMSAQAFHQGESSAAFQAAHARF VAAAAKVNTLLDVAQANLGEAAGTYVAADAAAASTYTGF, SEQ ID NO:3) and EsxH (MSQIMYNPAMLGHAGDMAGYAGTLQSLGAEIAVEQAALQSAWQGDTGITYQAWQAQ WNQAMEDLVRAYHAMSSTHEANTMAMMARDTAEAAKWGG, SEQ ID NO:9) iii) PE35 (MEKMSHDPIAADIGTQVSDNALHGVTAGSTALTSVTGLVPAGADEVSAQAATAFTSEGI QLLASNASAQDQLHRAGEAVQDVARTYSQIDDGAAGVFAE, SEQ ID NO:10) and PPE68 (MLWHAMPPELNTARLMAGAGPAPMLAAAAGWQTLSAALDAQAVELTARLNSLGEA WTGGGSDKALAAATPMVVWLQTASTQAKTRAMQATAQAAAYTQAMATTPSLPEIAAN HITQAVLTATNFFGINTIPIALTEMDYFIRMWNQAALAMEVYQAETAVNTLFEKLEPMAS ILDPGASQSTTNPIFGMPSPGSSTPVGQLPPAATQTLGQLGEMSGPMQQLTQPLQQVTSLF SQVGGTGGGNPADEEAAQMGLLGTSPLSNHPLAGGSGPSAGAGLLRAESLPGAGGSLTR TPLMSQLIEKPVAPSVMPAAAAGSSATGGAAPVGAGAMGQGAQSGGSTRPGLVAPAPL AQEREEDDEDDWDEEDDW, SEQ ID NO:25) iv) PPE20 (MTEPWIAFPPEVHSAMLNYGAGVGPMLISATQNGELSAQYAEAASEVEELLGVVASEG WQGQAAEAFVAAYMPFLAWLIQASADCVEMAAQQHVVIEAYTAAVELMPTQVELAAN QIKLAVLVATNFFGINTIPIAINEAEYVEMWVRAATTMATYSTVSRSALSAMPHTSPPPLI LKSDELLPDTGEDSDEDGHNHGGHSHGGHARMIDNFFAEILRGVSAGRIVWDPVNGTLN GLDYDDYVYPGHAIWWLARGLEFFQDGEQFGELLFTNPTGAFQFLLYVVVVDLPTHIAQ IATWLGQYPQLLSAALTGVIAHLGAITGLAGLSGLSAIPSAAIPAVVPELTPVAAAPPMLA VAGVGPAVAAPGMLPASAPAPAAAAGATAAGPTPPATGFGGFPPYLVGGGGPGIGFGSG QSAHAKAAASDSAAAESAAQASARAQARAARRGRSAAKARGHRDEFVTMDMGFDAA APAPEHQPGARASDCGAGPIGFAGTVRKEAVVKAAGLTTLAGDDFGGGPTMPMMPGT WTHDQGVFDEHR, SEQ ID NO:11) and Attorney Docket No; 29539-0808WO1 / MGH 2024-658 PE15 (VTLRVVPESLAGASAAIEAVTARLAAAHAAAAPFIAAVIPPGSDSVSVCNAVEFSVHGS QHVAMAAQGVEELGRSGVGVAESGASYAARDALAAASYLSGGL, SEQ ID NO:23) v) PPE51 (MDFALLPPEVNSARMYTGPGAGSLLAAAGGWDSLAAELATTAEAYGSVLSGLAALHW RGPAAESMAVTAAPYIGWLYTTAEKTQQTAIQARAAALAFEQAYAMTLPPPVVAANRI QLLALIATNFFGQNTAAIAATEAQYAEMWAQDAAAMYGYATASAAAALLTPFSPPRQT TNPAGLTAQAAAVSQATDPLSLLIETVTQALQALTIPSFIPEDFTFLDAIFAGYATVGVTQ DVESFVAGTIGAESNLGLLNVGDENPAEVTPGDFGIGELVSATSPGGGVSASGAGGAASV GNTVLASVGRANSIGQLSVPPSWAAPSTRPVSALSPAGLTTLPGTDVAEHGMPGVPGVP VAAGRASGVLPRYGVRLTVMAHPPAAG, SEQ ID NO:15) and PE19 (MSFVTTQPEALAAAAANLQGIGTTMNAQNAAAAAPTTGVVPAAADEVSALTAAQFAA HAQMYQTVSAQAAAIHEMFVNTLVASSGSYAATEAANAAAAG, SEQ ID NO:27) vi) PPE60 (VVDFGALPPEINSARMYAGPGSASLVAAAKMWDSVASDLFSAASAFQSVVWGLTVGS WIGSSAGLMAAAASPYVAWMSVTAGQAQLTAAQVRVAAAAYETAYRLTVPPPVIAEN RTELMTLTATNLLGQNTPAIEANQAAYSQMWGQDAEAMYGYAATAATATEALLPFED APLITNPGGLLEQAVAVEEAIDTAAANQLMNNVPQALQQLAQPAQGVVPSSKLGGLWT AVSPHLSPLSNVSSIANNHMSMMGTGVSMTNTLHSMLKGLAPAAAQAVETAAENGVW AMSSLGSQLGSSLGSSGLGAGVAANLGRAASVGSLSVPPAWAAANQAVTPAARALPLT SLTSAAQTAPGHMLGGLPLGHSVNAGSGINNALRVPARAYAIPRTPAAG, SEQ ID NO:16) and PE31 (VSFTAQPEMLAAAAGELRSLGATLKASNAAAAVPTTGVVPPAADEVSLLLATQFRTHA ATYQTASAKAAVIHEQFVTTLATSASSYADTEAANAVVTG, SEQ ID NO:24) vii) PE13 (VSFVMAYPEMLAAAADTLQSIGATTVASNAAAAAPTTGVVPPAADEVSALTAAHFAA HAAMYQSVSARAAAIHDQFVATLASSASSYAATEVANAAAAS, SEQ ID NO:18) and PPE18 (MVDFGALPPEINSARMYAGPGSASLVAAAQMWDSVASDLFSAASAFQSVVWGLTVGS WIGSSAGLMVAAASPYVAWMSVTAGQAELTAAQVRVAAAAYETAYGLTVPPPVIAEN Attorney Docket No; 29539-0808WO1 / MGH 2024-658 RAELMILIATNLLGQNTPAIAVNEAEYGEMWAQDAAAMFGYAAATATATATLLPFEEA PEMTSAGGLLEQAAAVEEASDTAAANQLMNNVPQALQQLAQPTQGTTPSSKLGGLWKT VSPHRSPISNMVSMANNHMSMTNSGVSMTNTLSSMLKGFAPAAAAQAVQTAAQNGVR AMSSLGSSLGSSGLGGGVAANLGRAASVGSLSVPQAWAAANQAVTPAARALPLTSLTS AAERGPGQMLGGLPVGQMGARAGGGLSGVLRVPPRPYVMPHSPAAG, SEQ ID NO:26); and wherein MHC Class II heterodimeric pairs are selected from: i) PE15 (VTLRVVPESLAGASAAIEAVTARLAAAHAAAAPFIAAVIPPGSDSVSVCNAVEFSVHGS QHVAMAAQGVEELGRSGVGVAESGASYAARDALAAASYLSGGL, SEQ ID NO:23) and PPE20 (MTEPWIAFPPEVHSAMLNYGAGVGPMLISATQNGELSAQYAEAASEVEELLGVVASEG WQGQAAEAFVAAYMPFLAWLIQASADCVEMAAQQHVVIEAYTAAVELMPTQVELAAN QIKLAVLVATNFFGINTIPIAINEAEYVEMWVRAATTMATYSTVSRSALSAMPHTSPPPLI LKSDELLPDTGEDSDEDGHNHGGHSHGGHARMIDNFFAEILRGVSAGRIVWDPVNGTLN GLDYDDYVYPGHAIWWLARGLEFFQDGEQFGELLFTNPTGAFQFLLYVVVVDLPTHIAQ IATWLGQYPQLLSAALTGVIAHLGAITGLAGLSGLSAIPSAAIPAVVPELTPVAAAPPMLA VAGVGPAVAAPGMLPASAPAPAAAAGATAAGPTPPATGFGGFPPYLVGGGGPGIGFGSG QSAHAKAAASDSAAAESAAQASARAQARAARRGRSAAKARGHRDEFVTMDMGFDAA APAPEHQPGARASDCGAGPIGFAGTVRKEAVVKAAGLTTLAGDDFGGGPTMPMMPGT WTHDQGVFDEHR, SEQ ID NO:11) ii) PE31 (VSFTAQPEMLAAAAGELRSLGATLKASNAAAAVPTTGVVPPAADEVSLLLATQFRTHA ATYQTASAKAAVIHEQFVTTLATSASSYADTEAANAVVTG, SEQ ID NO:24) and PPE60 (VVDFGALPPEINSARMYAGPGSASLVAAAKMWDSVASDLFSAASAFQSVVWGLTVGS WIGSSAGLMAAAASPYVAWMSVTAGQAQLTAAQVRVAAAAYETAYRLTVPPPVIAEN RTELMTLTATNLLGQNTPAIEANQAAYSQMWGQDAEAMYGYAATAATATEALLPFED APLITNPGGLLEQAVAVEEAIDTAAANQLMNNVPQALQQLAQPAQGVVPSSKLGGLWT AVSPHLSPLSNVSSIANNHMSMMGTGVSMTNTLHSMLKGLAPAAAQAVETAAENGVW AMSSLGSQLGSSLGSSGLGAGVAANLGRAASVGSLSVPPAWAAANQAVTPAARALPLT SLTSAAQTAPGHMLGGLPLGHSVNAGSGINNALRVPARAYAIPRTPAAG, SEQ ID NO:16) Attorney Docket No; 29539-0808WO1 / MGH 2024-658 iii) PPE51 (MDFALLPPEVNSARMYTGPGAGSLLAAAGGWDSLAAELATTAEAYGSVLSGLAALHW RGPAAESMAVTAAPYIGWLYTTAEKTQQTAIQARAAALAFEQAYAMTLPPPVVAANRI QLLALIATNFFGQNTAAIAATEAQYAEMWAQDAAAMYGYATASAAAALLTPFSPPRQT TNPAGLTAQAAAVSQATDPLSLLIETVTQALQALTIPSFIPEDFTFLDAIFAGYATVGVTQ DVESFVAGTIGAESNLGLLNVGDENPAEVTPGDFGIGELVSATSPGGGVSASGAGGAASV GNTVLASVGRANSIGQLSVPPSWAAPSTRPVSALSPAGLTTLPGTDVAEHGMPGVPGVP VAAGRASGVLPRYGVRLTVMAHPPAAG, SEQ ID NO:15) and PE19 (MSFVTTQPEALAAAAANLQGIGTTMNAQNAAAAAPTTGVVPAAADEVSALTAAQFAA HAQMYQTVSAQAAAIHEMFVNTLVASSGSYAATEAANAAAAG, SEQ ID NO:27) iv) PE5 (MTLRVVPEGLAAASAAVEALTARLAAAHASAAPVITAVVPPAADPVSLQTAAGFSAQG VEHAVVTAEGVEELGRAGVGVGESGASYLAGDAAAAATYGVVGG, SEQ ID NO:38) and PPE4 (MAAPIWMASPPEVHSALLSNGPGPGSLVAAATAWSQLSAEYASTAAELSGLLGAVPGW AWQGPSAEWYVAAHLPYVAWLTQASADAAGAAAQHEAAAAAYTTALAAMPTLAELA ANHVIHTVLVATNFFGINTIPITLNEADYVRMWLQAAAVMGLYQAASGAALASAPRTVP APTVMNPGGGAASTVGAVNPWQWLLALLQQLWNAYTGFYGWMLQLIWQFLQDPIGN SIKIIIAFLTNPIQALITYGPLLFALGYQIFFNLVGWPTWGMILSSPFLLPAGLGLGLAAIAFL PIVLAPAVIPPASTPLAAAAVAAGSVWPAVSMAVTGAGTAGAATPAAGAAPSAGAAPAP AAPATASFAYAVGGSGDWGPSLGPTVGGRGGIKAPAATVPAAAAAAATRGQSRARRRR RSELRDYGDEFLDMDSDSGFGPSTGDHGAQASERGAGTLGFAGTATKERRVRAVGLTA LAGDEFGNGPRMPMVPGTWEQGSNEPEAPDGSGRGGGDGLPHDSK, SEQ ID NO:40) v) PE29 (VTLRVVPEGLAAASAAVEALTARLAAAHAGAAPAITAVVAPAADPVSLQSAVGFSALG SEHAAIAGEGVEELGRSGVAVGESGIGYAAGDAVAAATYLVSGGSL, SEQ ID NO:39) and PPE48 (VTAPVWLASPPEVHSALLSAGPGPGSLQAAAAGWSALSAEYAAVAQELSVVVAAVG AGVWQGPSAELFVAAYVPYVAWLVQ, SEQ ID NO:41). Attorney Docket No; 29539-0808WO1 / MGH 2024-658 Immunogens described herein can be linked, operably or directly, to a separate or contiguous sequence that enhances the expression, stability, cell trafficking, processing and presentation, and / or immunogenicity of the epitope including, but not limited to, at least one of TOM20 (mitochondria), Human Ig Light Chain (endoplasmic reticulum), LAMP1-3 (lysosome), MITD (endosome), and NES (cytosol). In some embodiments, e.g., for LAMP1 / 2 / 3 targeting to the lysosome, a signal sequence (e.g., as listed in Table 3) is present on the N terminus and a LAMP1 / 2 / 3 transmembrane domain (e.g., as listed in Table 4) is present on the C terminus. TABLE 3. Signal Peptides SEQ ID NO: TOM20 MLATRVFSLVGKRAISTSVCVRAH 42. TABLE 4. Transmembrane Domains SEQ ID NO: LAMP1 NNMLIPIAVGGALAGLVLIVLIAYLIGRKRSHAGY TI 49 Immunogens as described herein can be linked directly to one another with a linker. In some embodiments, the linker is selected from the group consisting of: (1) consecutive glycine residues, at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 residues in length; (2) consecutive alanine residues, at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 residues in length;(3) two arginine residues (RR); (4) alanine, alanine, tyrosine (AAY); (5) a consensus sequence at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid residues in length that is processed efficiently by a mammalian proteasome; and (6) one or more native sequences flanking the epitope derived from the cognate protein of origin and that is at Attorney Docket No; 29539-0808WO1 / MGH 2024-658 least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 2-20 amino acid residues in length. In some embodiments, the linker comprises the sequence GPGPG (SEQ ID NO:52). In other embodiments, the linker comprises a non-immunogenic linker (e.g., GGS) or a self-cleaving P2A peptide sequence. Immunogens as described herein can be delivered to a subject as peptides or proteins using methods known in the art, e.g., as described in Tait et al., N Engl J Med 2019;381:2429-39 and Skeiky et al., The Journal of Immunology, 2004, 172:7618–7628. Immunogens as described herein can be delivered to and expressed in a subject’s cells by incorporating a nucleic acid encoding the immunogens in a vector, optionally an expression vector. As used herein, "expression vector" refers to a vector that comprises a recombinant polynucleotide including expression control sequences operatively linked to a nucleotide sequence to be expressed. An expression vector comprises sufficient cis- acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. In some embodiments, a recombinant expression vector can include additional immune-enhancer elements to increase epitope expression and / or de novo cytotoxic T cell responses in a subject. Immune-enhancer elements can include, but are not limited to, endoplasmic reticulum signal sequences (ERSS) to promote HLA class I presentation, sequences encoding a furin cleavage site (e.g., RRKR (SEQ ID NO:110), RGRRKRS (SEQ ID NO:111)), and / or a universal T-helper epitope such as a pan HLA-DR epitope (PADRE). The vector can also be “naked” DNA or RNA, e.g., mRNA, e.g., not in an expression vector. In some embodiments, the expression vector is a viral vector. The term "virus" is used herein to refer any of the obligate intracellular parasites having no protein-synthesizing or energy-generating mechanism. The virus may be an RNA virus (having a genome that is composed of RNA) or a DNA virus (having a genome composed of DNA). In some embodiments, the viral vector is a DNA virus vector. Exemplary DNA viruses include parvoviruses (e.g., adeno-associated viruses), adenoviruses, asfarviruses, herpesviruses (e.g., herpes simplex virus 1 and 2 (HSV-1 and HSV-2), epstein-barr virus (EBV), cytomegalovirus (CMV)), papillomoviruses (e.g., HPV), polyomaviruses (e.g., simian vacuolating virus 40 (SV40)), and poxviruses (e.g., vaccinia virus, cowpox virus, smallpox virus, fowlpox virus, sheeppox virus, myxoma virus). In some embodiments, the viral vector is a RNA virus vector. Exemplary RNA viruses include bunyaviruses (e.g., hantavirus), coronaviruses, ebolaviruses, Attorney Docket No; 29539-0808WO1 / MGH 2024-658 flaviviruses (e.g., yellow fever virus, west nile virus, dengue virus), hepatitis viruses (e.g., hepatitis A virus, hepatitis C virus, hepatitis E virus), influenza viruses (e.g., influenza virus type A, influenza virus type B, influenza virus type C), measles virus, mumps virus, noroviruses (e.g., Norwalk virus), poliovirus, respiratory syncytial virus (RSV), retroviruses (e.g., human immunodeficiency virus-1 (HIV-1)) and toroviruses. In some embodiments, the expression vector comprises a regulatory sequence or promoter operably linked to the nucleotide sequence encoding the immunogens as described herein. The term "operably linked" refers to a linkage of polynucleotide elements in a functional relationship. A nucleic acid sequence is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence. For instance, a promoter or enhancer is operably linked to a gene if it affects the transcription of the gene. Operably linked nucleotide sequences are typically contiguous. However, as enhancers generally function when separated from the promoter by several kilobases and intronic sequences may be of variable lengths, some polynucleotide elements may be operably linked but not directly flanked and may even function in trans from a different allele or chromosome. Nucleic acid sequences encoding immunogens as described herein preferably have strong promoters that are active in a variety of cell types. The promoters for eukaryotic nucleic acid sequences are typically present within the structural sequences encoding the immunogens. Although there are elements which regulate transcriptional activity within the 5' upstream region, the length of an active transcriptional unit may be considerably less than 500 base pairs. Additional exemplary promoters which may be employed include, but are not limited to, the retroviral LTR, the SV40 promoter, the human cytomegalovirus (CMV) promoter, the U6 promoter, or any other promoter (e.g., cellular promoters such as eukaryotic cellular promoters including, but not limited to, the histone, pol III, and β-actin promoters). Other viral promoters which may be employed include, but are not limited to, adenovirus promoters, TK promoters, and B19 parvovirus promoters. The selection of a suitable promoter will be apparent to those skilled in the art from the teachings contained herein. In some embodiments, an expression vector is an adeno-associated virus (AAV) vector. AAV is a small, nonenveloped icosahedral virus of the genus Dependoparvovirus and family Parvovirus. AAV has a single-stranded linear DNA genome of approximately 4.7 kb. AAV is capable of infecting both dividing and quiescent cells of several tissue types, with different AAV Attorney Docket No; 29539-0808WO1 / MGH 2024-658 serotypes exhibiting different tissue tropism. AAV includes numerous serologically distinguishable types including serotypes AAV-1 to AAV-12, as well as more than 100 serotypes from nonhuman primates (See, e.g., Srivastava (2008) J. Cell Biochem., 105(1): 17–24, and Gao et al. (2004) J. Virol., 78(12), 6381–6388). The serotype of the AAV vector used in the present invention can be selected by a skilled person in the art based on the efficiency of delivery, tissue tropism, and immunogenicity. For example, AAV-1, AAV-2, AAV-4, AAV-5, AAV-8, and AAV-9 can be used for delivery to the central nervous system; AAV-1, AAV-8, and AAV-9 can be used for delivery to the heart; AAV-2 can be used for delivery to the kidney; AAV-7, AAV-8, and AAV-9 can be used for delivery to the liver; AAV-4, AAV-5, AAV-6, AAV-9 can be used for delivery to the lung, AAV-8 can be used for delivery to the pancreas, AAV-2, AAV-5, and AAV-8 can be used for delivery to the photoreceptor cells; AAV-1, AAV-2, AAV-4, AAV-5, and AAV-8 can be used for delivery to the retinal pigment epithelium; AAV-1, AAV-6, AAV-7, AAV-8, and AAV-9 can be used for delivery to the skeletal muscle. In some embodiments, the AAV capsid protein comprises a sequence as disclosed in U.S. Patent No.7,198,951, such as, but not limited to, AAV-9 (SEQ ID NOs: 1-3 of U.S. Patent No.7,198,951), AAV-2 (SEQ ID NO: 4 of U.S. Patent No.7,198,951), AAV-1 (SEQ ID NO: 5 of U.S. Patent No.7,198,951), AAV-3 (SEQ ID NO: 6 of U.S. Patent No.7,198,951), and AAV-8 (SEQ ID NO: 7 of U.S. Patent No. 7,198,951). AAV serotypes identified from rhesus monkeys, e.g., rh.8, rh.10, rh.39, rh.43, and rh.74, are also contemplated in the instant invention. Besides the natural AAV serotypes, modified AAV capsids have been developed for improving efficiency of delivery, tissue tropism, and immunogenicity. Exemplary natural and modified AAV capsids are disclosed in U.S. Patent Nos.7,906,111, 9,493,788, and 7,198,951, and PCT Publication No. WO2017189964A2. The wild-type AAV genome contains two 145 nucleotide inverted terminal repeats (ITRs), which contain signal sequences directing AAV replication, genome encapsidation and integration. In addition to the ITRs, three AAV promoters, p5, p19, and p40, drive expression of two open reading frames encoding rep and cap genes. Two rep promoters, coupled with differential splicing of the single AAV intron, result in the production of four rep proteins (Rep 78, Rep 68, Rep 52, and Rep 40) from the rep gene. Rep proteins are responsible for genomic replication. The Cap gene is expressed from the p40 promoter, and encodes three capsid proteins (VP1, VP2, and VP3) which are splice variants of the cap gene. These proteins form the capsid of the AAV particle. Attorney Docket No; 29539-0808WO1 / MGH 2024-658 Because the cis-acting signals for replication, encapsidation, and integration are contained within the ITRs, some or all of the 4.3 kb internal genome may be replaced with foreign DNA, for example, an expression cassette for an exogenous nucleic acid sequence of interest encoding two or more optimal immunogens. Accordingly, in some embodiments, the AAV vector comprises a genome comprising an expression cassette for an exogenous nucleic acid sequence encoding immunogens as described herein epitopes flanked by a 5’ ITR and a 3’ ITR. The ITRs may be derived from the same serotype as the capsid or a derivative thereof. Alternatively, the ITRs may be of a different serotype from the capsid, thereby generating a pseudotyped AAV. In some embodiments, the ITRs are derived from AAV-2. In some embodiments, the ITRs are derived from AAV-5. At least one of the ITRs may be modified to mutate or delete the terminal resolution site, thereby allowing production of a self- complementary AAV vector. The rep and cap proteins can be provided in trans, for example, on a plasmid, to produce an AAV vector. A host cell line permissive of AAV replication must express the rep and cap genes, the ITR-flanked expression cassette, and helper functions provided by a helper virus, for example adenoviral genes E1a, E1b55K, E2a, E4orf6, and VA (Weitzman et al., Adeno-associated virus biology. Adeno-Associated Virus: Methods and Protocols, pp.1–23, 2011). Methods for generating and purifying AAV vectors have been described in detail (See e.g., Mueller et al., (2012) Current Protocols in Microbiology, 14D.1.1- 14D.1.21, Production and Discovery of Novel Recombinant Adeno-Associated Viral Vectors). Numerous cell types are suitable for producing AAV vectors, including HEK293 cells, COS cells, HeLa cells, BHK cells, Vero cells, as well as insect cells (See e.g. U.S. Patent Nos. 6,156,303, 5,387,484, 5,741,683, 5,691,176, 5,688,676, and 8,163,543, U.S. Patent Publication No.20020081721, and PCT Publication Nos. WO00 / 47757, WO00 / 24916, and WO96 / 17947). AAV vectors are typically produced in these cell types by one plasmid containing the ITR- flanked