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Cancer Antigens: Sources, Generation, and Presentation

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Handbook of Cancer and Immunology
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Abstract

Immune surveillance by T cells requires antigen presentation by molecules encoded by MHC (major histocompatibility complex) class I and class II genes in a process termed MHC restriction. MHC restriction is defined as a process in which protein antigens are proteolytically processed to short peptides, which are assembled with MHC molecules, and then displayed as peptide-bound MHC molecules at the surface of cells. Therefore, knowledge of peptide antigens presented by MHC molecules can yield information on the sources of tumor antigens, ways to track T cell responses to tumors, and targets for cancer vaccines and cell therapies. This chapter provides an overview of cancer antigens, their sources, and the mechanisms by which cells generate and present such antigens.

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References

  • Abi Habib J, Lesenfants J, Vigneron N, Van den Eynde BJ (2022) Functional differences between proteasome subtypes. Cell 11:421

    Article  CAS  Google Scholar 

  • Admon A (2021) Are there indeed spliced peptides in the Immunopeptidome? Mol Cell Proteomics 20:100099

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alspach E, Lussier DM, Miceli AP, Kizhvatov I, DuPage M, Luoma AM et al (2019) MHC-II neoantigens shape tumour immunity and response to immunotherapy. Nature 574:696–701

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Amobi A, Qian F, Lugade AA, Odunsi K (2017) Tryptophan catabolism and cancer immunotherapy targeting IDO mediated immune suppression. Adv Exp Med Biol 1036:129–144

    Article  CAS  PubMed  Google Scholar 

  • Androlewicz MJ, Anderson KS, Cresswell P (1993) Evidence that transporters associated with antigen processing translocate a major histocompatibility complex class I-binding peptide into the endoplasmic reticulum in an ATP-dependent manner. Proc Natl Acad Sci U S A 90:9130–9134

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Androlewicz MJ, Ortmann B, van Endert PM, Spies T, Cresswell P (1994) Characteristics of peptide and major histocompatibility complex class I/beta 2- microglobulin binding to the transporters associated with antigen processing (TAP1 and TAP2). Proc Natl Acad Sci U S A 91:12716–12720

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Anraku Y, Hirata R (1994) Protozyme: emerging evidence in nature. J Biochem 115:175–178

    Article  CAS  PubMed  Google Scholar 

  • Anton LC, Yewdell JW (2014) Translating DRiPs: MHC class I immunosurveillance of pathogens and tumors. J Leukoc Biol 95:551–562

    Article  PubMed  PubMed Central  Google Scholar 

  • Apcher S, Daskalogianni C, Lejeune F, Manoury B, Imhoos G, Heslop L et al (2011) Major source of antigenic peptides for the MHC class I pathway is produced during the pioneer round of mRNA translation. Proc Natl Acad Sci U S A 108:11572–11577

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Apcher S, Millot G, Daskalogianni C, Scherl A, Manoury B, Fahraeus R (2013) Translation of pre-spliced RNAs in the nuclear compartment generates peptides for the MHC class I pathway. Proc Natl Acad Sci U S A 110:17951–17956

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Apcher S, Prado Martins R, Fahraeus R (2016) The source of MHC class I presented peptides and its implications. Curr Opin Immunol 40:117–122

    Article  CAS  PubMed  Google Scholar 

  • Attig J, Young GR, Hosie L, Perkins D, Encheva-Yokoya V, Stoye JP et al (2019) LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly. Genome Res 29:1578–1590

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Babbitt BP, Allen PM, Matsueda G, Haber E, Unanue ER (1985) Binding of immunogenic peptides to Ia histocompatibility molecules. Nature 317:359–361

    Google Scholar 

  • Babbitt BP, Matsueda G, Haber E, Unanue ER, Allen PM (1986) Antigenic competition at the level of peptide-Ia binding. Proceedings of the National Academy of Sciences of the United States of America 83:4509–4513

    Google Scholar 

  • Bai P, Zhou Q, Wei P, Bai H, Chan SK, Kappler JW et al (2021) Rational discovery of a cancer neoepitope harboring the KRAS G12D driver mutation. Sci China Life Sci. https://doi.org/10.1007/s11427-020-1888-1

  • Bartok O, Pataskar A, Nagel R, Laos M, Goldfarb E, Hayoun D et al (2021) Antitumour immunity induces aberrant peptide presentation in melanoma. Nature 590:332–337

    Article  CAS  PubMed  Google Scholar 

  • Bashirova AA, Viard M, Naranbhai V, Grifoni A, Garcia-Beltran W, Akdag M et al (2020) HLA tapasin independence: broader peptide repertoire and HIV control. Proc Natl Acad Sci U S A 117:28232–28238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Batlle E, Clevers H (2017) Cancer stem cells revisited. Nat Med 23:1124–1134

    Article  CAS  PubMed  Google Scholar 

  • Becker JC, Guldberg P, Zeuthen J, Brocker EB, Straten PT (1999) Accumulation of identical T cells in melanoma and vitiligo-like leukoderma. J Invest Dermatol 113:1033–1038

    Article  CAS  PubMed  Google Scholar 

  • Becker JP, Helm D, Rettel M, Stein F, Hernandez-Sanchez A, Urban K et al (2021) NMD inhibition by 5-azacytidine augments presentation of immunogenic frameshift-derived neoepitopes. iScience 24:102389

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Benham AM, Gromme M, Neefjes J (1998) Allelic differences in the relationship between proteasome activity and MHC class I peptide loading. J Immunol 161:83–89

    Article  CAS  PubMed  Google Scholar 

  • Bettencourt P, Muller J, Nicastri A, Cantillon D, Madhavan M, Charles PD et al (2020) Identification of antigens presented by MHC for vaccines against tuberculosis. NPJ Vaccines 5:2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Billingham RE, Brent L, Medawar PB (1953) Actively acquired tolerance of foreign cells. Nature 172:603–606

    Article  CAS  PubMed  Google Scholar 

  • Birnbaum ME, Mendoza JL, Sethi DK, Dong S, Glanville J, Dobbins J et al (2014) Deconstructing the peptide-MHC specificity of T cell recognition. Cell 157:1073–1087

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bjorkman PJ, Saper MA, Samraoui B, Bennett WS, Strominger JL, Wiley DC (1987a) Structure of the human class I histocompatibility antigen, HLA-A2. Nature 329:506–512

    Article  CAS  PubMed  Google Scholar 

  • Bjorkman PJ, Saper MA, Samraoui B, Bennett WS, Strominger JL, Wiley DC (1987b) The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens. Nature 329:512–518

    Article  CAS  PubMed  Google Scholar 

  • Blanchard N, Kanaseki T, Escobar H, Delebecque F, Nagarajan NA, Reyes-Vargas E et al (2010) Endoplasmic reticulum aminopeptidase associated with antigen processing defines the composition and structure of MHC class I peptide repertoire in normal and virus-infected cells. J Immunol 184:3033–3042

    Article  CAS  PubMed  Google Scholar 

  • Blum JS, Wearsch PA, Cresswell P (2013) Pathways of antigen processing. Annu Rev Immunol 31:443–473

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boesteanu A, Brehm M, Mylin LM, Christianson GJ, Tevethia SS, Roopenian DC et al (1998) A molecular basis for how a single TCR interfaces multiple ligands. J Immunol 161:4719–4727

    Article  CAS  PubMed  Google Scholar 

  • Boon T, Van Pel A, De Plaen E, Chomez P, Lurquin C, Szikora JP et al (1989) Genes coding for T-cell-defined tum transplantation antigens: point mutations, antigenic peptides, and subgenic expression. Cold Spring Harb Symp Quant Biol 54(Pt 1):587–596

    Article  CAS  PubMed  Google Scholar 

  • Borrego F, Ulbrecht M, Weiss EH, Coligan JE, Brooks AG (1998) Recognition of human histocompatibility leukocyte antigen (HLA)-E complexed with HLA class I signal sequence-derived peptides by CD94/NKG2 confers protection from natural killer cell-mediated lysis. J Exp Med 187:813–818

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bourdetsky D, Schmelzer CE, Admon A (2014) The nature and extent of contributions by defective ribosome products to the HLA peptidome. Proc Natl Acad Sci U S A 111:E1591–E1599

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bousbaine D, Ploegh HL (2020) Antigen discovery tools for adaptive immune receptor repertoire research. Curr Opin Syst Biol 24:64–70

    Article  PubMed  PubMed Central  Google Scholar 

  • Bowles DJ, Marcus SE, Pappin DJ, Findlay JB, Eliopoulos E, Maycox PR et al (1986) Posttranslational processing of concanavalin A precursors in jackbean cotyledons. J Cell Biol 102:1284–1297

    Article  CAS  PubMed  Google Scholar 

  • Braud VM, Allan DS, O’Callaghan CA, Soderstrom K, D’Andrea A, Ogg GS et al (1998) HLA-E binds to natural killer cell receptors CD94/NKG2A, B and C. Nature 391:795–799

    Article  CAS  PubMed  Google Scholar 

  • Burgevin A, Saveanu L, Kim Y, Barilleau E, Kotturi M, Sette A et al (2008) A detailed analysis of the murine TAP transporter substrate specificity. PLoS One 3:e2402

    Article  PubMed  PubMed Central  Google Scholar 

  • Burnet M (1969) Self and not-self: cellular immunology book one. Melbourne University Press, Carlton, p 326

    Google Scholar 

  • Burnet M (1970a) Chapter VIII: Immunological surveillance. In: Immunological surveillance. Pergemon Press Pty Limited, Sidney, pp 161–185

    Chapter  Google Scholar 

  • Burnet M (1970b) Chapter VII: Antigenic qualities of neoplastic cells. In: Immunological surveillance. Pergemon Pvt Limited, Sydney, pp 145–160

    Chapter  Google Scholar 

  • Buus S, Colon S, Smith C, Freed JH, Miles C, Grey HM (1986a) Interaction between a “processed” ovalbumin peptide and Ia molecules. Proceedings of the National Academy of Sciences of the United States of America 83:3968–3971

    Google Scholar 

  • Buus S, Sette A, Colon SM, Jenis DM, Grey HM (1986b) Isolation and characterization of antigen-Ia complexes involved in T cell recognition. Cell 47: 1071–1077

    Google Scholar 

  • Cafri G, Gartner JJ, Zaks T, Hopson K, Levin N, Paria BC et al (2020) mRNA vaccine-induced neoantigen-specific T cell immunity in patients with gastrointestinal cancer. J Clin Invest 130:5976–5988

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cardinaud S, Moris A, Fevrier M, Rohrlich PS, Weiss L, Langlade-Demoyen P et al (2004) Identification of cryptic MHC I-restricted epitopes encoded by HIV-1 alternative reading frames. J Exp Med 199:1053–1063

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cardinaud S, Consiglieri G, Bouziat R, Urrutia A, Graff-Dubois S, Fourati S et al (2011) CTL escape mediated by proteasomal destruction of an HIV-1 cryptic epitope. PLoS Pathog 7:e1002049

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carreno BM, Magrini V, Becker-Hapak M, Kaabinejadian S, Hundal J, Petti AA et al (2015) Cancer immunotherapy. A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells. Science 348:803–808

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chapatte L, Ayyoub M, Morel S, Peitrequin AL, Levy N, Servis C et al (2006) Processing of tumor-associated antigen by the proteasomes of dendritic cells controls in vivo T-cell responses. Cancer Res 66:5461–5468

    Article  CAS  PubMed  Google Scholar 

  • Chen M, Bouvier M (2007) Analysis of interactions in a tapasin/class I complex provides a mechanism for peptide selection. EMBO J 26:1681–1690

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen L, Shi H, Koftori D, Sekine T, Nicastri A, Ternette N et al (2020) Identification of an unconventional Subpeptidome bound to the Behcet’s disease-associated HLA-B*51:01 that is regulated by endoplasmic reticulum aminopeptidase 1 (ERAP1). Mol Cell Proteomics 19:871–883

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chong C, Marino F, Pak H, Racle J, Daniel RT, Muller M et al (2018) Highthroughput and sensitive Immunopeptidomics platform reveals profound Interferongamma-mediated remodeling of the Human Leukocyte Antigen (HLA) Ligandome. Mol Cell Proteomics 17:533–548

    Article  CAS  PubMed  Google Scholar 

  • Chong C, Muller M, Pak H, Harnett D, Huber F, Grun D et al (2020) Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes. Nat Commun 11:1293

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cobbold M, De La Pena H, Norris A, Polefrone JM, Qian J, English AM et al (2013) MHC class I-associated phosphopeptides are the targets of memory-like immunity in leukemia. Sci Transl Med 5:203ra125

    Article  PubMed  PubMed Central  Google Scholar 

  • Coley WB (1893) The treatment of malignant tumors by repeated inoculations of erysipelas: with a report of ten original cases. Am J Med Sci 105:487–510

    Article  Google Scholar 

  • Coulie PG, Lehmann F, Lethe B, Herman J, Lurquin C, Andrawiss M et al (1995) A mutated intron sequence codes for an antigenic peptide recognized by cytolytic T lymphocytes on a human melanoma. Proc Natl Acad Sci U S A 92:7976–7980

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Croft NP, Purcell AW, Tscharke DC (2015) Quantifying epitope presentation using mass spectrometry. Mol Immunol 68:77–80

    Article  CAS  PubMed  Google Scholar 

  • Croft NP, Smith SA, Pickering J, Sidney J, Peters B, Faridi P et al (2019) Most viral peptides displayed by class I MHC on infected cells are immunogenic. Proc Natl Acad Sci U S A 116:3112–3117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cruz FM, Colbert JD, Merino E, Kriegsman BA, Rock KL (2017) The biology and underlying mechanisms of cross-presentation of exogenous antigens on MHC-I molecules. Annu Rev Immunol 35:149–176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dalet A, Robbins PF, Stroobant V, Vigneron N, Li YF, El-Gamil M et al (2011) An antigenic peptide produced by reverse splicing and double asparagine deamidation. Proc Natl Acad Sci U S A 108:E323–E331

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dash P, Fiore-Gartland AJ, Hertz T, Wang GC, Sharma S, Souquette A et al (2017) Quantifiable predictive features define epitope-specific T cell receptor repertoires. Nature 547:89–93

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Verteuil D, Muratore-Schroeder TL, Granados DP, Fortier MH, Hardy MP, Bramoulle A et al (2010) Deletion of immunoproteasome subunits imprints on the transcriptome and has a broad impact on peptides presented by major histocompatibility complex I molecules. Mol Cell Proteomics 9:2034–2047

    Article  PubMed  PubMed Central  Google Scholar 

  • De M, Jayarapu K, Elenich L, Monaco JJ, Colbert RA, Griffin TA (2003) Beta 2 subunit propeptides influence cooperative proteasome assembly. J Biol Chem 278:6153–6159

    Article  CAS  PubMed  Google Scholar 

  • Degen E, Williams DB (1991) Participation of a novel 88-kD protein in the biogenesis of murine class I histocompatibility molecules. J Cell Biol 112:1099–1115

    Article  CAS  PubMed  Google Scholar 

  • Depontieu FR, Qian J, Zarling AL, McMiller TL, Salay TM, Norris A et al (2009) Identification of tumor-associated, MHC class II-restricted phosphopeptides as targets for immunotherapy. Proc Natl Acad Sci U S A 106:12073–12078

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Destro F, Sforza F, Sicurella M, Marescotti D, Gallerani E, Baldisserotto A et al (2011) Proteasome inhibitors induce the presentation of an Epstein-Barr virus nuclear antigen 1-derived cytotoxic T lymphocyte epitope in Burkitt’s lymphoma cells. Immunology 133:105–114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Devlin JR, Alonso JA, Ayres CM, Keller GLJ, Bobisse S, Vander Kooi CW et al (2020) Structural dissimilarity from self drives neoepitope escape from immune tolerance. Nat Chem Biol 16:1269–1276

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Diekmann J, Adamopoulou E, Beck O, Rauser G, Lurati S, Tenzer S et al (2009) Processing of two latent membrane protein 1 MHC class I epitopes requires tripeptidyl peptidase II involvement. J Immunol 183:1587–1597