expression cassette, and one or more additional plasmids providing the additional AAV and helper virus genes. AAV of any serotype may be used in the present invention. Similarly, it is contemplated that any adenoviral type may be used, and a person of skill in the art will be able to identify AAV and adenoviral types suitable for the production of their desired recombinant AAV vector (rAAV). AAV particles may be purified, for example by affinity chromatography, iodixonal gradient, or CsCl gradient. AAV vectors may have single-stranded genomes that are 4.7 kb in Attorney Docket No; 29539-0808WO1 / MGH 2024-658 size, or are larger or smaller than 4.7 kb, including oversized genomes that are as large as 5.2 kb, or as small as 3.0 kb. Thus, where the exogenous gene of interest to be expressed from the AAV vector is small, the AAV genome may comprise a stuffer sequence. Further, vector genomes may be substantially self-complementary thereby allowing for rapid expression in the cell. In some embodiments, the genome of a self-complementary AAV vector comprises from 5' to 3': a 5' ITR; a first nucleic acid sequence comprising a promoter and / or enhancer operably linked to a nucleic acid sequence encoding immunogens as described herein; a modified ITR that does not have a functional terminal resolution site; a second nucleic acid sequence complementary or substantially complementary to the first nucleic acid sequence; and a 3' ITR. AAV vectors containing genomes of all types are suitable for use in the method of the present invention. Non-limiting examples of AAV vectors include pAAV-MCS (Agilent Technologies), pAAVK- EF1α-MCS (System Bio Catalog # AAV502A-1), pAAVK-EF1α-MCS1-CMV-MCS2 (System Bio Catalog # AAV503A-1), pAAV-ZsGreen1 (Clontech Catalog #6231), pAAV-MCS2 (Addgene Plasmid #46954), AAV-Stuffer (Addgene Plasmid #106248), pAAVscCBPIGpluc (Addgene Plasmid #35645), AAVS1_Puro_PGK1_3xFLAG_Twin_Strep (Addgene Plasmid #68375), pAAV-RAM-d2TTA::TRE-MCS-WPRE-pA (Addgene Plasmid #63931), pAAV-UbC (Addgene Plasmid #62806), pAAVS1-P-MCS (Addgene Plasmid #80488), pAAV-Gateway (Addgene Plasmid #32671), pAAV-Puro_siKD (Addgene Plasmid #86695), pAAVS1-Nst-MCS (Addgene Plasmid #80487), pAAVS1-Nst-CAG-DEST (Addgene Plasmid #80489), pAAVS1-P- CAG-DEST (Addgene Plasmid #80490), pAAVf-EnhCB-lacZnls (Addgene Plasmid #35642), and pAAVS1-shRNA (Addgene Plasmid #82697). These vectors can be modified to be suitable for therapeutic use. For example, an exogenous nucleic acid sequence of interest encoding immunogens as described herein can be inserted in a multiple cloning site, and a selection marker (e.g., puro or a gene encoding a fluorescent protein) can be deleted or replaced with another (same or different) exogenous gene of interest. Further examples of AAV vectors are disclosed in U.S. Patent Nos.5,871,982, 6,270,996, 7,238,526, 6,943,019, 6,953,690, 9,150,882, and 8,298,818, U.S. Patent Publication No.2009 / 0087413, and PCT Publication Nos. WO2017075335A1, WO2017075338A2, and WO2017201258A1. In some embodiments, the viral vector can be an adenoviral vector. Adenoviruses are medium-sized (90-100 nm), non-enveloped, icosahedral viruses composed of a nucleocapsid and a double-stranded linear DNA genome. The term "adenovirus" refers to any virus in the genus Attorney Docket No; 29539-0808WO1 / MGH 2024-658 Adenoviridiae including, but not limited to, human, bovine, ovine, equine, canine, porcine, murine, and simian adenovirus subgenera. Typically, an adenoviral vector is generated by introducing one or more mutations (e.g., a deletion, insertion, or substitution) into the adenoviral genome of the adenovirus so as to accommodate the insertion of a non-native nucleic acid sequence, for example, for gene transfer, into the adenovirus. A human adenovirus can be used as the source of the adenoviral genome for the adenoviral vector. For instance, an adenovirus can be of subgroup A (e.g., serotypes 12, 18, and 31), subgroup B (e.g., serotypes 3, 7, 11, 14, 16, 21, 34, 35, and 50), subgroup C (e.g., serotypes 1 , 2, 5, and 6), subgroup D (e.g., serotypes 8, 9, 10, 13, 15, 17, 19, 20, 22-30, 32, 33, 36-39, and 42-48), subgroup E (e.g., serotype 4), subgroup F (e.g., serotypes 40 and 41 ), an unclassified serogroup (e.g., serotypes 49 and 51), or any other adenoviral serogroup or serotype. In an exemplary implementation, the adenovirus vector is a serotype 5 adenovirus vector. Adenoviral serotypes 1 through 51 are available from the American Type Culture Collection (ATCC, Manassas, Virginia). Non-group C adenoviral vectors, methods of producing non-group C adenoviral vectors, and methods of using non- group C adenoviral vectors are disclosed in, for example, U.S. Patent Nos.5,801,030, 5,837,511, and 5,849,561, and PCT Publication Nos. WO1997 / 012986 and WO1998 / 053087. Non-human adenovirus (e.g., ape, simian, avian, canine, ovine, or bovine adenoviruses) can be used to generate the adenoviral vector (i.e., as a source of the adenoviral genome for the adenoviral vector). For example, the adenoviral vector can be based on a simian adenovirus, including both new world and old world monkeys (see, e.g., Virus Taxonomy: VHIth Report of the International Committee on Taxonomy of Viruses (2005)). A phylogeny analysis of adenoviruses that infect primates is disclosed in, e.g., Roy et al. (2009) PLoS Pathog. 5(7):e1000503. A gorilla adenovirus can be used as the source of the adenoviral genome for the adenoviral vector. Gorilla adenoviruses and adenoviral vectors are described in, e.g., PCT Publication Nos.WO2013 / 052799, WO2013 / 052811, and WO2013 / 052832. The adenoviral vector can also comprise a combination of subtypes and thereby be a "chimeric" adenoviral vector. The adenoviral vector can be replication-competent, conditionally replication- competent, or replication-deficient. A replication-competent adenoviral vector can replicate in typical host cells, i.e., cells typically capable of being infected by an adenovirus. A conditionally-replicating Attorney Docket No; 29539-0808WO1 / MGH 2024-658 adenoviral vector is an adenoviral vector that has been engineered to replicate under pre- determined conditions. For example, replication-essential gene functions, e.g., gene functions encoded by the adenoviral early regions, can be operably linked to an inducible, repressible, or tissue-specific transcription control sequence, e.g., a promoter. Conditionally-replicating adenoviral vectors are further described in U.S. Patent No.5,998,205. A replication-deficient adenoviral vector is an adenoviral vector that requires complementation of one or more gene functions or regions of the adenoviral genome that are required for replication, as a result of, for example, a deficiency in one or more replication- essential gene function or regions, such that the adenoviral vector does not replicate in typical host cells, especially those in a human to be infected by the adenoviral vector. The adenoviral vector can be replication-deficient, such that the replication- deficient adenoviral vector requires complementation of at least one replication-essential gene function of one or more regions of the adenoviral genome for propagation (e.g., to form adenoviral vector particles). The adenoviral vector can be deficient in one or more replication-essential gene functions of only the early regions (i.e., E1-E4 regions) of the adenoviral genome, only the late regions (i.e., L1-L5 regions) of the adenoviral genome, both the early and late regions of the adenoviral genome, or all adenoviral genes (i.e., a high capacity adenovector (HC-Ad)). See, e.g., Morsy et al. (1998) Proc. Natl. Acad. Sci. USA 95: 965-976, Chen et al. (1997) Proc. Natl. Acad. Sci. USA 94: 1645-1650, and Kochanek et al. (1999) Hum. Gene Ther.10(15):2451-9. Examples of replication-deficient adenoviral vectors are disclosed in U.S. Patent Nos.5,837,511, 5,851,806, 5,994,106, 6,127,175, 6,482,616, and 7,195,896, and PCT Publication Nos. WO1994 / 028152, WO1995 / 002697, WO1995 / 016772, WO1995 / 034671, WO1996 / 022378, WO1997 / 012986, WO1997 / 021826, and WO2003 / 022311. The replication-deficient adenoviral vector as described herein can be produced in complementing cell lines that provide gene functions not present in the replication-deficient adenoviral vector, but required for viral propagation, at appropriate levels in order to generate high titers of viral vector stock. Such complementing cell lines are known and include, but are not limited to, 293 cells (described in, e.g., Graham et al. (1977) J. Gen. Virol.36: 59-72), PER.C6 cells (described in, e.g., PCT Publication No. WO1997 / 000326, and U.S. Patent Nos. 5,994,128 and 6,033,908), and 293-ORF6 cells (described in, e.g., PCT Publication No. WO1995 / 034671 and Brough et al. (1997) J. Virol.71: 9206-9213). Other suitable Attorney Docket No; 29539-0808WO1 / MGH 2024-658 complementing cell lines to produce the replication-deficient adenoviral vector as described herein include complementing cells that have been generated to propagate adenoviral vectors encoding transgenes whose expression inhibits viral growth in host cells (see, e.g., U.S. Patent Publication No.2008 / 0233650). Additional suitable complementing cells are described in, for example, U.S. Patent Nos.6,677,156 and 6,682,929, and PCT Publication No. WO2003 / 020879. Formulations for adenoviral vector-containing compositions are further described in, for example, U.S. Patent Nos.6,225,289, and 6,514,943, and PCT Publication No. WO2000 / 034444. Additional exemplary adenoviral vectors, and / or methods for making or propagating adenoviral vectors are described in U.S. Patent Nos.5,559,099, 5,837,511, 5,846,782, 5,851,806, 5,994,106, 5,994,128, 5,965,541, 5,981,225, 6,040,174, 6,020,191, 6,083,716, 6,113,913, 6,303,362, 7,067,310, and 9,073,980. Commercially available adenoviral vector systems include the ViraPower™ Adenoviral Expression System available from Thermo Fisher Scientific, the AdEasy™ adenoviral vector system available from Agilent Technologies, and the Adeno-X™ Expression System 3 available from Takara Bio USA, Inc. In some embodiments, the recombinant vector can include DNA or messenger RNA (mRNA). One advantage of mRNA is that mRNA vaccines are capable of inducing a balanced immune response including both cellular and humoral immunity. In addition, mRNA vaccines can be designed to be self-adjuvanting. Alternatively, mRNA vaccines can be supplemented with one or more additional adjuvant molecules such as additional mRNAs encoding auxiliary adjuvant molecules. Functional synthetic mRNA may be obtained by in vitro transcription of a cDNA template, typically plasmid DNA (pDNA), using a bacteriophage RNA polymerase. Synthetic mRNA for use in an mRNA vector immunogen composition described herein can include a protein-encoding open reading frame (ORF) flanked at the minimum by two elements essential for the function of mature eukaryotic mRNA: a “cap,” i.e., a 7-methyl-guanosine residue joined to the 5′-end via a 5′-5′ triphosphate, and a poly(A) tail at the 3′-end. Therefore, in some embodiments, a pDNA template can include a bacteriophage promoter, an ORF, optionally a poly(d(A / T)) sequence transcribed into poly(A) and a unique restriction site for linearization of the plasmid to ensure defined termination of transcription. A linearized pDNA template can be transcribed into mRNA in a mixture including recombinant Attorney Docket No; 29539-0808WO1 / MGH 2024-658 RNA polymerase (T7, T3 or SP6) and nucleoside triphosphates. To obtain capped mRNA by transcription a cap analog like the dinucleotide m7G(5′)-ppp-(5′)G may be included in the reaction. If the cap analog is in excess of GTP, transcription initiates with the cap analog rather than GTP, yielding capped mRNA. Alternatively, the cap may be added enzymatically post transcription. A poly(A) tail may also be added post transcription if it is not provided by the pDNA template. Following transcription, the pDNA template as well as contaminating bacterial DNA is digested by DNase. The resultant mRNA transcript can be purified by a combination of precipitation and extraction steps. In order to be translated and elicit an antigen-specific immune response, an mRNA- vaccine has to reach the cytosol of target cells. However, as opposed to DNA vaccines, RNA vaccines only have to cross the plasma membrane, but not the nuclear envelope which may improve the probability of successful in vivo transfection. While locally administered naked mRNA can be taken up by cells, the efficacy of mRNA vaccines may benefit significantly from complexing agents which protect RNA from degradation. Complexing agents can be tailored to the specific route of delivery. Complexation may also enhance uptake by cells and / or improve delivery to the translation machinery in the cytoplasm. Thus, in some embodiments, mRNA for use in an immunogen composition can be complexed with either lipids or polymers. In some embodiments, the vector is a delivery vehicle comprised of lipid-based compositions, including lipid nanoparticle compositions include but are not limited those described in U.S. Patent Publication Number 20200206362, filed as U.S. Patent Application Serial number 16 / 599661 on October 11, 2019 and U.S. Patent Number 10,799,463, the contents of which are incorporated herein by reference. In some embodiments of the present disclosure, an RNA molecule is "replicon RNA" or “replicon RNA molecule” or simply a "replicon", in particular "self-replicating RNA" or "self- amplifying RNA" or “replicable RNA molecule”. A replicon RNA molecule is an RNA that is able to be replicated by an RNA-dependent RNA polymerase (replicase) by virtue of comprising nucleotide sequences that can be recognized by the replicase such that the RNA is replicated. The replicon does not necessarily encode the replicase, such that replicons can be replicated in cis (by the encoded replicase; also called a “cis-replicon”) or in trans (by a replicase provided in another manner, e.g., a separate replicase encoding nucleic acid, such as an mRNA; also called “trans-replicon”). Attorney Docket No; 29539-0808WO1 / MGH 2024-658 In saRNA vaccine constructs, the ORF encoding viral structural proteins is replaced with any antigen of choice, while the viral replicase remains an integral part of the vaccine and drives intracellular amplification of the RNA after immunization. Therefore, in some embodiments, the recombinant vector can include a saRNA vaccine construct where the ORF encoding viral structural proteins have been replaced with immunogens as described herein. In some embodiments, the replicon or self-replicating RNA is derived from or comprises elements derived from an ssRNA virus, in particular a positive-stranded ssRNA virus such as an alphavirus. Alphaviruses are typical representatives of positive-stranded RNA viruses. Alphaviruses replicate in the cytoplasm of infected cells (for review of the alphaviral life cycle see José et al., Future Microbiol., 2009, vol.4, pp.837–856). The total genome length of many alphaviruses typically ranges between 11,000 and 12,000 nucleotides, and the genomic RNA typically has a 5’-cap, and a 3’ poly(A) tail. The genome of alphaviruses encodes non-structural proteins (involved in transcription, modification and replication of viral RNA and in protein modification) and structural proteins (forming the virus particle). There are typically two open reading frames (ORFs) in the genome. The four non-structural proteins (nsP1–nsP4) are typically encoded together by a first ORF beginning near the 5′ terminus of the genome, while alphavirus structural proteins are encoded together by a second ORF which is found downstream of the first ORF and extends near the 3’ terminus of the genome. Typically, the first ORF is larger than the second ORF, the ratio being roughly 2:1. In cells infected by an alphavirus, only the nucleic acid sequence encoding non-structural proteins is translated from the genomic RNA, while the genetic information encoding structural proteins is translatable from a subgenomic transcript, which is an RNA molecule that resembles eukaryotic messenger RNA (mRNA; Gould et al., 2010, Antiviral Res., vol.87 pp.111–124). Following infection, i.e. at early stages of the viral life cycle, the (+) stranded genomic RNA directly acts like a messenger RNA for the translation of the open reading frame encoding the non-structural poly-protein (nsP1234). Alphavirus- derived vectors have been proposed for delivery of foreign genetic information into target cells or target organisms. In simple approaches, the open reading frame encoding alphaviral structural proteins is replaced by an open reading frame encoding a protein of interest. Alphavirus-based trans-replication systems rely on alphavirus nucleotide sequence elements on two separate nucleic acid molecules: one nucleic acid molecule encodes a viral replicase, and the other nucleic Attorney Docket No; 29539-0808WO1 / MGH 2024-658 acid molecule is capable of being replicated by said replicase in trans (hence the designation trans-replication system). Trans-replication requires the presence of both these nucleic acid molecules in a given host cell. The nucleic acid molecule capable of being replicated by the replicase in trans must comprise certain alphaviral sequence elements to allow recognition and RNA synthesis by the alphaviral replicase. Nucleic acids can be administered with one or more delivery vehicles that protect the nucleic acids from degradation, maximize delivery to on-target cells and minimize exposure to off-target cells. Such nucleic acid delivery vehicles may complex or encapsulate nucleic acids and include a range of materials, including polymers and lipids. In some embodiments, such nucleic acid delivery vehicles may form particles with nucleic acids, preferably RNA. RNA, in particular mRNA, described herein may be present in particles comprising (i) the RNA, and (ii) at least one cationic or cationically ionizable compound such as a polymer or lipid complexing the RNA. Electrostatic interactions between positively charged molecules such as polymers and lipids and negatively charged RNA are involved in particle formation. This results in complexation and spontaneous formation of nucleic acid, in particular RNA, particles. Different types of nucleic acid containing particles have been described previously to be suitable for delivery of RNA in particulate form (cf., e.g., Kaczmarek, J. C. et al., 2017, Genome Medicine 9, 60). For non-viral RNA delivery vehicles, nanoparticle encapsulation of nucleic acids physically protects the nucleic acids from degradation and, depending on the specific chemistry, can aid in cellular uptake and endosomal escape. In the context of the present disclosure, the term "particle" relates to a structured entity formed by molecules or molecule complexes, in particular particle forming compounds. In some embodiments, the particle contains an envelope (e.g., one or more layers or lamellas) made of one or more types of amphiphilic substances (e.g., amphiphilic lipids). In this context, the expression "amphiphilic substance" means that the substance possesses both hydrophilic and lipophilic properties. The envelope may also comprise additional substances (e.g., additional lipids) which do not have to be amphiphilic. Thus, the particle may be a monolamellar or multilamellar structure, wherein the substances constituting the one or more layers or lamellas comprise one or more types of amphiphilic substances (in particular selected from the group consisting of amphiphilic lipids) optionally in combination with additional substances (e.g., additional lipids) which do not have to be amphiphilic. In some embodiments, the term "particle" Attorney Docket No; 29539-0808WO1 / MGH 2024-658 relates to a micro- or nano-sized structure, such as a micro- or nano-sized compact structure. According to the present disclosure, the term "particle" includes nanoparticles. A "DNA particle", "RNA particle" or "DNA and RNA particle" can be used to deliver DNA and / or RNA to a target site of interest (e.g., cell, tissue, organ, and the like). A DNA and / or RNA particle may be formed from lipids comprising at least one cationic or cationically ionizable lipid. Without intending to be bound by any theory, it is believed that the cationic or cationically ionizable lipid combines together with the nucleic acids to form aggregates, and this aggregation results in colloidally stable particles. RNA particles described herein include lipid nanoparticle (LNP)-based and lipoplex (LPX)-based formulations. A lipoplex (LPX) described herein is obtainable from mixing two aqueous phases, namely a phase comprising RNA and a phase comprising a dispersion of lipids. In some embodiments, the lipid phase comprises liposomes. In some embodiments, liposomes are self-closed unilamellar or multilamellar vesicular particles wherein the lamellae comprise lipid bilayers and the encapsulated lumen comprises an aqueous phase. A prerequisite for using liposomes for nanoparticle formation is that the lipids in the mixture as required are able to form lamellar (bilayer) phases in the applied aqueous environment. In some embodiments, liposomes comprise unilamellar or multilamellar phospholipid bilayers enclosing an aqueous core (also referred to herein as an aqueous lumen). They may be prepared from materials possessing polar head (hydrophilic) groups and nonpolar tail (hydrophobic) groups. In some embodiments, cationic lipids employed in formulating liposomes designed for the delivery of RNA are amphiphilic in nature and consist of a positively charged (cationic) amine head group linked to a hydrocarbon chain or cholesterol derivative via glycerol. In some embodiments, lipoplexes are multilamellar liposome-based formulations that form upon electrostatic interaction of cationic liposomes with nucleic acids. In some embodiments, formed lipoplexes possess distinct internal arrangements of molecules that arise due to the transformation from liposomal structure into compact RNA–lipoplexes. In some embodiments, an LPX particle comprises an amphiphilic lipid, in particular cationic or cationically ionizable amphiphilic lipid, and RNA (especially mRNA) as described herein. In some embodiments, electrostatic interactions between positively charged liposomes Attorney Docket No; 29539-0808WO1 / MGH 2024-658 (made from one or more amphiphilic lipids, in particular cationic or cationically ionizable amphiphilic lipids) and negatively charged RNA (especially mRNA) results in complexation and spontaneous formation of RNA lipoplex particles. Positively charged liposomes may be generally synthesized using a cationic or cationically ionizable amphiphilic lipid, such as DOTMA and / or DODMA, and optionally additional lipids, such as DOPE or DSPC. In general, a lipid nanoparticle (LNP) is typically obtainable from direct mixing of RNA in an aqueous phase with lipids in a phase comprising an organic solvent, such as ethanol. In that case, lipids or lipid mixtures can be used for particle formation, which do not form lamellar (bilayer) phases in water. In some embodiments, LNPs comprise or consist of a cationic / cationically ionizable lipid and helper lipids such as phospholipids, cholesterol, and / or polymer-conjugated lipids (e.g., polyethylene glycol (PEG) lipids). In some embodiments, in the RNA LNPs described herein the RNA (in particular, mRNA) is bound by cationically ionizable lipid that occupies the central core of the LNP. In some embodiments, polymer-conjugated lipid forms the surface of the LNP, along with phospholipids. In some embodiments, cholesterol and cationically ionizable lipid in charged and uncharged forms can be distributed throughout the LNP. In some embodiments, RNA (e.g., mRNA) or other vectors described herein may be noncovalently associated with a particle as described herein. In embodiments, the RNA (especially mRNA) may be adhered to the outer surface of the particle (surface RNA (especially surface mRNA)) and / or may be contained in the particle (encapsulated RNA (especially encapsulated mRNA)). Given their high degree of chemical flexibility, polymers are commonly used materials for nanoparticle-based delivery. Typically, cationic polymers are used to electrostatically condense the negatively charged RNA into particles, in particular nanoparticles. These positively charged groups often consist of amines that change their state of protonation in the pH range between 5.5 and 7.5, thought to lead to an ion imbalance that results in endosomal rupture. Polymers such as poly-L-lysine, polyamidoamine, protamine and polyethyleneimine, as well as naturally occurring polymers such as chitosan have all been applied to nucleic acid delivery and are suitable as cationic polymers herein. In addition, some investigators have synthesized polymers specifically for nucleic acid delivery. Poly(β-amino esters), in particular, have gained Attorney Docket No; 29539-0808WO1 / MGH 2024-658 widespread use in nucleic acid delivery owing to their ease of synthesis and biodegradability. Such synthetic polymers are also suitable as cationic polymers herein. A "polymer," as used herein, is given its ordinary meaning, i.e., a molecular structure comprising one or more repeat units (monomers), connected by covalent bonds. The repeat units can all be identical, or in some cases, there can be more than one type of repeat unit present within the polymer. In some cases, the polymer is biologically derived, i.e., a biopolymer such as a protein. In some cases, additional moieties can also be present in the polymer, for example targeting moieties. If more than one type of repeat unit is present within the polymer, then the polymer is said to be a "copolymer." It is to be understood that the polymer being employed herein can be a copolymer. The repeat units forming the copolymer can be arranged in any fashion. For example, the repeat units can be arranged in a random order, in an alternating order, or as a "block" copolymer, i.e., comprising one or more regions each comprising a first repeat unit (e.g., a first block), and one or more regions each comprising a second repeat unit (e.g., a second block), etc. Block copolymers can have two (a diblock copolymer), three (a triblock copolymer), or more numbers of distinct blocks. In some embodiments, the polymer is biocompatible. Biocompatible polymers are polymers that typically do not result in significant cell death at moderate concentrations. In some embodiments, the biocompatible polymer is biodegradable, i.e., the polymer is able to degrade, chemically and / or biologically, within a physiological environment, such as within the body. In some embodiments, polymer may be protamine or polyalkyleneimine. The term "protamine" refers to any of various strongly basic proteins of relatively low molecular weight that are rich in arginine and are found associated especially with DNA in place of somatic histones in the sperm cells of various animals (as fish). In particular, the term "protamine" refers to proteins found in fish sperm that are strongly basic, are soluble in water, are not coagulated by heat, and yield chiefly arginine upon hydrolysis. In purified form, they are used in a long-acting formulation of insulin and to neutralize the anticoagulant effects of heparin. According to the disclosure, the term "protamine" as used herein is meant to comprise any protamine amino acid sequence obtained or derived from natural or biological sources including fragments thereof and multimeric forms of said amino acid sequence or fragment thereof as well Attorney Docket No; 29539-0808WO1 / MGH 2024-658 as (synthesized) polypeptides which are artificial and specifically designed for specific purposes and cannot be isolated from native or biological sources. In one embodiment, the polyalkyleneimine comprises polyethylenimine and / or polypropylenimine, preferably polyethyleneimine. A preferred polyalkyleneimine is polyethyleneimine (PEI). The average molecular weight of PEI is preferably 0.75∙102 to 107 Da, preferably 1000 to 105 Da, more preferably 10000 to 40000 Da, more preferably 15000 to 30000 Da, even more preferably 20000 to 25000 Da. Cationic polymers (including polycationic polymers) contemplated for use herein include any cationic polymers which are able to electrostatically bind nucleic acid. In one embodiment, cationic polymers contemplated for use herein include any cationic polymers with which nucleic acid can be associated, e.g. by forming complexes with the nucleic acid or forming vesicles in which the nucleic acid is enclosed or encapsulated. Particles described herein may also comprise polymers other than cationic polymers, i.e., non-cationic polymers and / or anionic polymers. Collectively, anionic and neutral polymers are referred to herein as non-cationic polymers. As described in more detail below, the immunogens as described herein can be used to form a therapeutic composition, such as a vaccine or pharmaceutical composition. While it is possible that a vaccine can comprise the immunogen composition in a pure or substantially pure form, it will be appreciated that the vaccine can additionally or optionally include the immunogen composition and a pharmaceutically acceptable carrier or other therapeutic agent. For example, the pharmaceutically acceptable carrier can include a physiologically acceptable diluent, such as sterile water or sterile isotonic saline. As used herein, the term “pharmaceutically acceptable carrier” can refer to any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like. Additional components that may be present with the immunogen composition can include adjuvants, preservatives, chemical stabilizers, and / or other proteins. It will be appreciated that the immunogen composition can be conjugated with one or more lipoproteins, administered in liposomal form, or with an adjuvant. For example, to be efficient, vaccines can include a strong adjuvant supplying a signal for the initiation and support of the adaptive immune response in addition to immunogens as described herein. Attorney Docket No; 29539-0808WO1 / MGH 2024-658 Typically, stabilizers, adjuvants, and preservatives are optimized to determine the best formulation for efficacy in a subject. Exemplary preservatives can include, but are not limited to, chiorobutanol, potassium sorbate, sorbic acid, sulfur dioxide, propyl gallate, the parabens, ethyl vanillin, glycerin, phenol, and parachiorophenol. Suitable stabilizing ingredients can include, for example, casamino acids, sucrose, gelatin, phenol red, N-Z amine, monopotassium diphosphate, lactose, lactalbumin hydrolysate, and dried milk. Other examples of pharmaceutically acceptable carriers are known in the art and described below. Immunogens as described herein described herein administered to a subject as tuberculosis vaccine can be used either prophylactically or therapeutically. When provided prophylactically, the vaccine can be provided in advance of any evidence of an active tuberculosis infection and thereby attenuate or prevent Mycobacterium tuberculosis infection. For example, a human subject at high risk for tuberculosis infection can be prophylactically treated with a vaccine comprising the T cell immunogen composition and a pharmaceutically acceptable carrier. When provided therapeutically, the vaccine can be used to enhance a subject’s own immune response to the antigens present as a result of tuberculosis infection. Thus, in some embodiments, a therapeutically and / or prophylactically effective amount of a vaccine as described herein is an amount that elicits an immune response to the immunogens and thereby prevents, inhibits, reducing the severity of tuberculosis infection in the subject. Inhibiting a viral infection can refer to inhibiting the onset of a viral infection, inhibiting an increase in an existing viral infection, or reducing the severity of the viral infection. In this regard, one of ordinary skill in the art will appreciate that while complete inhibition of the onset of a viral infection is desirable, any degree of inhibition of the onset of a viral infection is beneficial. Likewise, one of ordinary skill in the art will appreciate that while elimination of viral infection is desirable, any degree of inhibition of an increase in an existing viral infection or any degree of a reduction of a viral infection is beneficial. Inhibition of a viral infection can be assayed by methods known in the art, such as by assessing viral load. Viral loads can be measured by methods known in the art, such as by using PCR to detect the presence of viral nucleic acids or antibody-based assays to detect the presence of viral protein in a sample (e.g., blood) from a subject. Alternatively, the number of CD4+ T cells in a viral-infected subject can be measured. A treatment that inhibits an initial or further Attorney Docket No; 29539-0808WO1 / MGH 2024-658 decrease in CD4+ T cells in a viral-infected subject, or that results in an increase in the number of CD4+ T cells in a viral-infected subject, for example, may be considered an efficacious or therapeutic treatment. Optimal dosages to be administered may be readily determined by those skilled in the art, and will vary with the particular compound used, the strength of the preparation, the mode of administration, and the advancement of the disease condition. In addition, factors associated with the particular patient being treated, including patient age, weight, diet and time of administration, will result in the need to adjust dosages. The additional therapeutic agent may be used individually, sequentially, or in combination with one or more other therapeutic agents, such as antibacterial agents. Administration to a subject may be by the same or different route of administration or together in the same pharmaceutical formulation. Coadministration in the context of this invention is defined to mean the administration of more than one therapeutic agent in the course of a coordinated treatment to achieve an improved clinical outcome. Such coadministration may also be coextensive, that is, occurring during overlapping periods of time. Pharmaceutical compositions described herein can be formulated by standard techniques using one or more physiologically acceptable carriers or excipients. Suitable pharmaceutical carriers are described herein and in “Remington's Pharmaceutical Sciences” by E. W. Martin. Vaccines of the present invention can be formulated for administration by any suitable route, including via nasally or intradermal, subdermal, intravenous, intramuscular injection, with a syringe or other devices. Transdermal administration is also contemplated, as are inhalation or aerosol administration. For administration by inhalation, the compounds may be conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, for example, dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide, or other suitable gas. In the case of a pressurized aerosol, the dosage unit can be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, for example, gelatin for use in an inhaler or insufflator can be formulated containing a powder mix of the compound and a suitable powder base, for example, lactose or starch. Attorney Docket No; 29539-0808WO1 / MGH 2024-658 Suitable formulations for transdermal application include an effective amount of a compound of the present invention with carrier. Preferred carriers include absorbable pharmacologically acceptable solvents to assist passage through the skin of the host. For example, transdermal devices are in the form of a bandage comprising a backing member, a reservoir containing the compound optionally