    Article  CAS  PubMed  Google Scholar 

  • Dolan BP, Li L, Takeda K, Bennink JR, Yewdell JW (2010a) Defective ribosomal products are the major source of antigenic peptides endogenously generated from influenza A virus neuraminidase. J Immunol 184:1419–1424

    Article  CAS  PubMed  Google Scholar 

  • Dolan BP, Knowlton JJ, David A, Bennink JR, Yewdell JW (2010b) RNA polymerase II inhibitors dissociate antigenic peptide generation from normal viral protein synthesis: a role for nuclear translation in defective ribosomal product synthesis? J Immunol 185:6728–6733

    Article  CAS  PubMed  Google Scholar 

  • Dong G, Wearsch PA, Peaper DR, Cresswell P, Reinisch KM (2009) Insights into MHC class I peptide loading from the structure of the tapasin-ERp57 thiol oxidoreductase heterodimer. Immunity 30:21–32

    Article  PubMed  PubMed Central  Google Scholar 

  • Duan F, Duitama J, Al Seesi S, Ayres CM, Corcelli SA, Pawashe AP et al (2014) Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity. J Exp Med 211:2231–2248

    Article  PubMed  PubMed Central  Google Scholar 

  • Dudek NL, Tan CT, Gorasia DG, Croft NP, Illing PT, Purcell AW (2012) Constitutive and inflammatory immunopeptidome of pancreatic beta-cells. Diabetes 61:3018–3025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duraiswamy J, Burrows JM, Bharadwaj M, Burrows SR, Cooper L, Pimtanothai N et al (2003) Ex vivo analysis of T-cell responses to Epstein-Barr virusencoded oncogene latent membrane protein 1 reveals highly conserved epitope sequences in virus isolates from diverse geographic regions. J Virol 77:7401–7410

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ebstein F, Textoris-Taube K, Keller C, Golnik R, Vigneron N, Van den Eynde BJ et al (2016) Proteasomes generate spliced epitopes by two different mechanisms and as efficiently as non-spliced epitopes. Sci Rep 6:24032

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Engelhard VH, Obeng RC, Cummings KL, Petroni GR, Ambakhutwala AL, Chianese-Bullock KA et al (2020) MHC-restricted phosphopeptide antigens: preclinical validation and first-in-humans clinical trial in participants with high-risk melanoma. J Immunother Cancer 8:e000262

    Article  PubMed  PubMed Central  Google Scholar 

  • Erhard F, Halenius A, Zimmermann C, L’Hernault A, Kowalewski DJ, Weekes MP et al (2018) Improved Ribo-seq enables identification of cryptic translation events. Nat Methods 15:363–366

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Erhard F, Dolken L, Schilling B, Schlosser A (2020) Identification of the cryptic HLAI Immunopeptidome. Cancer Immunol Res 8:1018–1026

    Article  CAS  PubMed  Google Scholar 

  • Esquivel F, Yewdell J, Bennink J (1992) RMA/S cells present endogenously synthesized cytosolic proteins to class I-restricted cytotoxic T lymphocytes. J Exp Med 175:163–168

    Article  CAS  PubMed  Google Scholar 

  • Evans DM, Spencer CC, Pointon JJ, Su Z, Harvey D, Kochan G et al (2011) Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility. Nat Genet 43:761–767

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Evnouchidou I, Kamal RP, Seregin SS, Goto Y, Tsujimoto M, Hattori A et al (2011) Cutting edge: coding single nucleotide polymorphisms of endoplasmic reticulum aminopeptidase 1 can affect antigenic peptide generation in vitro by influencing basic enzymatic properties of the enzyme. J Immunol 186:1909–1913

    Article  CAS  PubMed  Google Scholar 

  • Falk K, Rotzschke O, Rammensee HG (1990) Cellular peptide composition governed by major histocompatibility complex class I molecules. Nature 348:248–251

    Article  CAS  PubMed  Google Scholar 

  • Falk K, Rotzschke O, Stevanovic S, Jung G, Rammensee HG (1991a) Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature 351:290–296

    Article  CAS  PubMed  Google Scholar 

  • Falk K, Rotzschke O, Deres K, Metzger J, Jung G, Rammensee HG (1991b) Identification of naturally processed viral nonapeptides allows their quantification in infected cells and suggests an allele-specific T cell epitope forecast. J Exp Med 174:425–434

    Article  CAS  PubMed  Google Scholar 

  • Fang Y, Mo F, Shou J, Wang H, Luo K, Zhang S et al (2020) A Pan-cancer clinical study of personalized Neoantigen vaccine monotherapy in treating patients with various types of advanced solid tumors. Clin Cancer Res 26:4511–4520

    Article  CAS  PubMed  Google Scholar 

  • Faridi P, Li C, Ramarathinam SH, Vivian JP, Illing PT, Mifsud NA et al (2018) A subset of HLA-I peptides are not genomically templated: evidence for cis- and trans-spliced peptide ligands. Sci Immunol 3:eaar3947

    Article  PubMed  Google Scholar 

  • Faridi P, Li C, Ramarathinam SH, Illing PT, Mifsud NA, Ayala R et al (2019) Response to comment on “A subset of HLA-I peptides are not genomically templated: evidence for cis- and trans-spliced peptide ligands”. Sci Immunol 4:eaaw8457

    Article  CAS  PubMed  Google Scholar 

  • Faridi P, Woods K, Ostrouska S, Deceneux C, Aranha R, Duscharla D et al (2020) Spliced peptides and cytokine-driven changes in the Immunopeptidome of melanoma. Cancer Immunol Res 8:1322–1334

    Article  PubMed  Google Scholar 

  • Faridi P, Dorvash M, Purcell AW (2021) Spliced HLA-bound peptides: a Black-Swan event in immunology. Clin Exp Immunol 204:179–188. https://doi.org/10.1111/cei.13589

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Feng D, Bond CJ, Ely LK, Maynard J, Garcia KC (2007) Structural evidence for a germline-encoded T cell receptor-major histocompatibility complex interaction ‘codon’. Nat Immunol 8:975–983

    Article  CAS  PubMed  Google Scholar 

  • Fior R (2019) Cancer – when cells break the rules and hijack their own planet. In: Fior R, Zilhao R (eds) Molecular and cell biology of cancer: when cells break the rules and hijack their own planet. Springer Nature, Cham, pp 1–20

    Chapter  Google Scholar 

  • Frankiw L, Baltimore D, Li G (2019) Alternative mRNA splicing in cancer immunotherapy. Nat Rev Immunol 19:675–687

    Article  CAS  PubMed  Google Scholar 

  • Fremont DH, Matsumura M, Stura EA, Peterson PA, Wilson IA (1992) Crystal structures of two viral peptides in complex with murine MHC class I H-2Kb. Science 257:919–927

    Article  CAS  PubMed  Google Scholar 

  • Gain C, Malik S, Bhattacharjee S, Ghosh A, Robertson ES, Das BB et al (2020) Proteasomal inhibition triggers viral oncoprotein degradation via autophagylysosomal pathway. PLoS Pathog 16:e1008105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garcia KC, Adams JJ, Feng D, Ely LK (2009) The molecular basis of TCR germline bias for MHC is surprisingly simple. Nat Immunol 10:143–147

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garcia-Medel N, Sanz-Bravo A, Barnea E, Admon A, Lopez de Castro JA (2012) The origin of proteasome-inhibitor resistant HLA class I peptidomes: a study with HLA-A*68:01. Mol Cell Proteomics 11:M111 011486

    Article  PubMed  Google Scholar 

  • Gee MH, Han A, Lofgren SM, Beausang JF, Mendoza JL, Birnbaum ME et al (2018) Antigen identification for orphan T cell receptors expressed on tumor-infiltrating lymphocytes. Cell 172:549–563 e516

    Article  CAS  PubMed  Google Scholar 

  • Gilchuk P, Spencer CT, Conant SB, Hill T, Gray JJ, Niu X et al (2013) Discovering naturally processed antigenic determinants that confer protective T cell immunity. J Clin Invest 123:1976–1987

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Glanville J, Huang H, Nau A, Hatton O, Wagar LE, Rubelt F et al (2017) Identifying specificity groups in the T cell receptor repertoire. Nature 547:94–98