with carriers, optionally a rate controlling barrier to deliver the compound to the skin of the host at a controlled and predetermined rate over a prolonged period of time and means to secure the device to the skin. Matrix transdermal formulations may also be used. In one implementation, a pharmaceutical composition is administered to a subject, preferably a human, at a therapeutically effective dose to prevent, treat, or control Mycobacterium tuberculosis. The dosage of pharmaceutical compositions administered is dependent on the species of warm-blooded animal (mammal), the body weight, age, individual condition, surface area of the area to be treated and on the form of administration. The size of the dose also will be determined by the existence, nature, and extent of any adverse effects that accompany the administration of a particular small molecule compound in a particular subject. Typically, a dosage of the active compounds of the present invention is a dosage that is sufficient to achieve the desired effect. Optimal dosing schedules can be calculated from measurements of compound accumulation in the body of a subject. In general, dosage may be given once or more daily, weekly, or monthly. Persons of ordinary skill in the art can easily determine optimum dosages, dosing methodologies and repetition rates. In another implementation, a pharmaceutical composition including a vaccine described herein is administered in a daily dose in the range from about 0.1 mg per kg of subject weight (0.1 mg / kg) to about 1 g / kg for multiple days. In another implementation, the daily dose is a dose in the range of about 5 mg / kg to about 500 mg / kg. In yet another implementation, the daily dose is about 10 mg / kg to about 250 mg / kg. In yet another implementation, the daily dose is about 25 mg / kg to about 150 mg / kg. A preferred dose is about 10 mg / kg. The daily dose can be administered once per day or divided into subdoses and administered in multiple doses, e.g., twice, three times, or four times per day. Following successful treatment, it may be desirable to have the subject undergo booster vaccination to prevent the recurrence of Mycobacterium tuberculosis. As can be appreciated Attorney Docket No; 29539-0808WO1 / MGH 2024-658 from the disclosure above, the present invention has a wide variety of applications. The invention is further illustrated by the following examples, which are only illustrative and are not intended to limit the definition and scope of the invention in any way. EXAMPLES The Examples are put forth for illustrative purposes only and are not intended to limit the scope of what the inventors regard as their invention. The success of mRNA vaccines in generating durable memory T cell responses (CD4+ and CD8+) presents a new opportunity for TB vaccine development by enabling a vaccine platform capable of poly-epitope vaccines and programmable antigen targeting36–41. Given human diversity, it was hypothesized that poly-epitope vaccines would be better suited to generate T cell responses capable of human population coverage which is now studied using mice engineered to express human MHC alleles42,43. Materials and Methods All experiments were carried out with at least three independent biological replicates. Appropriate statistical analyses were used for all experiments (e.g., via GraphPad Prism) and data assessed for the normality of distributions. The Student’s t-test (for normal distributions) or Mann-Whitney test (for non-normal distributions) were used when comparing two groups. To compare multiple groups, an ANOVA test followed by an appropriate post-test (Dunnett’s, Bonferroni’s, or Tukey's post-tests) was used. Statistical packages appropriate for proteomic analysis were used within Proteome Discoverer version 2.4 (DDA) and Scaffold DIA version 2.0 (DIA) to calculate false discovery rates for peptide and protein identification and to perform the appropriate comparisons between samples. For microscopy-based assays, researchers were blinded to their samples during the acquisition and analysis stages and a second researcher independently verified the phenotypes. When possible, automated image- analysis was used to score phenotypes33. Analysis pipelines were checked for errors by manually counting a subset of randomly selected images. Mtb-infected Primary Human Macrophages (MF) Generation: MF were generated by isolating CD14+ monocytes from HLA-typed leukopaks as previously describes33. Monocytes are differentiated to MF using 25 ng / mL M-CSF for 6 days. Phenotyping by flow cytometry is conducted prior to infection to confirm MF differentiation. Analysis of Attorney Docket No; 29539-0808WO1 / MGH 2024-658 monocyte-derived MF is prioritized given their abundance in granulomas; however, future studies will study other phagocytes known to be infected during Mtb infection. Mtb Infection: MF were infected with mycobacteria at an MOI of 2 for 4h prior to removing extracellular bacteria. Samples were lysed at 24, 72, and 144h for immunopeptidomics studies. Immunopeptidomics: Samples were subjected to an MHC-I or MHC-II immunoprecipitation (IP) using monoclonal antibodies which recognize conserved epitopes on human MHC-I or MHC-II (I: W6 / 32, II: Tu39). Following IP, peptides were eluted from MHC complexes. For discovery analyses, samples were fractionated prior to MS analyses. All Mtb peptide IDs were validated by manual inspection of MS / MS fragmentation spectra and synthetic peptide confirmation. For targeted SureQuant analyses, samples were prepared as described above (Rigor) with heavy isotope coded peptides added for quantitative analyses. These approaches have been used extensively for the analysis of Mtb-derived peptide presentation32,33. All validated Mtb peptides were subsequently analyzed to determine their sequence conservation across diverse sequenced clinical isolates. Mouse Experiments: Equal numbers of male and female mice are used; if there are no differences, male and female mice will be combined in all analyses. Groups of mice will typically range in size from 3-7 mice per group. This is based on a sample size calculation as follows: using a two−sided unpaired Student's t test to compare two groups of mice with an alpha probability of 0.05, a power of 0.8, and an effect size ranging from 1.6−2.3 x SD, a sample size of 3−7 mice per group is required to detect a statistically meaningful difference. M. tuberculosis culture: Mycobacterium tuberculosis (Mtb) H37Rv was grown in Difco Middlebrook 7H9 media supplemented with 10% OADC, 0.2% glycerol, and 0.05% Tween-80 to mid-log phase. Human cell isolation, differentiation, and culture: Deidentified buffy coats were obtained from Massachusetts General Hospital, except for donor C (obtained from StemCell). Samples are acquired and provided to research groups with no identifying information. PBMCs were isolated by density-based centrifugation using Ficoll (GE Healthcare). CD14+ monocytes were isolated from PBMCs using a CD14 positive-selection kit (Stemcell). Isolated monocytes were differentiated in R10 media [RPMI 1640 without phenol red (Gibco) supplemented with 10% heat-inactivated FBS (Gibco), 1% HEPES (Corning), 1% L- Attorney Docket No; 29539-0808WO1 / MGH 2024-658 glutamine (Sigma)] supplemented with 25 ng / mL GM-CSF (Biolegend, 572902) and 25 ng / mL IL-4 (Biolegend, 574006). Monocytes were cultured on tissue culture treated T75 flasks (VWR) for 6 days. Media was replaced with fresh cytokine-containing media every 3 days. HLA genotyping: Genomic DNA was extracted from 5x106PBMCs using a Qiagen DNeasy kit. HLA typing was performed using a targeted next generation sequencing (NGS) method. Briefly, locus-specific primers were used to amplify a total of 26 polymorphic exons of HLA-A & B (exons 1–4), C (exons 1–5), E (exon 3), DPA1 (exon 2), DPB1 (exons 2–4), DQA1 (exon 1–3), DQB1 (exons 2 & 3), DRB1 (exons 2 & 3), and DRB3 / 4 / 5 (exon 2) genes with Fluidigm Access Array system (Fluidigm Corporation, South San Francisco, CA 94080 USA). The 26 Fluidigm PCR amplicons were harvested from Fluidigm Access Allay IFC and pooled. Quality and quantity were checked using a Caliper LabChip GX Touch HT Nucleic Acid Analyzer (PerkinElmer, Waltham, MA 02452 USA). The PCR product library was quantitated and subjected to sequencing on an Illumina MiSeq sequencer (Illumina, San Diego, CA 92122 USA). HLA alleles and genotypes were called using the Omixon HLA Explore (version 2.0.0) software (Omixon Biocomputing Ltd., Budapest, Hungary). HLA genotyping data for donor C was instead provided by StemCell. M. tuberculosis infection: The Mtb culture was pelleted by centrifugation, washed once with PBS, resuspended in R10 media and centrifuged at low speed (500 rpm for 5 minutes) to pellet clumps, leaving a uniform suspension of bacteria in the supernatant.50 million hMDCs were infected at MOI 2.5 for 4 hr and then washed with PBS to remove extracellular Mtb. Infected hMDCs were cultured in R10 media for 72 hours before harvesting. MHC immunoprecipitation: hMDCs were harvested by collecting the culture media (containing any cells in suspension), washing adherent cells with PBS, incubating remaining adherent cells with PBS supplemented with 4 mM EDTA for 15 minutes at 37 °C, gently scraping with a cell scraper, collecting the detached cells, and washing the flask with PBS and collecting the wash. The harvested cells were then pelleted, washed with PBS, and lysed in 1 mL of MHC lysis buffer [20 mM Tris, 150 mM sodium chloride, pH 8.0, supplemented with 1% CHAPS, 1 x HALT protease and phosphatase inhibitor cocktail (Pierce), and 0.2 mM phenylmethylsulfonyl fluoride (Sigma-Aldrich)]. Attorney Docket No; 29539-0808WO1 / MGH 2024-658 BSL3 protocol: Lysate from Mtb-infected (or mock-infected) cells was sonicated using a Q500 ultrasonic water bath sonicator (Qsonica) in five 30 second pulses at an amplitude of 60%, cleared by centrifugation at 16,000 x g for 5 minutes, and sterile filtered twice using 0.2 μm filter cartridges (Pall NanoSep). Lysates were then added to protein A sepharose beads pre-conjugated with 0.5 mg of pan-MHC-I antibody (clone W6 / 32) or 0.1 mg of pan-MHC-II antibody (clone Tü39), prepared as previously described,92and incubated rotating at 4 °C overnight (12–14 hours). Beads were then washed and peptide-MHC complexes eluted as previously described.92MHC-I peptide isolation: C18 SpinTips (Protea) were washed with 0.1% trifluoroacetic acid, activated with 90% acetonitrile supplemented with 0.1% formic acid, and washed with 0.1% formic acid. Eluate from MHC-I IPs was applied to the column by centrifugation. The column was washed with 0.1% formic acid, and peptides were eluted by applying elution solvent (28% acetonitrile with 0.1% formic acid) by centrifugation twice. Eluates were snap-frozen in liquid nitrogen and lyophilized. MHC-II peptide isolation: MHC-II-associated peptides were purified using 10 kDa molecular weight cutoff filters (Cytiva NanoSep) as previously described,92snap-frozen in liquid nitrogen, and lyophilized. MS analyses: For all MS analyses, samples were analyzed using an Orbitrap Exploris 480 mass spectrometer (Thermo Fisher Scientific) coupled with an UltiMate 3000 RSLC Nano LC system (Dionex), Nanospray Flex ion source (Thermo Fisher Scientific), and column oven heater (Sonation). The MHC peptide sample was loaded onto a fused silica capillary chromatography column with an integrated electrospray tip (~1 μm orifice) prepared and packed in-house with 10 cm of 1.9 μm C18 beads (ReproSil-Pur). MHC peptide samples were resuspended in 0.1% formic acid and loaded at a flow rate of 300 nL / minute. Peptides were eluted using a flow rate of 100 nL / minute. Standard mass spectrometry parameters were as follows: spray voltage, 2.0 kV; no sheath or auxiliary gas flow; ion transfer tube temperature, 275 °C. MHC-I peptides were eluted using a gradient of 6–25% buffer B (70% Acetonitrile, 0.1% formic acid) over 75 min, 25–45% over 5 min, 45–100% over 5 min, hold for 1 min, and 100% to 3% over 2 min. MHC-II peptides were eluted using a gradient of 6–12% buffer B (70% Acetonitrile, 0.1% formic acid) over 10 min, 12–20% over 45 min, 20–25% over 10 min, 25-45% over 5 Attorney Docket No; 29539-0808WO1 / MGH 2024-658 minutes, 45-97% over 2 minutes, hold for 1 min, and 97% to 3% over 2 min. Full scan mass spectra (120,000 resolution 350–1200 m / z for MHC-I, 350-1800 m / z for MHC-II) were detected in the orbitrap analyzer after accumulation of 3x106ions (normalized AGC target of 300%) or 25 ms. For every full scan, MS / MS scans were collected during a 3 s cycle time. Ions were isolated (0.4 m / z isolation width) using the standard AGC target and automatic determination of maximum injection time, fragmented by HCD with 30% CE, and scanned at a resolution of 120,000. Charge states <2 and >4 were excluded. In DDA analyses, precursors were excluded from selection for 30 seconds if fragmented n=2 times within a 20- second window. For PathMHC PRM analyses, inclusion list masses were matched by m / z and charge state, with a mass tolerance of 5 ppm. Acquisition was scheduled for a window of 3 minutes centered on the observed retention time of the target precursor ion in the DDA analysis in which it was originally detected. Precursors were excluded from selection for 4 seconds after being fragmented 1 time. For analyses of MHC-I peptides from hMDCs infected with Mtb, 40% of the sample was used for each analysis while 20% was reserved for subsequent validation using SureQuant. DDA-only MHC-I analyses of MHC-I peptides from Mtb-infected hMDCs were performed without prior offline fractionation (donor E), or with offline fractionation by reversed-phase HPLC as previously described33(donor D). PathMHC computational pipeline: The PathMHC pipeline first identifies MS1 peaks (features) using Dinosaur (version 1.2.0), then aligns these features between a sample from infected cells and a mock-infected control using DeepRTalign (version 1.1.3). MS1 features detected in the infected sample are excluded if they are mapped to a feature in the mock- infected control by DeepRTalign, or if they match a peptide already identified by DDA from a provided list of peptide-spectrum matches to within a mass tolerance of 10 ppm and retention time tolerance defined by the peak boundaries set by Dinosaur. The remaining MS1 features (i.e., those not previously identified by DDA and with no corresponding peak in the mock-infected control) are then scored using AutoMS, using an XIC length of 40 seconds and an XIC mass tolerance of 10 ppm for MHC-I peptides and 40 ppm for MHC-II peptides. A final inclusion list is generated consisting of precursors meeting the following criteria: For Attorney Docket No; 29539-0808WO1 / MGH 2024-658 MHC-I, charge state 2-4, retention time less than 90 minutes (from the end of sample loading), AutoMS signal to noise ratio score (SNR) > 1 or AutoMS score > 0.2. For MHC-II, charge state 2-3, retention time less than 90 minutes, AutoMS signal to noise ratio (SNR) > 1.5 or AutoMS score > 0.3. MS data search and manual inspection: All mass spectra were analyzed with Proteome Discoverer (PD, version 3.0) and searched using Sequest with rescoring using INFERYS and Percolator against a custom database comprising the Uniprot human proteome (UP000005640) together with either the Uniprot Mycobacterium tuberculosis H37Rv proteome (UP000001584) or the Mycobacterium smegmatis mc2155 proteome (UP000006158). No enzyme was used, and variable modifications included oxidized methionine for all analyses. Peptide-spectrum matches from MHC-I analyses were filtered with the following criteria: search engine rank = 1, length between 8 and 13 amino acids, XCorr ≥ 2.0, spectral angle ≥ 0.6, and percolator q-value < 0.05. Peptide-spectrum matches from MHC-II analyses were filtered with the following criteria: search engine rank = 1, length between 8 and 30 amino acids, XCorr ≥ 2.0, spectral angle ≥ 0.6, and percolator q- value < 0.05. Identifications (IDs) of putative Mtb-derived peptides were rejected if any peptide- spectrum matches (PSMs) for the same peptide were found in the unfiltered DDA MS data for the corresponding mock-infected control. For each putative Mtb peptide identified, MS / MS spectra and extracted ion chromatograms (XIC) were manually inspected, and the ID was only accepted for further validation if it met the following criteria: (1) MS / MS spectra contained enough information to unambiguously assign a majority of the peptide sequence; (2) neutral losses were consistent with the chemical properties of the peptide; (3) manual de novo sequencing did not reveal an alternate peptide sequence that would explain a greater number of MS / MS spectrum peaks; (4) XIC showed a peak in MS intensity at the mass to charge ratio (m / z) of the peptide precursor ion at the retention time at which it was identified that did not appear in the corresponding mock-infected control. Peptides that met these criteria were further validated using SureQuant (see below). Synthetic standard survey MS analyses: DDA MS analysis of the SIL peptide mixture was performed as described above (see MS analyses) with the following modifications: Attorney Docket No; 29539-0808WO1 / MGH 2024-658 Peptides were eluted using a gradient of 6–35% buffer B over 30 min, 35–45% over 2 min, 45–100% over 3 min, and 100% to 2% over 1 min. No dynamic exclusion was used. A second set of survey analyses was performed on the mixture of SIL peptides with background matrix using the full SureQuant acquisition method (see below). SIL peptides were spiked into a mixture of MHC-I peptides purified as described above from THP-1 cells differentiated into macrophages via 24 hr of treatment with 150 nM phorbol myristate acetate (PMA), which provided a representative background matrix. Because SIL amino acids are not 100% pure, SIL peptide concentrations were adjusted and survey analyses were repeated until the SIL peptide could be reliably detected while minimizing background signal detected at the mass of the biological peptide. In the final SIL standard mixture, 100 fmol of each peptide was used per sample for all epitopes except two peptides for which 10 fmol was used per sample (KIYSEADEAWRK (SEQ ID NO:84) and RADEEQQQAL (SEQ ID NO:81)). Validation of candidate Mtb peptides by SureQuant MS analysis: Stable isotope labeled (SIL) synthetic peptide standards were ordered from BioSynth as a crude peptide library. Standard MS parameters and MS1 scan parameters were as described above, except that a scan range of 380-1200 m / z was used. The custom SureQuant method was built based on the template provided in the Thermo Orbitrap Exploris Series 2.0 method editor. After the optimal charge state and most intense product ions were determined via a survey analysis of the synthetic SIL peptide standards alone (see above), a method branch was created for each m / z offset between the SIL peptide and biological peptide as previously described.35The m / z tolerance for detection of SIL standards was set at 10 ppm. A resolution of 15,000 and automatically determined ion accumulation time was used for MS / MS scans of the SIL standards, and a resolution of 240,000 with a maximum accumulation time of 1 s was used for MS / MS scans of the biological peptide. An MS / MS scan of the light (biological) peptide was triggered upon detection of 3 or more of the top 6 product ions (mass tolerance 20 ppm) in a scan of the corresponding SIL standard. Results were analyzed using Skyline Daily Build 24.1.1.202. Attorney Docket No; 29539-0808WO1 / MGH 2024-658 Example 1: Antigen Presentation by Mtb-infected Human Macrophages (MF) Define Which Antigens are Presented by Infected MF and How Mtb Processes Control Their Presentation Studies of Mtb-derived peptide presentation have revealed important biological observations with translational implications. First, there is no Mtb protein presented across all MHC-I alleles33. This suggests that polyepitope vaccines will be needed to effectively elicit CD8+ T cells via vaccination across human diversity. CFP10 has now been identified as an antigen presented on MHC-II across all donors tested to date and therefore, CFP10 is a high value antigen for eliciting CD4+ T cell responses and a priority for devising strategies that optimize presentation of the appropriate CFP10-derived peptides on MHC-II. As both shared and unique Mtb proteins are presented on MHC-I and MHC-II, harnessing CD4+ and CD8+ T cell responses will require potentially distinct vaccine strategies. Only EsxB (CFP10), EsxG, and PPE51 were presented on MHC-I and MHC-II. Strategies to facilitate antigen presentation of vaccine-derived antigens on MHC-I and MHC-II are described herein below. Mass spectrometry-based approaches have now been developed to rigorously identify and quantify Mtb-derived peptide presentation on MHC-I and MHC-II in Mtb-infected primary human cells using as few as one million cells32,33,35. Here, the use of these methods applied to virulent Mtb in a BSL3 setting are described to address a critical gap in our understanding of what Mtb antigens are presented by infected phagocytes. These methods operate in an unbiased discovery or targeted mode (SureQuant). SureQuant facilitates targeted and quantitative analysis of antigen presentation during Mtb infection. SureQuant-MHC is a targeted mass spectrometry (MS) method based on parallel reaction monitoring, in which endogenous peptides are quantified relative to synthetic heavy-isotope coded peptide standards spiked into the biological sample at known concentrations33–35,45–47. SureQuant quantification occurs by comparing the light-to-heavy ratio of the intensities of multiple co-eluting fragment ions per peptide and requires matching MS / MS fragmentation spectra and coelution of the synthetic and endogenous versions of the peptide, thus providing accurate quantification and effectively eliminating false positive identifications (Figure 2). Parallel reaction monitoring (PRM) based approaches are used for quality control in pharmaceutical drug production and in both pre- clinical and clinical assays47. Attorney Docket No; 29539-0808WO1 / MGH 2024-658 By identifying proteins presented on MHC-I and MHC-II, direct evidence of Mtb protein interaction with components of host antigen presentation pathways is provided using SureQuant- MHC. Performing antigen presentation studies in Mtb-infected primary human macrophages (MF) lacking the peptide transporter, TAP, it is possible to determine which Mtb proteins gain access to the cytosol (Figure 3). Using these methods overcomes the need for T cell clones to study antigen presentation thus facilitating the study of antigen presentation and immunodominance in new ways. Immunodominance refers to the observation that immune responses are only mounted against a subset of peptides from a protein29,30. By unbiased immunopeptidomics, a peptide derived from EsxA presented on the MHC-I allele HLA- A*02:01 was detected. Next, a high-throughput binding assay was performed to identify additional EsxA-derived peptides that bind HLA- A*02:01. After identifying these peptides, SureQuant was used to determine if these peptides were generated during Mtb infection and presented on HLA-A*02:01. Uninfected or Mtb- infected HLA-A*02:01+ MF. In both conditions, the synthetic peptides that were spiked were detected, thus demonstrating that these peptides, if present, can be detected by mass spectrometry. Only the EsxA peptide identified by unbiased immunopeptidomics was detected and not the other peptides that bound in a high- throughput binding assay (Figure 4)33. The same principles are true for EsxG. This approach was extended to track more peptides derived from type 7 secretion system (T7SS) substrates and their presentation on HLA- A*02:01 as a proof of concept. A total of 286 peptides derived from T7SS substrates which can bind HLA-A*02:01 in vitro were tracked. Only 2 of these peptides were presented during Mtb infection, suggesting that while T7SS substrates are enriched, only a small fraction of these peptides can bind MHC-I and be presented during infection, which is consistent with this present model of immunodominance. These data further suggest that MHC binding alone is not sufficient to predict presentation during Mtb infection. Sequences, source proteins, associated HLA alleles, and donors for each validated Mtb- derived MHC-I peptide are shown in Figure 5. Sequences, source proteins, and donors for each Mtb-derived MHC-II peptide are shown in Figure 6. Each of these peptides was tracked by mass spectrometry (SureQuant) to confirm their MHC-I / II presentation on Mtb-infected human monocyte-derived dendritic cells33, Figure 7, (and data not shown). Partial mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et Attorney Docket No; 29539-0808WO1 / MGH 2024-658 al., 2022) partner repository with the dataset identifiers PXD037837 (DDA data) and PXD037843 (SureQuant data). By defining antigens presented by Mtb-infected MF as well as identifying vaccine designs that recapitulate the presentation of antigens that are presented during infection, the development of new TB vaccines will incorporate human diversity and lessons from immunodominance. Example 2: mRNA Delivery of an EsxJ-derived Peptide Generated T a Cell Response The in vitro delivery of mRNA to primary human-monocyte derived MF has now been optimized to allow for direct comparison of antigen presentation. Previous subunit TB vaccines have not been characterized using this lens. A T cell clone that recognizes an EsxJ-derived peptide (QTVEDEARRMW) on HLA- B*57:01 (detected by mass spectrometry) was utilized. An mRNA vaccine was engineered to encode a full-length EsxJ mRNA or relevant EsxJ-peptide with or without an MHC-I trafficking domain (MITD). Activation of the T cell clone by EsxJ mRNAs with or without the MITD was detected (Figure 7). These data show that mRNA vaccines as described herein generate relevant peptide-MHC complexes. Example 3. Lysosomal Signal Sequences Increase the Quantity of Peptide-MHC Complex Produced To directly assess the effect of subcellular localization of mRNA-encoded Mtb antigens on MHC-II peptide presentation, in vitro transcription templates were designed for production of nucleotide-modified mRNA encoding EsxB or EsxG, translationally fused to signals targeting them to a range of subcellular compartments, namely the cytosol, endosomes, or lysosomes. mRNAs encoding different Mtb genes were delivered to human monocyte-derived dendritic cells, and 24 hours later, samples were lysed for MHC-II immunopeptidomics. Transfections were performed as follows: For each flask of 1 ✕ 107hMDCs, 15 μL of MessengerMax lipofectamine (Thermo) was mixed with 125 μL Opti-MEM (Gibco), vortexed for 3 seconds, and incubated for 10 minutes at room temperature.10 pmol of mRNA was diluted in 125 μL of Opti- MEM, added to the lipofectamine / Opti-MEM mixture (for a final volume 250 μL of Opti-MEM) and incubated at room temperature for an additional 5 minutes. The mixture was then added to the media of the flask of hMDCs.4 hours after adding the mRNA / lipofectamine / Opti-MEM Attorney Docket No; 29539-0808WO1 / MGH 2024-658 mixture, the media was removed, the cells were washed with PBS, and fresh R10 media was added. hMDCs were incubated overnight (16-18 hours) after mRNA transfection before being harvested for MHC-II peptide isolation. For subsequent MHC immunoprecipitation, hMDCs were harvested by collecting the culture media (containing any cells in suspension), washing adherent cells with PBS, incubating remaining adherent cells with PBS supplemented with 4 mM EDTA for 15 minutes at 37 °C, gently scraping with a cell scraper, collecting the detached cells, and washing the flask with PBS and collecting the wash. Harvested cells were pelleted by centrifugation. The harvested cells were then washed with PBS, and lysed in 1 mL of MHC lysis buffer [20 mM Tris, 150 mM sodium chloride, pH 8.0, supplemented with 1% CHAPS, 1 x HALT protease and phosphatase inhibitor cocktail (Pierce), and 0.2 mM phenylmethylsulfonyl fluoride (Sigma-Aldrich)]. Lysate from mRNA-transfected hMDCs was sonicated using a probe sonicator in three 10 second pulses at an amplitude of 30% and cleared by centrifugation at 16,000 x g for 5 minutes. For quantitative SureQuant experiments, lysate protein concentrations were normalized by BCA assay and 100 fmol of each of three soluble peptide-DRA1*01:01- DRB1*07:01 complexes containing SIL peptides (heavy isotope-labeled peptide-MHCs – hipMHCs) (ImmunAware custom order) were spiked into each sample to be used as internal standards. Lysates were then added to protein A sepharose beads pre-conjugated with pan- MHC-II antibody (clone Tü39) – or other antibody, where specified – prepared as previously described.18For untargeted discovery MS experiments, 0.25 mg of antibody was used. For targeted MS experiments, 0.1 mg of antibody was used. Beads were incubated with lysate rotating at 4 °C overnight (12–14 hours). Beads were then washed and peptide-MHC complexes eluted. Quantitative SureQuant analyses were performed as described hereinabove. Data were analyzed using Skyline Daily Build 22.1.9.208. For each target peptide, the intensities of the three most intense product ions were integrated over the time during which the peptide was scanned. These intensities were normalized by the integrated intensities of the corresponding product ions from the corresponding SIL standard over the same time interval, and these ratios were averaged. Finally, these averaged light / heavy ratios were normalized by the average of the corresponding ratios for the hipMHC standard peptides and normalized to a reference condition. Using extracted ion chromatograms of peptide fragment ions, the quantity of peptide-MHC complex formation as a function of appended signal sequence (LAMP1, LAMP2, LAMP3) was Attorney Docket No; 29539-0808WO1 / MGH 2024-658 compared. It was determined that lysosomal signal sequences increased the quantity of peptide- MHC complex produced when equimolar quantities of mRNA were administered (FIGs.9A-C). Example 4. Codelivery of Mtb Antigens Can Improve Antigen Presentation of EsxB EsxB and EsxA are naturally cosecreted by Mtb as a heterodimer. Codelivery of a lysosome-targeted EsxB with a lysosome-targeted EsxA was tested to determine whether coexpression would enhance presentation of EsxB on MHC-II. hMDCs were transfected with mRNAs encoding lysosome-targeted EsxB alone or co-transfected with lysosome-targeted EsxA and EsxB. Representative SureQuant fragment ion chromatograms for EsxB-derived MHC-II peptides presented by HLA-DRB1*01:01-expressing hMDCs are shown in Figure 10, left panel. Quantification of EsxB-derived MHC-II peptides presented by HLA-DRB1*01:01- expressing hMDCs transfected with mRNAs encoding lysosome-targeted EsxB alone or co- transfected with lysosome-targeted EsxA and EsxB are shown in Figure 10, right panel. It was determined that codelivery of EsxA with EsxB enhanced presentation on MHC-II (Figure 10). Example 5. PathMHC identified potential TB vaccine targets presented on MHC-I We next applied PathMHC to analyze the MHC-I repertoire of hMDCs infected with Mtb to identify potential TB vaccine targets. The PathMHC workflow requires MHC peptide samples isolated from cells infected with a pathogen of interest and from mock-infected control cells. First, each sample is divided in two equal parts, and one half of each sample (infected and mock- infected) is analyzed by untargeted MS (DDA). Second, the untargeted MS data are analyzed using a computational pipeline that finds precursor ions that are specific to infected cells and absent in the mock-infected control, excluding those already identified in the untargeted analysis (see Methods). Finally, this set of putatively infection-specific precursor ions is used as an inclusion list for a targeted MS analysis of the remaining half of each sample using parallel reaction monitoring (PRM) to identify pathogen-derived peptides previously missed in the untargeted analysis. The PathMHC computational pipeline comprised three steps: First, LC-MS features (i.e., precursor ions) were annotated using the feature detection algorithm Dinosaur.93Second, the LC- MS features were aligned across the two samples using DeepRTAlign,94and features in the infected sample that were not paired with any feature in the mock-infected control were selected for further analysis. Finally, LC-MS features that had a charge state and retention time consistent Attorney Docket No; 29539-0808WO1 / MGH 2024-658 with MHC peptides were scored for quality (including signal-to-noise ratio) using the autoencoder-based scoring algorithm AutoMS.95Peaks that met scoring thresholds are added to the inclusion list for the follow-up targeted analysis with PRM. hMDCs were infected with Mtb at an MOI of 2.5 for 72 hours prior to isolation of MHC-I peptides (Figure 11A). Mtb-derived peptides comprised 0.116% of MHC-I peptide IDs in infected hMDCs in DDA analyses and 0.156% on average in PRM analyses (Figure 11B), suggesting a modest enrichment despite the low overall prevalence of Mtb peptides in this system. We obtained a total of 19 Mtb-derived peptide IDs (16 unique epitopes), including 4 identified in PRM analyses that had not been previously identified by DDA (2 unique epitopes) (Figure 11C). Peptides identified by PathMHC PRM analyses that were previously missed in DDA analyses derived from EspC and the EsxJ family of proteins – EsxJ, EsxK, EsxP, and EsxW (abbreviated here as EsxJKPW). We next examined whether these Mtb-derived peptides identified using our in vitro experiments showed evidence of immunogenicity in individuals with prior evidence of Mtb exposure. We queried the Immune Epitope Database (IEDB),64which catalogs studies of immunogenic peptides identified in human cohorts. Not every Mtb-derived peptide has been comprehensively tested for human immunogenicity, so a lack of a reported T cell response to a given peptide in IEDB does not indicate lack of immunogenicity. We found that five of the peptides we detected by PathMHC are immunogenic in people (LLDEGKQSL – EsxA, LLDAHIPQL – EsxG, AEMKTDAATL – EsxB, EMKTDAATL – EsxB, and QEAGNFERI – EsxB).96,12The overall space of possible 8- to 11-mer Mtb peptides that could hypothetically be candidate MHC-I epitopes is large, so matching immunogenic epitopes by coincidence is unlikely. These results demonstrate that the application of PathMHC to Mtb- infected samples in vitro can identify immunogenic peptides with in vivo relevance. We validated the Mtb MHC-I peptide IDs we obtained from PathMHC by SureQuant33(a targeted MS method that compares biological MHC peptides with stable isotope labeled synthetic standards to demonstrate identical retention times and MS / MS spectra) along with 5 other epitopes that had been separately identified in DDA-only analysis of MHC-I peptides from hMDCs (FIG.12). Unsupervised clustering of MHC-I peptides using Gibbs clustering97,98resulted in clusters with sequence motifs that matched the known peptide binding preferences of HLA alleles expressed by each donor. Each Mtb-derived peptide was predicted to bind at least one class I human leukocyte antigen (HLA) allele expressed by the corresponding donor by the Attorney Docket No; 29539-0808WO1 / MGH 2024-658 MHC peptide prediction algorithm NetMHCpan99. These results increased our confidence that the peptides identified were authentic Mtb MHC-I epitopes. REFERENCES 1. Kyu, H. H. et al. The global burden of tuberculosis: results from the Global Burden of Disease Study 2015. Lancet Infect. Dis.18, 261–284 (2018). 