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gomez HL, Felipe-Medina N, Condezo YB, Garcia-Valiente R, Ramos I, Suja JA et al (2019) The PSMA8 subunit of the spermatoproteasome is essential for proper meiotic exit and mouse fertility. PLoS Genet 15:e1008316

    Article  Google Scholar 

  • Goto Y, Ogawa K, Nakamura TJ, Hattori A, Tsujimoto M (2015) Substrate-dependent nitric oxide synthesis by secreted endoplasmic reticulum aminopeptidase 1 in macrophages. J Biochem 157:439–449

    Article  CAS  PubMed  Google Scholar 

  • Granados DP, Sriranganadane D, Daouda T, Zieger A, Laumont CM, Caron-Lizotte O et al (2014) Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides. Nat Commun 5:3600

    Article  PubMed  Google Scholar 

  • Grandea AG 3rd, Golovina TN, Hamilton SE, Sriram V, Spies T, Brutkiewicz RR et al (2000) Impaired assembly yet normal trafficking of MHC class I molecules in Tapasin mutant mice. Immunity 13:213–222

    Article  CAS  PubMed  Google Scholar 

  • Griffin TA, Nandi D, Cruz M, Fehling HJ, Kaer LV, Monaco JJ et al (1998) Immunoproteasome assembly: cooperative incorporation of interferon gamma (IFN-gamma)-inducible subunits. J Exp Med 187:97–104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grubaugh D, Flechtner JB, Higgins DE (2013) Proteins as T cell antigens: methods for high-throughput identification. Vaccine 31:3805–3810

    Article  CAS  PubMed  Google Scholar 

  • Guan J, Yang SJ, Gonzalez F, Yin Y, Shastri N (2017) Antigen processing in the endoplasmic reticulum is monitored by semi-invariant alphabeta TCRs specific for a conserved peptide-Qa-1(b) MHC class Ib ligand. J Immunol 198:2017–2027

    Article  CAS  PubMed  Google Scholar 

  • Gubin MM, Zhang X, Schuster H, Caron E, Ward JP, Noguchi T et al (2014) Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens. Nature 515:577–581

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guillaume B, Stroobant V, Bousquet-Dubouch MP, Colau D, Chapiro J, Parmentier N et al (2012) Analysis of the processing of seven human tumor antigens by intermediate proteasomes. J Immunol 189:3538–3547

    Article  CAS  PubMed  Google Scholar 

  • Guilloux Y, Lucas S, Brichard VG, Van Pel A, Viret C, De Plaen E et al (1996) A peptide recognized by human cytolytic T lymphocytes on HLA-A2 melanomas is encoded by an intron sequence of the N-acetylglucosaminyltransferase V gene. J Exp Med 183:1173–1183

    Article  CAS  PubMed  Google Scholar 

  • Haj AK, Breitbach ME, Baker DA, Mohns MS, Moreno GK, Wilson NA et al (2020) High-throughput identification of MHC Class I binding peptides using an Ultradense peptide Array. J Immunol 204:1689–1696

    Article  CAS  PubMed  Google Scholar 

  • Hall SS (1997) Life, death, and the immune system. Henry Holt and Company, New York, p 544

    Google Scholar 

  • Hammer GE, Gonzalez F, Champsaur M, Cado D, Shastri N (2006) The aminopeptidase ERAAP shapes the peptide repertoire displayed by major histocompatibility complex class I molecules. Nat Immunol 7:103–112

    Article  CAS  PubMed  Google Scholar 

  • Hammer GE, Gonzalez F, James E, Nolla H, Shastri N (2007) In the absence of aminopeptidase ERAAP, MHC class I molecules present many unstable and highly immunogenic peptides. Nat Immunol 8:101–108

    Article  CAS  PubMed  Google Scholar 

  • Hanada K, Yewdell JW, Yang JC (2004) Immune recognition of a human renal cancer antigen through post-translational protein splicing. Nature 427:252–256

    Article  CAS  PubMed  Google Scholar 

  • Hebert DN, Foellmer B, Helenius A (1996) Calnexin and calreticulin promote folding, delay oligomerization and suppress degradation of influenza hemagglutinin in microsomes. EMBO J 15:2961–2968

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Heemels MT, Schumacher TN, Wonigeit K, Ploegh HL (1993) Peptide translocation by variants of the transporter associated with antigen processing. Science 262:2059–2063

    Article  CAS  PubMed  Google Scholar 

  • Herberts CA, van Gaans-van den Brink J, van der Heeft M, van Wijk J, Hoekman AJ et al (2003) Autoreactivity against induced or upregulated abundant self-peptides in HLA-A*0201 following measles virus infection. Hum Immunol 64:44–55

    Article  CAS  PubMed  Google Scholar 

  • Hickman HD, Luis AD, Bardet W, Buchli R, Battson CL, Shearer MH et al (2003) Cutting edge: class I presentation of host peptides following HIV infection. J Immunol 171:22–26

    Article  CAS  PubMed  Google Scholar 

  • Hilf N, Kuttruff-Coqui S, Frenzel K, Bukur V, Stevanovic S, Gouttefangeas C et al (2019) Actively personalized vaccination trial for newly diagnosed glioblastoma. Nature 565:240–245

    Article  CAS  PubMed  Google Scholar 

  • Holmes FL (1967) Origins of the concept of the milieur intérieur. In: Grande F, Visscher MB (eds) Claude Bernard and Experimental Medicine. Shenkman, Cambridge, MA, pp 179–191

    Google Scholar 

  • Holmes FL (1986) Claude Bernard, the milieu intérieur, and regulatory physiology. Hist Philos Life Sci 8:3–25

    CAS  PubMed  Google Scholar 

  • Hong SW, Kim SM, Jin DH, Kim YS, Hur DY (2017) RPS27a enhances EBVencoded LMP1-mediated proliferation and invasion by stabilizing of LMP1. Biochem Biophys Res Commun 491:303–309

    Article  CAS  PubMed  Google Scholar 

  • Huang J, Brameshuber M, Zeng X, Xie J, Li QJ, Chien YH et al (2013) A single peptide-major histocompatibility complex ligand triggers digital cytokine secretion in CD4(+) T cells. Immunity 39:846–857

    Article  CAS  PubMed  Google Scholar 

  • Hunt DF, Henderson RA, Shabanowitz J, Sakaguchi K, Michel H, Sevilir N et al (1992a) Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. Science 255:1261–1263

    Article  CAS  Google Scholar 

  • Hunt DF, Michel H, Dickinson TA, Shabanowitz J, Cox AL, Sakaguchi K et al (1992b) Peptides presented to the immune system by the murine class II major histocompatibility complex molecule I-Ad. Science 256:1817–1820

    Article  CAS  PubMed  Google Scholar 

  • Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147:789–802

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Inobe T, Matouschek A (2014) Paradigms of protein degradation by the proteasome. Curr Opin Struct Biol 24:156–164

    Article  CAS  PubMed  Google Scholar 

  • Ivanova M, Tsvetkova G, Lukanov T, Stoimenov A, Hadjiev E, Shivarov V (2020) Probable HLA-mediated immunoediting of JAK2 V617F-driven oncogenesis. Exp Hematol 92:75–88 e10

    Article  CAS  PubMed  Google Scholar 

  • Jackson MR, Cohen-Doyle MF, Peterson PA, Williams DB (1994) Regulation of MHC class I transport by the molecular chaperone, calnexin (p 88, IP90). Science 263:384–387

    Article  CAS  PubMed  Google Scholar 

  • Jagger BW, Wise HM, Kash JC, Walters KA, Wills NM, Xiao YL et al (2012) An overlapping protein-coding region in influenza A virus segment 3 modulates the host response. Science 337:199–204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • James E, Bailey I, Sugiyarto G, Elliott T (2013) Induction of protective antitumor immunity through attenuation of ERAAP function. J Immunol 190:5839–5846

    Article  CAS  PubMed  Google Scholar 

  • Jappe EC, Kringelum J, Trolle T, Nielsen M (2018) Predicted MHC peptide binding promiscuity explains MHC class I ‘hotspots’ of antigen presentation defined by mass spectrometry eluted ligand data. Immunology 154:407–417