2. Pai, M., Kasaeva, T. & Swaminathan, S. Covid-19’s Devastating Effect on Tuberculosis Care — A Path to Recovery. N. Engl. J. Med.386, 1490–1493 (2022). 3. Portnoy, A. et al. The cost and cost-effectiveness of novel tuberculosis vaccines in low- and middle-income countries: A modeling study. PLOS Med.20, e1004155 (2023). 4. Weerasuriya, C. K. et al. The epidemiologic impact and cost-effectiveness of new tuberculosis vaccines on multidrug-resistant tuberculosis in India and China. BMC Med.19, 60 (2021). 5. Scanga, C. A. et al. Depletion of Cd4+ T Cells Causes Reactivation of Murine Persistent Tuberculosis despite Continued Expression of Interferon γ and Nitric Oxide Synthase 2. J. Exp. Med.192, 347–358 (2000). 6. Diedrich, C. R. et al. SIV and CD4 depletion distinctly reactivate latent Mycobacterium. Tuberculosis infection. J. Immunol.204, 225.35-225.35 (2020). 7. Flynn, J. L., Goldstein, M. M., Triebold, K. J., Koller, B. & Bloom, B. R. Major histocompatibility complex class I-restricted T cells are required for resistance to Mycobacterium tuberculosis infection. Proc. Natl. Acad. Sci. U. S. A.89, 12013–12017 (1992). 8. Guleria, I., Mukherjee, R. & Kaufmann, S. H. E. In vivo depletion of CD4 and CD8 T lymphocytes impairs Mycobacterium w vaccine-induced protection against M. tubercolosis in mice. Med. Microbiol. Immunol. (Berl.) 182, 129–135 (1993). 9. Chen, C. Y. et al. A Critical Role for CD8 T Cells in a Nonhuman Primate Model of Tuberculosis. PLOS Pathog.5, e1000392 (2009). 10. Lin, P. L. & Flynn, J. L. CD8 T cells and Mycobacterium tuberculosis infection. Semin. Immunopathol.37, 239–249 (2015). 11. Lewinsohn, D. A. et al. Comprehensive definition of human immunodominant CD8 antigens in tuberculosis. NPJ Vaccines 2, 8 (2017). Attorney Docket No; 29539-0808WO1 / MGH 2024-658 12. Lewinsohn, D. A. et al. Immunodominant tuberculosis CD8 antigens preferentially restricted by HLA-B. PLoS Pathog.3, 1240–1249 (2007). 13. Lewinsohn, D. M. et al. Human Mycobacterium tuberculosis CD8 T Cell Antigens / Epitopes Identified by a Proteomic Peptide Library. PLOS ONE 8, e67016 (2013). 14. Arlehamn, C. S. L. et al. A Quantitative Analysis of Complexity of Human Pathogen- Specific CD4 T Cell Responses in Healthy M. tuberculosis Infected South Africans. PLOS Pathog.12, e1005760 (2016). 15. Lindestam Arlehamn, C. S., Lewinsohn, D., Sette, A. & Lewinsohn, D. Antigens for CD4 and CD8 T Cells in Tuberculosis. Cold Spring Harb. Perspect. Med.4, a018465 (2014). 16. Glanville, J. et al. Identifying specificity groups in the T cell receptor repertoire. Nature 547, 94–98 (2017). 17. Huang, H., Wang, C., Rubelt, F., Scriba, T. J. & Davis, M. M. Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening. Nat. Biotechnol.38, 1194–1202 (2020). 18. Musvosvi, M. et al. T cell receptor repertoires associated with control and disease progression following Mycobacterium tuberculosis infection. Nat. Med.29, 258–269 (2023). 19. Lewinsohn, D. M. et al. Secreted Proteins from Mycobacterium tuberculosis Gain Access to the Cytosolic MHC Class-I Antigen-Processing Pathway1. J. Immunol.177, 437–442 (2006). 20. Lin, P. L. et al. CD4 T Cell Depletion Exacerbates Acute Mycobacterium tuberculosis While Reactivation of Latent Infection Is Dependent on Severity of Tissue Depletion in Cynomolgus Macaques. AIDS Res. Hum. Retroviruses 28, 1693–1702 (2012). 21. Goulder, P. J. R. & Watkins, D. I. Impact of MHC class I diversity on immune control of immunodeficiency virus replication. Nat. Rev. Immunol.8, 619–630 (2008). 22. Huisman, B. D., Balivada, P. A. & Birnbaum, M. E. Yeast display platform with expression of linear peptide epitopes for high-throughput assessment of peptide-MHC-II binding. J. Biol. Chem.299, 102913 (2023). 23. Huisman, B. D., Dai, Z., Gifford, D. K. & Birnbaum, M. E. A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding. eLife 11, e78589 (2022). 24. Rappazzo, C. G., Huisman, B. D. & Birnbaum, M. E. Repertoire-scale determination of class II MHC peptide binding via yeast display improves antigen prediction. Nat. Commun.11, 4414 (2020). Attorney Docket No; 29539-0808WO1 / MGH 2024-658 25. Greenbaum, J. et al. Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes. Immunogenetics 63, 325–335 (2011). 26. Peters, B. et al. A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules. PLOS Comput. Biol.2, e65 (2006). 27. Wieczorek, M. et al. Major Histocompatibility Complex (MHC) Class I and MHC Class II Proteins: Conformational Plasticity in Antigen Presentation. Front. Immunol.8, (2017). 28. Trowsdale, J. & Knight, J. C. Major Histocompatibility Complex Genomics and Human Disease. Annu. Rev. Genomics Hum. Genet.14, 301–323 (2013). 29. Yewdell, J. W. Confronting Complexity: Real-World Immunodominance in Antiviral CD8+ T Cell Responses. Immunity 25, 533–543 (2006). 30. Yewdell, J. W. & Bennink, J. R. Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses. Annu. Rev. Immunol.17, 51–88 (1999). 31. Nyendak, M. et al. Adenovirally-Induced Polyfunctional T Cells Do Not Necessarily Recognize the Infected Target: Lessons from a Phase I Trial of the AERAS-402 Vaccine. Sci. Rep.6, 36355 (2016). 32. Flyer, D. C. et al. Identification by mass spectrometry of CD8(+)-T-cell Mycobacterium tuberculosis epitopes within the Rv0341 gene product. Infect. Immun.70, 2926–2932 (2002). 33. Leddy, O., White, F. M. & Bryson, B. D. Immunopeptidomics reveals determinants of Mycobacterium tuberculosis antigen presentation on MHC class I. eLife 12, e84070 (2023). 34. Stopfer, L. E. et al. MEK inhibition enhances presentation of targetable MHC-I tumor antigens in mutant melanomas. Proc. Natl. Acad. Sci. U. S. A.119, e2208900119 (2022). 35. Stopfer, L. E. et al. Absolute quantification of tumor antigens using embedded MHC-I isotopologue calibrants. Proc. Natl. Acad. Sci. U. S. A.118, e2111173118 (2021). 36. Moss, P. The T cell immune response against SARS-CoV-2. Nat. Immunol.23, 186–193 (2022). 37. Painter, M. M. et al. Rapid induction of antigen-specific CD4+ T cells is associated with coordinated humoral and cellular immunity to SARS-CoV-2 mRNA vaccination. Immunity 54, 2133-2142.e3 (2021). 38. Lim, J. M. E. et al. A comparative characterization of SARS-CoV-2-specific T cells induced by mRNA or inactive virus COVID-19 vaccines. Cell Rep. Med.3, 100793 (2022). Attorney Docket No; 29539-0808WO1 / MGH 2024-658 39. Kuse, N. et al. Long-term memory CD8+ T cells specific for SARS-CoV-2 in individuals who received the BNT162b2 mRNA vaccine. Nat. Commun.13, 5251 (2022). 40. Goel, R. R. et al. mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern. Science 374, abm0829 (2021). 41. Mateus, J. et al. Low-dose mRNA-1273 COVID-19 vaccine generates durable memory enhanced by crossreactive T cells. Science 374, eabj9853 (2021). 42. Pasquetto, V. et al. HLA-A*0201, HLA-A*1101, and HLA-B*0702 transgenic mice recognize numerous poxvirus determinants from a wide variety of viral gene products. J. Immunol. Baltim. Md 1950175, 5504–5515 (2005). 43. Boucherma, R. et al. HLA-A*01:03, HLA-A*24:02, HLA-B*08:01, HLA-B*27:05, HLA- B*35:01, HLAB* 44:02, and HLA-C*07:01 Monochain Transgenic / H-2 Class I Null Mice: Novel Versatile Preclinical Models of Human T Cell Responses. J. Immunol.191, 583–593 (2013). 44. Cole, S. T. et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537–544 (1998). 45. Stopfer, L. E. et al. High-Density, Targeted Monitoring of Tyrosine Phosphorylation Reveals Activated Signaling Networks in Human Tumors. Cancer Res.81, 2495–2509 (2021). 46. Stopfer, L. E., D’Souza, A. D. & White, F. M.1,2,3, MHC: a review of mass-spectrometry- based immunopeptidomics methods for relative and absolute quantification of pMHCs. Immuno- Oncol. Technol.11, 100042 (2021). 47. Arieta, C. M. et al. The T-cell-directed vaccine BNT162b4 encoding conserved non-spike antigens protects animals from severe SARS-CoV-2 infection. Cell 186, 2392-2409.e21 (2023). 48. Champion, P. A. D., Stanley, S. A., Champion, M. M., Brown, E. J. & Cox, J. S. C-Terminal Signal Sequence Promotes Virulence Factor Secretion in Mycobacterium tuberculosis. Science 313, 1632–1636 (2006). 49. Watson, R. O., Manzanillo, P. S. & Cox, J. S. Extracellular M. tuberculosis DNA Targets Bacteria for Autophagy by Activating the Host DNA-Sensing Pathway. Cell 150, 803–815 (2012). 50. Manzanillo, P. S., Shiloh, M. U., Portnoy, D. A. & Cox, J. S. Mycobacterium Tuberculosis Activates the DNA-Dependent Cytosolic Surveillance Pathway within Macrophages. Cell Host Microbe 11, 469–480 (2012). Attorney Docket No; 29539-0808WO1 / MGH 2024-658 51. Bettencourt, P. et al. Identification of antigens presented by MHC for vaccines against tuberculosis. Npj Vaccines 5, 1–14 (2020). 52. Kamath, A., Woodworth, J. S. M. & Behar, S. M. Antigen-Specific CD8+ T Cells and the Development of Central Memory during Mycobacterium tuberculosis Infection1. J. Immunol. 177, 6361–6369 (2006). 53. Caruso, A. M. et al. Mice Deficient in CD4 T Cells Have Only Transiently Diminished Levels of IFN-γ, Yet Succumb to Tuberculosis1. J. Immunol.162, 5407–5416 (1999). 54. Tascon, R. E., Stavropoulos, E., Lukacs, K. V. & Colston, M. J. Protection against Mycobacterium tuberculosis Infection by CD8+ T Cells Requires the Production of Gamma Interferon. Infect. Immun.66, 830–834 (1998). 55. Osman, M. M., Pagán, A. J., Shanahan, J. K. & Ramakrishnan, L. Mycobacterium marinum phthioceroldimycocerosates enhance macrophage phagosomal permeabilization and membrane damage. PloS One15, e0233252 (2020). 56. Quigley, J. et al. The Cell Wall Lipid PDIM Contributes to Phagosomal Escape and Host Cell Exit of Mycobacterium tuberculosis. mBio 8, 10.1128 / mbio.00148-17 (2017). 57. Lerner, T. R. et al. Phthiocerol dimycocerosates promote access to the cytosol and intracellular burden of Mycobacterium tuberculosis in lymphatic endothelial cells. BMC Biol. 16, 1 (2018). 58. Augenstreich, J. et al. ESX-1 and phthiocerol dimycocerosates of Mycobacterium tuberculosis act in concert to cause phagosomal rupture and host cell apoptosis. Cell. Microbiol. 19, e12726 (2017). 59. van der Wel, N. et al. M. tuberculosis and M. leprae Translocate from the Phagolysosome to the Cytosol in Myeloid Cells. Cell 129, 1287–1298 (2007). 60. Bell, S. L., Lopez, K. L., Cox, J. S., Patrick, K. L. & Watson, R. O. Galectin-8 Senses Phagosomal Damage and Recruits Selective Autophagy Adapter TAX1BP1 To Control Mycobacterium tuberculosis Infection in Macrophages. mBio 12, e0187120 (2021). 61. Morrison, H. M. et al. Deficiency in Galectin-3, -8, and -9 impairs immunity to chronic Mycobacterium tuberculosis infection but not acute infection with multiple intracellular pathogens. PLOS Pathog.19, e1011088 (2023). 62. Mehra, A. et al. Mycobacterium tuberculosis Type VII Secreted Effector EsxH Targets Host ESCRT to Impair Trafficking. PLOS Pathog.9, e1003734 (2013). Attorney Docket No; 29539-0808WO1 / MGH 2024-658 63. Mittal, E. et al. Mycobacterium tuberculosis Type VII Secretion System Effectors Differentially Impact the ESCRT Endomembrane Damage Response. mBio 9, e01765-18 (2018). 64. Vita, R. et al. The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res.47, D339–D343 (2019). 65. Boisson-Dupuis, S. et al. Tuberculosis and impaired IL-23-dependent IFN-γ immunity in humans homozygous for a common TYK2 missense variant. Sci. Immunol.3, eaau8714 (2018). 66. Ogishi, M. et al. Inherited human ITK deficiency impairs IFN-γ immunity and underlies tuberculosis. J. Exp. Med.220, e20220484 (2023). 67. Rosain, J. et al. Human IRF1 governs macrophagic IFN-γ immunity to mycobacteria. Cell 186, 621-645.e33 (2023). 68. Gideon, H. P. et al. Variability in tuberculosis granuloma T cell responses exists, but a balance of pro- and anti-inflammatory cytokines is associated with sterilization. PLoS Pathog. 11, e1004603 (2015). 69. Gideon, H. P. et al. Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control. Immunity 55, 827-846.e10 (2022). 70. Lyadova, I. V. & Panteleev, A. V. Th1 and Th17 Cells in Tuberculosis: Protection, Pathology, and Biomarkers. Mediators Inflamm.2015, 854507 (2015). 71. Ilghari, D. et al. Solution Structure of the Mycobacterium tuberculosis EsxG^EsxH Complex. J. Biol. Chem.286, 29993–30002 (2011). 72. Tufariello, J. M. et al. Separable roles for Mycobacterium tuberculosis ESX-3 effectors in iron acquisition and virulence. Proc. Natl. Acad. Sci.113, E348–E357 (2016). 73. Tak, U., Dokland, T. & Niederweis, M. Pore-forming Esx proteins mediate toxin secretion by Mycobacterium tuberculosis. Nat. Commun.12, 394 (2021). 74. Poweleit, N. et al. The structure of the endogenous ESX-3 secretion system. eLife 8, e52983 (2019). 75. Atmakuri, K. & Fortune, S. M. Regulation of protein secretion by ... protein secretion? Cell Host Microbe 4, 190–191 (2008). 76. Fortune, S. M. et al. Mutually dependent secretion of proteins required for mycobacterial virulence. Proc. Natl. Acad. Sci. U. S. A.102, 10676–10681 (2005). 77. Houben, E. N. G., Korotkov, K. V. & Bitter, W. Take five - Type VII secretion systems of Mycobacteria. Biochim. Biophys. Acta 1843, 1707–1716 (2014). Attorney Docket No; 29539-0808WO1 / MGH 2024-658 78. Lightbody, K. L. et al. Molecular features governing the stability and specificity of functional complex formation by Mycobacterium tuberculosis CFP-10 / ESAT-6 family proteins. J. Biol. Chem.283, 17681–17690 (2008). 79. Renshaw, P. S. et al. Structure and function of the complex formed by the tuberculosis virulence factors CFP-10 and ESAT-6. EMBO J.24, 2491–2498 (2005). 80. Anderson, B. R. et al. Nucleoside modifications in RNA limit activation of 2′-5′- oligoadenylate synthetase and increase resistance to cleavage by RNase L. Nucleic Acids Res. 39, 9329–9338 (2011). 81. Orlandini von Niessen, A. G. et al. Improving mRNA-Based Therapeutic Gene Delivery by Expression-Augmenting 3′ UTRs Identified by Cellular Library Screening. Mol. Ther.27, 824– 836 (2019). 82. Cao, J. et al. High-throughput 5′ UTR engineering for enhanced protein production in non- viral gene therapies. Nat. Commun.12, 4138 (2021). 83. Trepotec, Z., Geiger, J., Plank, C., Aneja, M. K. & Rudolph, C. Segmented poly(A) tails significantly reduce recombination of plasmid DNA without affecting mRNA translation efficiency or half-life. RNA 25, 507–518 (2019). 84. Aditham, A. et al. Chemically Modified mocRNAs for Highly Efficient Protein Expression in Mammalian Cells. ACS Chem. Biol.17, 3352–3366 (2022). 85. la Cour, T. et al. Analysis and prediction of leucine-rich nuclear export signals. Protein Eng. Des. Sel.17, 527–536 (2004). 86. Wu, T. C. et al. Engineering an intracellular pathway for major histocompatibility complex class II presentation of antigens. Proc. Natl. Acad. Sci.92, 11671–11675 (1995). 87. Kreiter, S. et al. Increased Antigen Presentation Efficiency by Coupling Antigens to MHC Class I Trafficking Signals1. J. Immunol.180, 309–318 (2008). 88. Moradian, H., Roch, T., Lendlein, A. & Gossen, M. mRNA Transfection-Induced Activation of Primary Human Monocytes and Macrophages: Dependence on Carrier System and Nucleotide Modification. Sci. Rep.10, 4181 (2020). 89. Sahin, U. & Türeci, Ö. Personalized vaccines for cancer immunotherapy. Science 359, 1355– 1360 (2018). 90. Sahin, U. et al. Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer. Nature 547, 222–226 (2017). Attorney Docket No; 29539-0808WO1 / MGH 2024-658 91. Melzi, E. et al. Membrane-bound mRNA immunogens lower the threshold to activate HIV Env V2 apex directed broadly neutralizing B cell precursors in humanized mice. Immunity 55, 2168-2186.e6 (2022). 92. Stopfer, L. E., Mesfin, J. M., Joughin, B. A., Lauffenburger, D. A. & White, F. M. Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4 / 6 inhibition. Nat. Commun.11, 2760 (2020). 93. Teleman, J., Chawade, A., Sandin, M., Levander, F. & Malmström, J. Dinosaur: A Refined Open-Source Peptide MS Feature Detector. J. Proteome Res.15, 2143–2151 (2016). 94. Liu, Y. et al. DeepRTAlign: toward accurate retention time alignment for large cohort mass spectrometry data analysis. Nat. Commun.14, 8188 (2023). 95. Ji, H. & Tian, J. Deep denoising autoencoder-assisted continuous scoring of peak quality in high-resolution LC−MS data. Chemom. Intell. Lab. Syst.231, 104694 (2022). 96. Tully, G. et al. Highly Focused T Cell Responses in Latent Human Pulmonary Mycobacterium tuberculosis Infection. J. Immunol.174, 2174–2184 (2005). 97. Andreatta, M., Lund, O. & Nielsen, M. Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. Bioinformatics 29, 8–14 (2013). 98. Andreatta, M., Alvarez, B. & Nielsen, M. GibbsCluster: unsupervised clustering and alignment of peptide sequences. Nucleic Acids Res.45, W458–W463 (2017). 99. Reynisson, B., Alvarez, B., Paul, S., Peters, B. & Nielsen, M. NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res.48, W449– W454 (2020). OTHER EMBODIMENTS It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. All references cited herein, including patents, patent applications, papers, text books, and the like, and the references cited therein, to the extent that they are not already, are hereby incorporated herein by reference in their entirety. Although the forgoing invention has been described in some detail by way of illustration and example for clarity and understanding, it will Attorney Docket No; 29539-0808WO1 / MGH 2024-658 be readily apparent to one ordinary skill in the art in light of the teachings of this invention that certain variations, changes, modifications and substitution of equivalents may be made thereto without necessarily departing from the spirit and scope of this invention. As a result, the embodiments described herein are subject to various modifications, changes and the like, with the scope of this invention being determined solely by reference to the claims appended hereto. Those of skill in the art will readily recognize a variety of non-critical parameters that could be changed, altered or modified to yield essentially similar results.

Claims

Attorney Docket No; 29539-0808WO1 / MGH 2024-658 WHAT IS CLAIMED IS:

1. A vector comprising a multi-epitope immunogen, wherein the vector comprises a nucleotide sequence encoding: i) four or more MHC Class I epitopes, wherein the four or more MHC Class I epitopes are selected from SEAYQGVQQKW (SEQ ID NO:53), LQNLARTI (SEQ ID NO:54), NHVNFFQEL (SEQ ID NO:55), RMWASAQNI (SEQ ID NO:56), HQAIVRDV (SEQ ID NO:57), KLADFGLVRA (SEQ ID NO:58), LLDEGKQSL (SEQ ID NO:59), AAWGGSGSEAY (SEQ ID NO:60), QEQASQQIL (SEQ ID NO:61), QTVEDEARRMW (SEQ ID NO:62), VYLTAHNAL (SEQ ID NO:63), EAVQDVARTY (SEQ ID NO:64), AEILRGVSA (SEQ ID NO:65), EVHSAMLNY (SEQ ID NO:66), IHDQFVATL (SEQ ID NO:67), NASPVAQSY (SEQ ID NO:68), VPLEGGGRL (SEQ ID NO:69), TQHDAADALF (SEQ ID NO:70), LPFEDAPLI (SEQ ID NO:71), ELDEISTNIRQAGVQY (SEQ ID NO:72), QAIVRDVL (SEQ ID NO:73), KQKQELDEI (SEQ ID NO:74), GELRSLGATL (SEQ ID NO:75), TLRVVPESL (SEQ ID NO:76), MEDLVRAY (SEQ ID NO:77), QEAGNFERI (SEQ ID NO:78), AEHQAIVRDVL (SEQ ID NO:79), AEMKTDAATL (SEQ ID NO:80), RFMTDPHAMR (SEQ ID NO:81), SLLDEGKQSLTKL (SEQ ID NO:82), AVVRFQEAANK (SEQ ID NO:83), KIYSEADEAWRK (SEQ ID NO:84), EMKTDAATL (SEQ ID NO:85), and LLDAHIPQL (SEQ ID NO:86), and combinations thereof, or epitopes having at least 65% to about 99% homology to MHC Class I epitopes selected from SEAYQGVQQKW (SEQ ID NO:53), LQNLARTI (SEQ ID NO:54), NHVNFFQEL (SEQ ID NO:55), RMWASAQNI (SEQ ID NO:56), HQAIVRDV (SEQ ID NO:57), KLADFGLVRA (SEQ ID NO:58), LLDEGKQSL (SEQ ID NO:59), AAWGGSGSEAY (SEQ ID NO:60), QEQASQQIL (SEQ ID NO:61), QTVEDEARRMW (SEQ ID NO:62), VYLTAHNAL (SEQ ID NO:63), EAVQDVARTY (SEQ ID NO:64), AEILRGVSA (SEQ ID NO:65), EVHSAMLNY (SEQ ID NO:66), IHDQFVATL (SEQ ID NO:67), NASPVAQSY (SEQ ID NO:68), VPLEGGGRL (SEQ ID NO:69), TQHDAADALF (SEQ ID NO:70), LPFEDAPLI (SEQ ID NO:71), ELDEISTNIRQAGVQY (SEQ ID NO:72), QAIVRDVL (SEQ ID NO:73), KQKQELDEI (SEQ ID NO:74), GELRSLGATL (SEQ ID NO:75), TLRVVPESL (SEQ ID NO:76), MEDLVRAY (SEQ ID NO:77), QEAGNFERI (SEQ ID NO:78), AEHQAIVRDVL (SEQ ID NO:79), AEMKTDAATL (SEQ ID NO:80), RFMTDPHAMR (SEQ ID NO:81), SLLDEGKQSLTKL (SEQ IDAttorney Docket No; 29539-0808WO1 / MGH 2024-658 NO:82), AVVRFQEAANK (SEQ ID NO:83), KIYSEADEAWRK (SEQ ID NO:84), EMKTDAATL (SEQ ID NO:85), and LLDAHIPQL (SEQ ID NO:86), and combinations thereof, and ii) two or more MHC Class II epitopes, wherein the two or more MHC Class II epitopes are selected from AEMKTDAATL (SEQ ID NO:80), RADEEQQQAL (SEQ ID NO:81), ISTNIRQAGVQYSRADEE (SEQ ID NO:82), AAVVRFQEAANKQK, AAVVRFQEAANKQKQ (SEQ ID NO:83), GAAGTAAQAAVVR (SEQ ID NO:84), LQGQWRGAAGTAAQAA (SEQ ID NO:85), SLQGQWRGAAGTAAQAA (SEQ ID NO:86), QGQWRGAAGTAAQA (SEQ ID NO:87), ESSAAFQAAHARFVAAA (SEQ ID NO:88), GESSAAFQAAHARFVAAA (SEQ ID NO:89), SAAFQAAHARFVAAA (SEQ ID NO:90), SSAAFQAAHARFVAAA (SEQ ID NO:91), AAGTYVAADAAAAST (SEQ ID NO:92), VGPQVVNINTKLGYNNA (SEQ ID NO:93), VQVAATEVRR (SEQ ID NO:94), SQRVDPSAASGQDSTEARPA (SEQ ID NO:95), PSAASGQDSTEARPA (SEQ ID NO:96), AIPAYEPEPGKPAPA (SEQ ID NO:97), SGASYAARDALAAASY (SEQ ID NO:98), GHDEESPGAQSLT (SEQ ID NO:99), THAATYQTASAKAAVIHE (SEQ ID NO:100), SGPKVVIDGKDQNVTG (SEQ ID NO:101), DVVDDPAFVLHGNHPVR (SEQ ID NO:102), DAGGTYQPHPAEAVVEK (SEQ ID NO:103), DAGGTYQPHPAEAVVE (SEQ ID NO:104), RQPEPEVDTA (SEQ ID NO:105), LPPPVVAANRIQL (SEQ ID NO:106), PEAVIVSTARSPIG (SEQ ID NO:107), ASAAVEALTARLAAAH (SEQ ID NO:108), IGTTMNAQNAAAAAPT (SEQ ID NO:109), and GTTMNAQNAAAAAPT (SEQ ID NO:110), and combinations thereof, or epitopes having at least 65% to about 99% homology to MHC Class II epitopes selected from AEMKTDAATL (SEQ ID NO:80), RADEEQQQAL (SEQ ID NO:81), ISTNIRQAGVQYSRADEE (SEQ ID NO:82), AAVVRFQEAANKQK, AAVVRFQEAANKQKQ (SEQ ID NO:83), GAAGTAAQAAVVR (SEQ ID NO:84), LQGQWRGAAGTAAQAA (SEQ ID NO:85), SLQGQWRGAAGTAAQAA (SEQ ID NO:86), QGQWRGAAGTAAQA (SEQ ID NO:87), ESSAAFQAAHARFVAAA (SEQ ID NO:88), GESSAAFQAAHARFVAAA (SEQ ID NO:89), SAAFQAAHARFVAAA (SEQ ID NO:90), SSAAFQAAHARFVAAA (SEQ ID NO:91), AAGTYVAADAAAAST (SEQ ID NO:92), VGPQVVNINTKLGYNNA (SEQ ID NO:93), VQVAATEVRR (SEQ ID NO:94), SQRVDPSAASGQDSTEARPA (SEQ IDAttorney Docket No; 29539-0808WO1 / MGH 2024-658 NO:95), PSAASGQDSTEARPA (SEQ ID NO:96), AIPAYEPEPGKPAPA (SEQ ID NO:97), SGASYAARDALAAASY (SEQ ID NO:98), GHDEESPGAQSLT (SEQ ID NO:99), THAATYQTASAKAAVIHE (SEQ ID NO:100), SGPKVVIDGKDQNVTG (SEQ ID NO:101), DVVDDPAFVLHGNHPVR (SEQ ID NO:102), DAGGTYQPHPAEAVVEK (SEQ ID NO:103), DAGGTYQPHPAEAVVE (SEQ ID NO:104), RQPEPEVDTA (SEQ ID NO:105), LPPPVVAANRIQL (SEQ ID NO:106), PEAVIVSTARSPIG (SEQ ID NO:107), ASAAVEALTARLAAAH (SEQ ID NO:108), IGTTMNAQNAAAAAPT (SEQ ID NO:109), and GTTMNAQNAAAAAPT (SEQ ID NO:110), and combinations thereof.

2. The vector of claim 1, wherein the four or more MHC Class I epitopes are selected from LQNLARTI (SEQ ID NO:54), NHVNFFQEL (SEQ ID NO:55), RMWASAQNI (SEQ ID NO:56), HQAIVRDV (SEQ ID NO:57), KLADFGLVRA (SEQ ID NO:58), QAIVRDVL (SEQ ID NO:73), KQKQELDEI (SEQ ID NO:74), GELRSLGATL (SEQ ID NO:75), TLRVVPESL (SEQ ID NO:76), MEDLVRAY (SEQ ID NO:77), and LLDAHIPQL (SEQ ID NO:86), and combinations thereof, or epitopes having at least 65% to about 99% homology to MHC Class I epitopes selected from, LQNLARTI (SEQ ID NO:54), NHVNFFQEL (SEQ ID NO:55), RMWASAQNI (SEQ ID NO:56), HQAIVRDV (SEQ ID NO:57), KLADFGLVRA (SEQ ID NO:58), QAIVRDVL (SEQ ID NO:73), KQKQELDEI (SEQ ID NO:74), GELRSLGATL (SEQ ID NO:75), TLRVVPESL (SEQ ID NO:76), MEDLVRAY (SEQ ID NO:77), and LLDAHIPQL (SEQ ID NO:86), and combinations thereof.