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jardetzky TS, Lane WS, Robinson RA, Madden DR, Wiley DC (1991) Identification of self peptides bound to purified HLA-B27. Nature 353:326–329

    Article  CAS  PubMed  Google Scholar 

  • Javitt A, Barnea E, Kramer MP, Wolf-Levy H, Levin Y, Admon A et al (2019) Proinflammatory cytokines Alter the Immunopeptidome landscape by modulation of HLA-B expression. Front Immunol 10:141

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang J, Natarajan K, Boyd LF, Morozov GI, Mage MG, Margulies DH (2017) Crystal structure of a TAPBPR-MHC I complex reveals the mechanism of peptide editing in antigen presentation. Science 358:1064–1068

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jin N, Wang Y, Crawford F, White J, Marrack P, Dai S et al (2015) N-terminal additions to the WE14 peptide of chromogranin A create strong autoantigen agonists in type 1 diabetes. Proc Natl Acad Sci U S A 112:13318–13323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kalaora S, Lee JS, Barnea E, Levy R, Greenberg P, Alon M et al (2020) Immunoproteasome expression is associated with better prognosis and response to checkpoint therapies in melanoma. Nat Commun 11:896

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanaseki T, Blanchard N, Hammer GE, Gonzalez F, Shastri N (2006) ERAAP synergizes with MHC class I molecules to make the final cut in the antigenic peptide precursors in the endoplasmic reticulum. Immunity 25:795–806

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kawakami Y, Robbins PF, Rosenberg SA (1996) Human melanoma antigens recognized by T lymphocytes. Keio J Med 45:100–108

    Article  CAS  PubMed  Google Scholar 

  • Keskin DB, Anandappa AJ, Sun J, Tirosh I, Mathewson ND, Li S et al (2019) Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial. Nature 565:234–239

    Article  CAS  PubMed  Google Scholar 

  • Khanna R, Burrows SR, Nicholls J, Poulsen LM (1998) Identification of cytotoxic T cell epitopes within Epstein-Barr virus (EBV) oncogene latent membrane protein 1 (LMP1): evidence for HLA A2 supertype-restricted immune recognition of EBVinfected cells by LMP1-specific cytotoxic T lymphocytes. Eur J Immunol 28:451–458

    Article  CAS  PubMed  Google Scholar 

  • Khodadoust MS, Olsson N, Wagar LE, Haabeth OA, Chen B, Swaminathan K et al (2017) Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens. Nature 543:723–727

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kingsbury DJ, Griffin TA, Colbert RA (2000) Novel propeptide function in 20 S proteasome assembly influences beta subunit composition. J Biol Chem 275:24156–24162

    Article  CAS  PubMed  Google Scholar 

  • Kirino Y, Bertsias G, Ishigatsubo Y, Mizuki N, Tugal-Tutkun I, Seyahi E et al (2013) Genome-wide association analysis identifies new susceptibility loci for Behcet’s disease and epistasis between HLA-B*51 and ERAP1. Nat Genet 45:202–207

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kittlesen DJ, Thompson LW, Gulden PH, Skipper JC, Colella TA, Shabanowitz J et al (1998) Human melanoma patients recognize an HLA-A1-restricted CTL epitope from tyrosinase containing two cysteine residues: implications for tumor vaccine development. J Immunol 160:2099–2106

    Article  CAS  PubMed  Google Scholar 

  • Klein J (1975) Biology of the mouse histocompatibility – 2 complex: principles of Immunogenetics applied to a single system. Springer-Verlag, New York, p 620

    Book  Google Scholar 

  • Knuth A, Wolfel T, Klehmann E, Boon T, K. H. (1989) Meyer zum Buschenfelde, Cytolytic T-cell clones against an autologous human melanoma: specificity study and definition of three antigens by immunoselection. Proc Natl Acad Sci U S A 86:2804–2808

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kong Y, Rose CM, Cass AA, Williams AG, Darwish M, Lianoglou S et al (2019) Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nat Commun 10:5228

    Article  PubMed  PubMed Central  Google Scholar 

  • Koopmann JO, Post M, Neefjes JJ, Hammerling GJ, Momburg F (1996) Translocation of long peptides by transporters associated with antigen processing (TAP). Eur J Immunol 26:1720–1728

    Article  CAS  PubMed  Google Scholar 

  • Kortleve D, Coelho RML, Hammerl D, Debets R (2022) Cancer germline antigens and tumor-agnostic CD8(+) T cell evasion. Trends Immunol. https://doi.org/10.1016/j.it.2022.03.006

  • Kowalewski DJ, Schuster H, Backerta L, Berlina C, Kahn S, Kanz L et al (2014) HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL). Proc Natl Acad Sci U S A 112(2):E166–E175

    PubMed  PubMed Central  Google Scholar 

  • Krangel MS, Orr HT, Strominger JL (1979) Assembly and maturation of HLA-A and HLA-B antigens in vivo. Cell 18:979–991

    Article  CAS  PubMed  Google Scholar 

  • Kubiniok P, Marcu A, Bichmann L, Kuchenbecker L, Schuster H, Hamelin D et al (2020) The global architecture shaping the heterogeneity and tissue-dependency of the MHC class I Immunopeptidome is evolutionarily conserved. bioRxiv. https://doi.org/10.1101/2020.1109.1128.317750

  • Kumar A, Suryadevara NC, Wolf KJ, Wilson JT, Di Paolo RJ, Brien JD et al (2020) Heterotypic immunity against vaccinia virus in an HLA-B*07:02 transgenic mousepox infection model. Sci Rep 10:13167

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kwun HJ, da Silva SR, Shah IM, Blake N, Moore PS, Chang Y (2007) Kaposi’s sarcoma-associated herpesvirus latency-associated nuclear antigen 1 mimics Epstein-Barr virus EBNA1 immune evasion through central repeat domain effects on protein processing. J Virol 81:8225–8235

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Labadie BW, Bao R, Luke JJ (2019) Reimagining IDO pathway inhibition in cancer immunotherapy via downstream focus on the tryptophan-kynurenine-aryl hydrocarbon Axis. Clin Cancer Res 25:1462–1471

    Article  CAS  PubMed  Google Scholar 

  • Lanska DJ (2014) Walter Bradford Cannon. In: Encyclopedia of the neurological sciences, vol 1. Clsevier, Inc., pp 580–583

    Chapter  Google Scholar 

  • Laumont CM, Daouda T, Laverdure JP, Bonneil E, Caron-Lizotte O, Hardy MP et al (2016) Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames. Nat Commun 7:10238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Laumont CM, Vincent K, Hesnard L, Audemard E, Bonneil E, Laverdure JP et al (2018) Noncoding regions are the main source of targetable tumor-specific antigens. Sci Transl Med 10:eaau5516

    Article  CAS  PubMed  Google Scholar 

  • Lee SP, Brooks JM, Al-Jarrah H, Thomas WA, Haigh TA, Taylor GS et al (2004) CD8 T cell recognition of endogenously expressed epstein-barr virus nuclear antigen 1. J Exp Med 199:1409–1420

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lev A, Princiotta MF, Zanker D, Takeda K, Gibbs JS, Kumagai C et al (2010) Compartmentalized MHC class I antigen processing enhances immunosurveillance by circumventing the law of mass action. Proc Natl Acad Sci U S A 107:6964–6969

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Levitskaya J, Sharipo A, Leonchiks A, Ciechanover A, Masucci MG (1997) Inhibition of ubiquitin/proteasome-dependent protein degradation by the Gly-Ala repeat domain of the Epstein-Barr virus nuclear antigen 1. Proc Natl Acad Sci U S A 94:12616–12621

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lichti CF (2021) Identification of spliced peptides in pancreatic islets uncovers errors leading to false assignments. Proteomics 21:e2000176

    Article  PubMed  Google Scholar 

  • Liepe J, Marino F, Sidney J, Jeko A, Bunting DE, Sette A et al (2016) A large fraction of HLA class I ligands are proteasome-generated spliced peptides. Science 354:354–358

    Article  CAS  PubMed  Google Scholar 

  • Lopez de Castro JA (2018) How ERAP1 and ERAP2 shape the Peptidomes of disease-associated MHC-I proteins. Front Immunol 9:2463

    Article  PubMed  PubMed Central  Google Scholar 

  • Lu X, Gibbs JS, Hickman HD, David A, Dolan BP, Jin Y et al (2012) Endogenous viral antigen processing generates peptide-specific MHC class I cell-surface clusters. Proc Natl Acad Sci U S A 109:15407–15412

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu SX, De Neef E, Thomas JD, Sabio E, Rousseau B, Gigoux M et al (2021) Pharmacologic modulation of RNA splicing enhances anti-tumor immunity. Cell. https://doi.org/10.1016/j.cell.2021.05.038

  • Luckey CJ, Marto JA, Partridge M, Hall E, White FM, Lippolis JD et al (2001) Differences in the expression of human class I MHC alleles and their associated peptides in the presence of proteasome inhibitors. J Immunol 167:1212–1221

    Article  CAS  PubMed  Google Scholar 

  • Luedtke B, Pooler LM, Choi EY, Tranchita AM, Reinbold CJ, Brown AC et al (2003) A single nucleotide polymorphism in the Emp3 gene defines the H4 minor histocompatibility antigen. Immunogenetics 55:284–295

    Article  CAS  PubMed  Google Scholar 

  • Lurquin C, Van Pel A, Mariame B, De Plaen E, Szikora JP, Janssens C et al (1989) Structure of the gene of tum- transplantation antigen P91A: the mutated exon encodes a peptide recognized with Ld by cytolytic T cells. Cell 58:293–303

    Article  CAS  PubMed  Google Scholar 

  • Maby P, Bindea G, Mlecnik B, Galon J (2021) License to kill: microsatellite instability and immune contexture. Onco Targets Ther 10:1905935

    Google Scholar 

  • Madden DR, Gorga JC, Strominger JL, Wiley DC (1991) The structure of HLA-B27 reveals nonamer self-peptides bound in an extended conformation. Nature 353:321–325

    Article  CAS  PubMed  Google Scholar 

  • Malarkannan S, Horng T, Shih PP, Schwab S, Shastri N (1999) Presentation of out-of-frame peptide/MHC class I complexes by a novel translation initiation mechanism. Immunity 10:681–690

    Article  CAS  PubMed  Google Scholar 

  • Marcilla M, Cragnolini JJ, Lopez de Castro JA (2007) Proteasome-independent HLAB27 ligands arise mainly from small basic proteins. Mol Cell Proteomics 6:923–938

    Article  CAS  PubMed  Google Scholar 

  • Marcu A, Bichmann L, Kuchenbecker L, Kowalewski D, Freudenmann L, Backert L et al (2020) The HLA ligand atlas – a resource of natural HLA ligands presented on benign tissues. bioRxiv. https://doi.org/10.1101/778944

  • Marrack P, Scott-Browne JP, Dai S, Gapin L, Kappler JW (2008) Evolutionarily conserved amino acids that control TCR-MHC interaction. Annu Rev Immunol 26:171–203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martin-Esteban A, Gomez-Molina P, Sanz-Bravo A, Lopez de Castro JA (2014) Combined effects of ankylosing spondylitis-associated ERAP1 polymorphisms outside the catalytic and peptide-binding sites on the processing of natural HLAB27 ligands. J Biol Chem 289:3978–3990

    Article  CAS  PubMed  Google Scholar 

  • Martin-Esteban A, Guasp P, Barnea E, Admon A, Lopez de Castro JA (2016) Functional interaction of the ankylosing spondylitis-associated endoplasmic reticulum aminopeptidase 2 with the HLA-B*27 Peptidome in human cells. Arthritis Rheumatol 68:2466–2475

    Article  CAS  PubMed  Google Scholar 

  • Martin-Esteban A, Sanz-Bravo A, Guasp P, Barnea E, Admon A, Lopez de Castro JA (2017) Separate effects of the ankylosing spondylitis associated ERAP1 and ERAP2 aminopeptidases determine the influence of their combined phenotype on the HLA-B*27 peptidome. J Autoimmun 79:28–38

    Article  CAS  PubMed  Google Scholar 

  • Matsumura M, Fremont DH, Peterson PA, Wilson IA (1992) Emerging principles for the recognition of peptide antigens by MHC class I molecules. Science 257:927–934

    Article  CAS  PubMed  Google Scholar 

  • Mazza C, Auphan-Anezin N, Gregoire C, Guimezanes A, Kellenberger C, Roussel A et al (2007) How much can a T-cell antigen receptor adapt to structurally distinct antigenic peptides? EMBO J 26:1972–1983

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McGlincy NJ, Ingolia NT (2017) Transcriptome-wide measurement of translation by ribosome profiling. Methods 126:112–129

    Article  PubMed  PubMed Central  Google Scholar 

  • McMurtrey C, Trolle T, Sansom T, Remesh SG, Kaever T, Bardet W et al (2016) Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove. elife 5:e12556

    Article  PubMed  PubMed Central  Google Scholar 

  • Medawar PB (1958) The immunology of transplantation. Harvey Lect 52:144–176

    CAS  Google Scholar 

  • Meij P, Leen A, Rickinson AB, Verkoeijen S, Vervoort MB, Bloemena E et al (2002) Identification and prevalence of CD8(+) T-cell responses directed against Epstein- Barr virus-encoded latent membrane protein 1 and latent membrane protein 2. Int J Cancer 99:93–99

    Article  CAS  PubMed  Google Scholar 

  • Michaux A, Larrieu P, Stroobant V, Fonteneau JF, Jotereau F, Van den Eynde BJ et al (2014) A spliced antigenic peptide comprising a single spliced amino acid is produced in the proteasome by reverse splicing of a longer peptide fragment followed by trimming. J Immunol 192:1962–1971

    Article  CAS  PubMed  Google Scholar 

  • Milner E, Barnea E, Beer I, Admon A (2006) The turnover kinetics of major histocompatibility complex peptides of human cancer cells. Mol Cell Proteomics 5:357–365

    Article  CAS  PubMed  Google Scholar 

  • Milner E, Gutter-Kapon L, Bassani-Strenberg M, Barnea E, Beer I, Admon A (2013) The effect of proteasome inhibition on the generation of the human leukocyte antigen (HLA) peptidome. Mol Cell Proteomics 12:1853–1864

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mohammed F, Cobbold M, Zarling AL, Salim M, Barrett-Wilt GA, Shabanowitz J et al (2008) Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self. Nat Immunol 9:1236–1243

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morel S, Levy F, Burlet-Schiltz O, Brasseur F, Probst-Kepper M, Peitrequin AL et al (2000) Processing of some antigens by the standard proteasome but not by the immunoproteasome results in poor presentation by dendritic cells. Immunity 12:107–117

    Article  CAS  PubMed  Google Scholar 

  • Morris GP, Allen PM (2012) How the TCR balances sensitivity and specificity for the recognition of self and pathogens. Nat Immunol 13:121–128

    Article  CAS  PubMed  Google Scholar 

  • Murata S, Sasaki K, Kishimoto T, Niwa S, Hayashi H, Takahama Y et al (2007) Regulation of CD8+ T cell development by thymus-specific proteasomes. Science 316:1349–1353

    Article  CAS  PubMed  Google Scholar 

  • Murata S, Takahama Y, Kasahara M, Tanaka K (2018) The immunoproteasome and thymoproteasome: functions, evolution and human disease. Nat Immunol 19:923–931

    Article  CAS  PubMed  Google Scholar 

  • Mylonas R, Beer I, Iseli C, Chong C, Pak HS, Gfeller D et al (2018) Estimating the contribution of proteasomal spliced peptides to the HLA-I Ligandome. Mol Cell Proteomics 17:2347–2357

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nagarajan NA, de Verteuil DA, Sriranganadane D, Yahyaoui W, Thibault P, Perreault C et al (2016) ERAAP shapes the Peptidome associated with classical and nonclassical MHC class I molecules. J Immunol 197:1035–1043

    Article  CAS  PubMed  Google Scholar 

  • Netzer N, Goodenbour JM, David A, Dittmar KA, Jones RB, Schneider JR et al (2009) Innate immune and chemically triggered oxidative stress modifies translational fidelity. Nature 462:522–526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nitta T, Murata S, Sasaki K, Fujii H, Ripen AM, Ishimaru N et al (2010) Thymoproteasome shapes immunocompetent repertoire of CD8+ T cells. Immunity 32:29–40