3. The vector of claim 1, wherein the two or more MHC Class II epitopes are SLQGQWRGAAGTAAQAA (SEQ ID NO:86) and LQGQWRGAAGTAAQAA (SEQ ID NO:85) or epitopes having at least 65% to about 99% homology to SLQGQWRGAAGTAAQAA (SEQ ID NO:86) and LQGQWRGAAGTAAQAA (SEQ ID NO:85).

4. The vector of claim 1, wherein the vector further comprises a compartment targeting signal peptide selected from mitochondrial import receptor subunit TOM20 homolog (TOM20), Human immunoglobulin (Ig) light chain, lysosome associated membrane protein 1 (LAMP1), LAMP2, LAMP3, MHC-I trafficking domain (MITD), and nuclear export signal (NES).Attorney Docket No; 29539-0808WO1 / MGH 2024-658 5. The vector of claim 1, wherein two or more of the epitopes are separated by non- immunogenic linkers (GGS) or a self-cleaving P2A peptide sequence.

6. The vector of claim 1, wherein the nucleotide sequence comprises an RNA sequence.

7. The vector of claim 1, wherein the nucleotide sequence comprises a DNA sequence.

8. The vector of claim 1, wherein the vector is an RNA vector.

9. The vector of claim 8, wherein the RNA vector is replicon RNA or self-amplifying RNA.

10. The vector of claim 1, wherein the vector is a DNA vector.

11. The vector of claim 10, where in the DNA vector is a replication-deficient adenoviral vector selected from the group consisting of human adenovirus, rhesus adenovirus, simian adenovirus and gorilla adenovirus viral vectors.

12. The vector of any one of claims 1-11, for use in a method of preventing or treating an Mycobacterium tuberculosis infection in a subject, said method comprising administering the vector to the subject.

13. A vector comprising a multi-epitope immunogen, wherein the vector comprises a nucleotide sequence encoding at least one MHC Class I (Table 1) or MHC Class II (Table 2) heterodimeric pair, or combinations thereof, or nucleotide sequences having at least 65% to about 99% homology to at least one MHC Class I (Table 1) or MHC Class II (Table 2) heterodimeric pair, wherein the MHC Class I heterodimeric pairs are selected from: i) EsxA (MTEQQWNFAGIEAAASAIQGNVTSIHSLLDEGKQSLTKLAAAWGGSGSEAYQGVQQK WDATATELNNALQNLARTISEAGQAMASTEGNVTGMFA, SEQ ID NO:1) andAttorney Docket No; 29539-0808WO1 / MGH 2024-658 EsxB (MAEMKTDAATLAQEAGNFERISGDLKTQIDQVESTAGSLQGQWRGAAGTAAQAAVVR FQEAANKQKQELDEISTNIRQAGVQYSRADEEQQQALSSQMGF, SEQ ID NO:2) ii) EsxG (MSLLDAHIPQLVASQSAFAAKAGLMRHTIGQAEQAAMSAQAFHQGESSAAFQAAHARF VAAAAKVNTLLDVAQANLGEAAGTYVAADAAAASTYTGF, SEQ ID NO:3) and EsxH (MSQIMYNPAMLGHAGDMAGYAGTLQSLGAEIAVEQAALQSAWQGDTGITYQAWQAQ WNQAMEDLVRAYHAMSSTHEANTMAMMARDTAEAAKWGG, SEQ ID NO:9) iii) PE35 (MEKMSHDPIAADIGTQVSDNALHGVTAGSTALTSVTGLVPAGADEVSAQAATAFTSEGI QLLASNASAQDQLHRAGEAVQDVARTYSQIDDGAAGVFAE, SEQ ID NO:10) and PPE68 (MLWHAMPPELNTARLMAGAGPAPMLAAAAGWQTLSAALDAQAVELTARLNSLGEA WTGGGSDKALAAATPMVVWLQTASTQAKTRAMQATAQAAAYTQAMATTPSLPEIAAN HITQAVLTATNFFGINTIPIALTEMDYFIRMWNQAALAMEVYQAETAVNTLFEKLEPMAS ILDPGASQSTTNPIFGMPSPGSSTPVGQLPPAATQTLGQLGEMSGPMQQLTQPLQQVTSLF SQVGGTGGGNPADEEAAQMGLLGTSPLSNHPLAGGSGPSAGAGLLRAESLPGAGGSLTR TPLMSQLIEKPVAPSVMPAAAAGSSATGGAAPVGAGAMGQGAQSGGSTRPGLVAPAPL AQEREEDDEDDWDEEDDW, SEQ ID NO:25) iv) PPE20 (MTEPWIAFPPEVHSAMLNYGAGVGPMLISATQNGELSAQYAEAASEVEELLGVVASEG WQGQAAEAFVAAYMPFLAWLIQASADCVEMAAQQHVVIEAYTAAVELMPTQVELAAN QIKLAVLVATNFFGINTIPIAINEAEYVEMWVRAATTMATYSTVSRSALSAMPHTSPPPLI LKSDELLPDTGEDSDEDGHNHGGHSHGGHARMIDNFFAEILRGVSAGRIVWDPVNGTLN GLDYDDYVYPGHAIWWLARGLEFFQDGEQFGELLFTNPTGAFQFLLYVVVVDLPTHIAQ IATWLGQYPQLLSAALTGVIAHLGAITGLAGLSGLSAIPSAAIPAVVPELTPVAAAPPMLA VAGVGPAVAAPGMLPASAPAPAAAAGATAAGPTPPATGFGGFPPYLVGGGGPGIGFGSG QSAHAKAAASDSAAAESAAQASARAQARAARRGRSAAKARGHRDEFVTMDMGFDAA APAPEHQPGARASDCGAGPIGFAGTVRKEAVVKAAGLTTLAGDDFGGGPTMPMMPGT WTHDQGVFDEHR, SEQ ID NO:11) andAttorney Docket No; 29539-0808WO1 / MGH 2024-658 PE15 (VTLRVVPESLAGASAAIEAVTARLAAAHAAAAPFIAAVIPPGSDSVSVCNAVEFSVHGS SEQ ID NO:23) v) PPE51 (MDFALLPPEVNSARMYTGPGAGSLLAAAGGWDSLAAELATTAEAYGSVLSGLAALHW RGPAAESMAVTAAPYIGWLYTTAEKTQQTAIQARAAALAFEQAYAMTLPPPVVAANRI QLLALIATNFFGQNTAAIAATEAQYAEMWAQDAAAMYGYATASAAAALLTPFSPPRQT TNPAGLTAQAAAVSQATDPLSLLIETVTQALQALTIPSFIPEDFTFLDAIFAGYATVGVTQ DVESFVAGTIGAESNLGLLNVGDENPAEVTPGDFGIGELVSATSPGGGVSASGAGGAASV GNTVLASVGRANSIGQLSVPPSWAAPSTRPVSALSPAGLTTLPGTDVAEHGMPGVPGVP VAAGRASGVLPRYGVRLTVMAHPPAAG, SEQ ID NO:15) and PE19 (MSFVTTQPEALAAAAANLQGIGTTMNAQNAAAAAPTTGVVPAAADEVSALTAAQFAA HAQMYQTVSAQAAAIHEMFVNTLVASSGSYAATEAANAAAAG, SEQ ID NO:27) vi) PPE60 (VVDFGALPPEINSARMYAGPGSASLVAAAKMWDSVASDLFSAASAFQSVVWGLTVGS WIGSSAGLMAAAASPYVAWMSVTAGQAQLTAAQVRVAAAAYETAYRLTVPPPVIAEN RTELMTLTATNLLGQNTPAIEANQAAYSQMWGQDAEAMYGYAATAATATEALLPFED APLITNPGGLLEQAVAVEEAIDTAAANQLMNNVPQALQQLAQPAQGVVPSSKLGGLWT AVSPHLSPLSNVSSIANNHMSMMGTGVSMTNTLHSMLKGLAPAAAQAVETAAENGVW AMSSLGSQLGSSLGSSGLGAGVAANLGRAASVGSLSVPPAWAAANQAVTPAARALPLT SLTSAAQTAPGHMLGGLPLGHSVNAGSGINNALRVPARAYAIPRTPAAG, SEQ ID NO:16) and PE31 (VSFTAQPEMLAAAAGELRSLGATLKASNAAAAVPTTGVVPPAADEVSLLLATQFRTHA ATYQTASAKAAVIHEQFVTTLATSASSYADTEAANAVVTG, SEQ ID NO:24) vii) PE13 (VSFVMAYPEMLAAAADTLQSIGATTVASNAAAAAPTTGVVPPAADEVSALTAAHFAA HAAMYQSVSARAAAIHDQFVATLASSASSYAATEVANAAAAS, SEQ ID NO:18) and PPE18 (MVDFGALPPEINSARMYAGPGSASLVAAAQMWDSVASDLFSAASAFQSVVWGLTVGS WIGSSAGLMVAAASPYVAWMSVTAGQAELTAAQVRVAAAAYETAYGLTVPPPVIAENAttorney Docket No; 29539-0808WO1 / MGH 2024-658 RAELMILIATNLLGQNTPAIAVNEAEYGEMWAQDAAAMFGYAAATATATATLLPFEEA PEMTSAGGLLEQAAAVEEASDTAAANQLMNNVPQALQQLAQPTQGTTPSSKLGGLWKT VSPHRSPISNMVSMANNHMSMTNSGVSMTNTLSSMLKGFAPAAAAQAVQTAAQNGVR AMSSLGSSLGSSGLGGGVAANLGRAASVGSLSVPQAWAAANQAVTPAARALPLTSLTS AAERGPGQMLGGLPVGQMGARAGGGLSGVLRVPPRPYVMPHSPAAG, SEQ ID NO:26); and wherein MHC Class II heterodimeric pairs are selected from: vi) PE15 (VTLRVVPESLAGASAAIEAVTARLAAAHAAAAPFIAAVIPPGSDSVSVCNAVEFSVHGS QHVAMAAQGVEELGRSGVGVAESGASYAARDALAAASYLSGGL, SEQ ID NO:23) and PPE20 (MTEPWIAFPPEVHSAMLNYGAGVGPMLISATQNGELSAQYAEAASEVEELLGVVASEG WQGQAAEAFVAAYMPFLAWLIQASADCVEMAAQQHVVIEAYTAAVELMPTQVELAAN QIKLAVLVATNFFGINTIPIAINEAEYVEMWVRAATTMATYSTVSRSALSAMPHTSPPPLI LKSDELLPDTGEDSDEDGHNHGGHSHGGHARMIDNFFAEILRGVSAGRIVWDPVNGTLN GLDYDDYVYPGHAIWWLARGLEFFQDGEQFGELLFTNPTGAFQFLLYVVVVDLPTHIAQ IATWLGQYPQLLSAALTGVIAHLGAITGLAGLSGLSAIPSAAIPAVVPELTPVAAAPPMLA VAGVGPAVAAPGMLPASAPAPAAAAGATAAGPTPPATGFGGFPPYLVGGGGPGIGFGSG QSAHAKAAASDSAAAESAAQASARAQARAARRGRSAAKARGHRDEFVTMDMGFDAA APAPEHQPGARASDCGAGPIGFAGTVRKEAVVKAAGLTTLAGDDFGGGPTMPMMPGT WTHDQGVFDEHR, SEQ ID NO:11) vii) PE31 (VSFTAQPEMLAAAAGELRSLGATLKASNAAAAVPTTGVVPPAADEVSLLLATQFRTHA ATYQTASAKAAVIHEQFVTTLATSASSYADTEAANAVVTG, SEQ ID NO:24) and PPE60 (VVDFGALPPEINSARMYAGPGSASLVAAAKMWDSVASDLFSAASAFQSVVWGLTVGS WIGSSAGLMAAAASPYVAWMSVTAGQAQLTAAQVRVAAAAYETAYRLTVPPPVIAEN RTELMTLTATNLLGQNTPAIEANQAAYSQMWGQDAEAMYGYAATAATATEALLPFED APLITNPGGLLEQAVAVEEAIDTAAANQLMNNVPQALQQLAQPAQGVVPSSKLGGLWT AVSPHLSPLSNVSSIANNHMSMMGTGVSMTNTLHSMLKGLAPAAAQAVETAAENGVW AMSSLGSQLGSSLGSSGLGAGVAANLGRAASVGSLSVPPAWAAANQAVTPAARALPLT SLTSAAQTAPGHMLGGLPLGHSVNAGSGINNALRVPARAYAIPRTPAAG, SEQ ID NO:16)Attorney Docket No; 29539-0808WO1 / MGH 2024-658 viii) PPE51 (MDFALLPPEVNSARMYTGPGAGSLLAAAGGWDSLAAELATTAEAYGSVLSGLAALHW RGPAAESMAVTAAPYIGWLYTTAEKTQQTAIQARAAALAFEQAYAMTLPPPVVAANRI QLLALIATNFFGQNTAAIAATEAQYAEMWAQDAAAMYGYATASAAAALLTPFSPPRQT TNPAGLTAQAAAVSQATDPLSLLIETVTQALQALTIPSFIPEDFTFLDAIFAGYATVGVTQ DVESFVAGTIGAESNLGLLNVGDENPAEVTPGDFGIGELVSATSPGGGVSASGAGGAASV GNTVLASVGRANSIGQLSVPPSWAAPSTRPVSALSPAGLTTLPGTDVAEHGMPGVPGVP VAAGRASGVLPRYGVRLTVMAHPPAAG, SEQ ID NO:15) and PE19 (MSFVTTQPEALAAAAANLQGIGTTMNAQNAAAAAPTTGVVPAAADEVSALTAAQFAA HAQMYQTVSAQAAAIHEMFVNTLVASSGSYAATEAANAAAAG, SEQ ID NO:27) ix) PE5 (MTLRVVPEGLAAASAAVEALTARLAAAHASAAPVITAVVPPAADPVSLQTAAGFSAQG VEHAVVTAEGVEELGRAGVGVGESGASYLAGDAAAAATYGVVGG, SEQ ID NO:38) and PPE4 (MAAPIWMASPPEVHSALLSNGPGPGSLVAAATAWSQLSAEYASTAAELSGLLGAVPGW AWQGPSAEWYVAAHLPYVAWLTQASADAAGAAAQHEAAAAAYTTALAAMPTLAELA ANHVIHTVLVATNFFGINTIPITLNEADYVRMWLQAAAVMGLYQAASGAALASAPRTVP APTVMNPGGGAASTVGAVNPWQWLLALLQQLWNAYTGFYGWMLQLIWQFLQDPIGN SIKIIIAFLTNPIQALITYGPLLFALGYQIFFNLVGWPTWGMILSSPFLLPAGLGLGLAAIAFL PIVLAPAVIPPASTPLAAAAVAAGSVWPAVSMAVTGAGTAGAATPAAGAAPSAGAAPAP AAPATASFAYAVGGSGDWGPSLGPTVGGRGGIKAPAATVPAAAAAAATRGQSRARRRR RSELRDYGDEFLDMDSDSGFGPSTGDHGAQASERGAGTLGFAGTATKERRVRAVGLTA LAGDEFGNGPRMPMVPGTWEQGSNEPEAPDGSGRGGGDGLPHDSK, SEQ ID NO:40) x) PE29 (VTLRVVPEGLAAASAAVEALTARLAAAHAGAAPAITAVVAPAADPVSLQSAVGFSALG SEHAAIAGEGVEELGRSGVAVGESGIGYAAGDAVAAATYLVSGGSL, SEQ ID NO:39) and PPE48 (VTAPVWLASPPEVHSALLSAGPGPGSLQAAAAGWSALSAEYAAVAQELSVVVAAVG AGVWQGPSAELFVAAYVPYVAWLVQ, SEQ ID NO:41).Attorney Docket No; 29539-0808WO1 / MGH 2024-658 14. The vector of claim 13, wherein the vector further comprises a compartment targeting signal peptide selected from TOM20, Human Ig Light Chain, LAMP1, LAMP2, LAMP3, MITD, and NES.

15. The vector of claim 13, wherein the nucleotide sequence comprises an RNA sequence.

16. The vector of claim 13, wherein the nucleotide sequence comprises a DNA sequence.

17. The vector of claim 13, wherein the vector is an RNA vector.

18. The vector of claim 17, wherein the RNA vector is replicon RNA or self-amplifying RNA.

19. The vector of claim 17, wherein the vector is a DNA vector.

20. The vector of claim 19, where in the DNA vector is a replication-deficient adenoviral vector selected from the group consisting of human adenovirus, rhesus adenovirus, simian adenovirus and gorilla adenovirus viral vectors.

21. The vector of any one of claims 13-20, for use in a method of preventing or treating an Mycobacterium tuberculosis infection in a subject, said method comprising administering the vector to the subject.

Images