    Article  CAS  PubMed  Google Scholar 

  • Nitta T, Kochi Y, Muro R, Tomofuji Y, Okamura T, Murata S et al (2017) Human thymoproteasome variations influence CD8 T cell selection. Sci Immunol 2:eaan5165

    Article  PubMed  Google Scholar 

  • Norment AM, Salter RD, Parham P, Engelhard VH, Littman DR (1988) Cell-cell adhesion mediated by CD8 and MHC class I molecules. Nature 336:79–81

    Article  CAS  PubMed  Google Scholar 

  • Ogiso Y, Tomida A, Tsuruo T (2002) Nuclear localization of proteasomes participates in stress-inducible resistance of solid tumor cells to topoisomerase II-directed drugs. Cancer Res 62:5008–5012

    CAS  PubMed  Google Scholar 

  • Ohigashi I, Frantzeskakis M, Jacques A, Fujimori S, Ushio A, Yamashita F et al (2021) The thymoproteasome hardwires the TCR repertoire of CD8+ T cells in the cortex independent of negative selection. J Exp Med 218:e20201904

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Osterbye T, Nielsen M, Dudek NL, Ramarathinam SH, Purcell AW, Schafer-Nielsen C et al (2020) HLA Class II specificity assessed by high-density peptide microarray interactions. J Immunol 205:290–299

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ott PA, Hu Z, Keskin DB, Shukla SA, Sun J, Bozym DJ et al (2017) An immunogenic personal neoantigen vaccine for patients with melanoma. Nature 547:217–221

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ou WJ, Cameron PH, Thomas DY, Bergeron JJ (1993) Association of folding intermediates of glycoproteins with calnexin during protein maturation. Nature 364:771–776

    Article  CAS  PubMed  Google Scholar 

  • Ouspenskaia T, Law T, Clauser K, Klaeger S, Sarkizova S, Aguet F et al (2021) Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer. BioRxiv. https://doi.org/10.1101/2020.1102.1112.945840

  • Overwijk WW, Lee DS, Surman DR, Irvine KR, Touloukian CE, Chan CC et al (1999) Vaccination with a recombinant vaccinia virus encoding a “self” antigen induces autoimmune vitiligo and tumor cell destruction in mice: requirement for CD4(+) T lymphocytes. Proc Natl Acad Sci U S A 96:2982–2987

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Paes W, Leonov G, Partridge T, Chikata T, Murakoshi H, Frangou A et al (2019) Contribution of proteasome-catalyzed peptide cis-splicing to viral targeting by CD8(+) T cells in HIV-1 infection. Proc Natl Acad Sci U S A 116:24748–24759

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Paes W, Leonov G, Partridge T, Nicastri A, Ternette N, Borrow P (2020) Elucidation of the signatures of proteasome-catalyzed peptide splicing. Front Immunol 11:563800

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Paul S, Croft NP, Purcell AW, Tscharke DC, Sette A, Nielsen M et al (2020) Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system. PLoS Comput Biol 16:e1007757

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peh CA, Burrows SR, Barnden M, Khanna R, Cresswell P, Moss DJ et al (1998) HLA-B27-restricted antigen presentation in the absence of tapasin reveals polymorphism in mechanisms of HLA class I peptide loading. Immunity 8:531–542

    Article  CAS  PubMed  Google Scholar 

  • Peters B, Nielsen M, Sette A (2020) T cell epitope predictions. Annu Rev Immunol 38:123–145

    Article  CAS  PubMed  Google Scholar 

  • Pettmann J, Huhn A, Abu Shah E, Kutuzov MA, Wilson DB, Dustin ML et al (2021) The discriminatory power of the T cell receptor. elife 10:e67092

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Platteel AC, Mishto M, Textoris-Taube K, Keller C, Liepe J, Busch DH et al (2016) CD8(+) T cells of listeria monocytogenes-infected mice recognize both linear and spliced proteasome products. Eur J Immunol 46:1109–1118

    Article  CAS  PubMed  Google Scholar 

  • Platteel ACM, Liepe J, Textoris-Taube K, Keller C, Henklein P, Schalkwijk HH et al (2017) Multi-level strategy for identifying proteasome-catalyzed spliced epitopes targeted by CD8(+) T cells during bacterial infection. Cell Rep 20:1242–1253

    Article  CAS  PubMed  Google Scholar 

  • Ploegh HL, Orr HT, Strominger JL (1981) Major histocompatibility antigens: the human (HLA-A, -B, -C) and murine (H-2K, H-2D) class I molecules. Cell 24:287–299

    Article  CAS  PubMed  Google Scholar 

  • Prasad S, Starck SR, Shastri N (2016) Presentation of cryptic peptides by MHC Class I is enhanced by inflammatory stimuli. J Immunol 197:2981–2991

    Article  CAS  PubMed  Google Scholar 

  • Princiotta MF, Finzi D, Qian SB, Gibbs J, Schuchmann S, Buttgereit F et al (2003) Quantitating protein synthesis, degradation, and endogenous antigen processing. Immunity 18:343–354

    Article  CAS  PubMed  Google Scholar 

  • Purbhoo MA, Irvine DJ, Huppa JB, Davis MM (2004) T cell killing does not require the formation of a stable mature immunological synapse. Nat Immunol 5:524–530

    Article  CAS  PubMed  Google Scholar 

  • Qian MX, Pang Y, Liu CH, Haratake K, Du BY, Ji DY et al (2013) Acetylationmediated proteasomal degradation of core histones during DNA repair and spermatogenesis. Cell 153:1012–1024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rajagopalan S, Brenner MB (1994) Calnexin retains unassembled major histocompatibility complex class I free heavy chains in the endoplasmic reticulum. J Exp Med 180:407–412

    Article  CAS  PubMed  Google Scholar 

  • Rajagopalan S, Xu Y, Brenner MB (1994) Retention of unassembled components of integral membrane proteins by calnexin. Science 263:387–390

    Article  CAS  PubMed  Google Scholar 

  • Reed B, Crawford F, Hill RC, Jin N, White J, Krovi SH et al (2021) Lysosomal cathepsin creates chimeric epitopes for diabetogenic CD4 T cells via transpeptidation. J Exp Med 218:e20192135

    Article  CAS  PubMed  Google Scholar 

  • Reeves E, Edwards CJ, Elliott T, James E (2013) Naturally occurring ERAP1 haplotypes encode functionally distinct alleles with fine substrate specificity. J Immunol 191:35–43

    Article  CAS  PubMed  Google Scholar 

  • Reits EA, Vos JC, Gromme M, Neefjes J (2000) The major substrates for TAP in vivo are derived from newly synthesized proteins. Nature 404:774–778

    Article  CAS  PubMed  Google Scholar 

  • Reya T, Morrison SJ, Clarke MF, Weissman IL (2001) Stem cells, cancer, and cancer stem cells. Nature 414:105–111

    Article  CAS  PubMed  Google Scholar 

  • Reynisson B, Alvarez B, Paul S, Peters B, Nielsen M (2020) 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rizvi SM, Raghavan M (2006) Direct peptide-regulatable interactions between MHC class I molecules and tapasin. Proc Natl Acad Sci U S A 103:18220–18225

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rizvi SM, Salam N, Geng J, Qi Y, Bream JH, Duggal P et al (2014) Distinct assembly profiles of HLA-B molecules. J Immunol 192:4967–4976

    Article  CAS  PubMed  Google Scholar 

  • Robbins PF, Lu YC, El-Gamil M, Li YF, Gross C, Gartner J et al (2013) Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells. Nat Med 19:747–752

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Robinson J, Barker DJ, Georgiou X, Cooper MA, Flicek P, Marsh SGE (2020) IPDIMGT/HLA database. Nucleic Acids Res 48:D948–D955

    CAS  PubMed  Google Scholar 

  • Rolfs Z, Muller M, Shortreed MR, Smith LM, Bassani-Sternberg M (2019) Comment on “A subset of HLA-I peptides are not genomically templated: evidence for cis-and trans-spliced peptide ligands”. Sci Immunol 4:eaaw1622

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rotzschke O, Falk K, Deres K, Schild H, Norda M, Metzger J et al (1990) Isolation and analysis of naturally processed viral peptides as recognized by cytotoxic T cells. Nature 348:252–254

    Article  CAS  PubMed  Google Scholar 

  • Roudko V, Bozkus CC, Orfanelli T, McClain CB, Carr C, O’Donnell T et al (2020) Shared immunogenic poly-epitope frameshift mutations in microsatellite unstable tumors. Cell 183:1634–1649 e1617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ruiz Cuevas MV, Hardy MP, Holly J, Bonneil E, Durette C, Courcelles M et al (2021) Most non-canonical proteins uniquely populate the proteome or immunopeptidome. Cell Rep 34:108815

    Article  CAS  PubMed  Google Scholar 

  • Sahin U, Derhovanessian E, Miller M, Kloke BP, Simon P, Lower M et al (2017) Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer. Nature 547:222–226

    Article  CAS  PubMed  Google Scholar 

  • Saini SK, Orskov AD, Bjerregaard AM, Unnikrishnan A, Holmberg-Thyden S, Borch A et al (2020) Human endogenous retroviruses form a reservoir of T cell targets in hematological cancers. Nat Commun 11:5660

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sakata E, Eisele MR, Baumeister W (2021) Molecular and cellular dynamics of the 26S proteasome. Biochim Biophys Acta Proteins Proteom 1869:140583

    Article  CAS  PubMed  Google Scholar 

  • Salter RD, Norment AM, Chen BP, Clayberger C, Krensky AM, Littman DR et al (1989) Polymorphism in the alpha 3 domain of HLA-A molecules affects binding to CD8. Nature 338:345–347

    Article  CAS  PubMed  Google Scholar 

  • Salter RD, Benjamin RJ, Wesley PK, Buxton SE, Garrett TP, Clayberger C et al (1990) A binding site for the T-cell co-receptor CD8 on the alpha 3 domain of HLAA2. Nature 345:41–46

    Article  CAS  PubMed  Google Scholar 

  • Saper M, Bjorkman PJ, Wiley DC (1991) Refined structure of the human histocompatibility antigen at 26 A resolution. J Mol Biol 219:277–319

    Article  CAS  PubMed  Google Scholar 

  • Saric T, Chang SC, Hattori A, York IA, Markant S, Rock KL et al (2002) An IFNgamma-induced aminopeptidase in the ER, ERAP1, trims precursors to MHC class I-presented peptides. Nat Immunol 3:1169–1176

    Article  CAS  PubMed  Google Scholar 

  • Sarkizova S, Klaeger S, Le PM, Li LW, Oliveira G, Keshishian H et al (2020) A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nat Biotechnol 38:199–209

    Article  CAS  PubMed  Google Scholar 

  • Saveanu L, Carroll O, Lindo V, Del Val M, Lopez D, Lepelletier Y et al (2005) Concerted peptide trimming by human ERAP1 and ERAP2 aminopeptidase complexes in the endoplasmic reticulum. Nat Immunol 6:689–697

    Article  CAS  PubMed  Google Scholar 

  • Schmidt J, Smith AR, Magnin M, Racle J, Devlin JR, Bobisse S et al (2021) Prediction of neo-epitope immunogenicity reveals TCR recognition determinants and provides insight into immunoediting. Cell Rep Med 2:100194

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schubert U, Anton LC, Gibbs J, Norbury CC, Yewdell JW, Bennink JR (2000) Rapid degradation of a large fraction of newly synthesized proteins by proteasomes. Nature 404:770–774

    Article  CAS  PubMed  Google Scholar 

  • Schumacher TN, Kantesaria DV, Heemels MT, Ashton-Rickardt PG, Shepherd JC, Fruh K et al (1994) Peptide length and sequence specificity of the mouse TAP1/TAP2 translocator. J Exp Med 179:533–540

    Article  CAS  PubMed  Google Scholar 

  • Schwab SR, Li KC, Kang C, Shastri N (2003) Constitutive display of cryptic translation products by MHC class I molecules. Science 301:1367–1371

    Article  CAS  PubMed  Google Scholar 

  • Schwab SR, Shugart JA, Horng T, Malarkannan S, Shastri N (2004) Unanticipated antigens: translation initiation at CUG with leucine. PLoS Biol 2:e366

    Article  PubMed  PubMed Central  Google Scholar 

  • Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J et al (2011) Global quantification of mammalian gene expression control. Nature 473:337–342

    Article  PubMed  Google Scholar 

  • Schwarz K, de Giuli R, Schmidtke G, Kostka S, van den Broek M, Kim KB et al (2000) The selective proteasome inhibitors lactacystin and epoxomicin can be used to either up- or down-regulate antigen presentation at nontoxic doses. J Immunol 164:6147–6157

    Article  CAS  PubMed  Google Scholar 

  • Sendoel A, Dunn JG, Rodriguez EH, Naik S, Gomez NC, Hurwitz B et al (2017) Translation from unconventional 5′ start sites drives tumour initiation. Nature 541:494–499

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Serwold T, Gonzalez F, Kim J, Jacob R, Shastri N (2002) ERAAP customizes peptides for MHC class I molecules in the endoplasmic reticulum. Nature 419:480–483

    Article  CAS  PubMed  Google Scholar 

  • Sette A, Ceman S, Kubo RT, Sakaguchi K, Appella E, Hunt DF et al (1992) Invariant chain peptides in most HLA-DR molecules of an antigen-processing mutant. Science 258:1801–1804

    Article  CAS  PubMed  Google Scholar 

  • Shastri N, Nguyen V, Gonzalez F (1995) Major histocompatibility class I molecules can present cryptic translation products to T-cells. J Biol Chem 270:1088–1091

    Article  CAS  PubMed  Google Scholar 

  • Shastri N, Schwab S, Serwold T (2002) Producing nature’s gene-chips: the generation of peptides for display by MHC class I molecules. Annu Rev Immunol 20:463–493

    Article  CAS  PubMed  Google Scholar 

  • Shepherd JC, Schumacher TN, Ashton-Rickardt PG, Imaeda S, Ploegh HL, Janeway CA Jr et al (1993) TAP1-dependent peptide translocation in vitro is ATP dependent and peptide selective. Cell 74:577–584

    Article  CAS  PubMed  Google Scholar 

  • Smith CC, Beckermann KE, Bortone DS, De Cubas AA, Bixby LM, Lee SJ et al (2018) Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma. J Clin Invest 128:4804–4820

    Article  PubMed  PubMed Central  Google Scholar 

  • Snell GD, Dausset J, Nathenson SG (1976) Histocompatibility. Academic, New York, p 416

    Google Scholar 

  • Spencer CT, Bezbradica JS, Ramos MG, Arico CD, Conant SB, Gilchuk P et al (2015) Viral infection causes a shift in the self peptide repertoire presented by human MHC class I molecules. Proteomics Clin Appl 9:1035–1052

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stamogiannos A, Koumantou D, Papakyriakou A, Stratikos E (2015) Effects of polymorphic variation on the mechanism of Endoplasmic Reticulum Aminopeptidase 1. Mol Immunol 67:426–435

    Article  CAS  PubMed  Google Scholar 

  • Starck SR, Jiang V, Pavon-Eternod M, Prasad S, McCarthy B, Pan T et al (2012) Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I. Science 336:1719–1723

    Article  CAS  PubMed  Google Scholar 

  • Starck SR, Tsai JC, Chen K, Shodiya M, Wang L, Yahiro K et al (2016) Translation from the 5′ untranslated region shapes the integrated stress response. Science 351:aad3867

    Article  PubMed  PubMed Central  Google Scholar 

  • Strange A, Capon F, Spencer CC, Knight J, Weale ME, Allen MH et al (2010) A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. Nat Genet 42:985–990

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sun Y, Sijts AJ, Song M, Janek K, Nussbaum AK, Kral S et al (2002) Expression of the proteasome activator PA28 rescues the presentation of a cytotoxic T lymphocyte epitope on melanoma cells. Cancer Res 62:2875–2882

    CAS  PubMed  Google Scholar 

  • Sweeney C, Quek L, Gration B, Vyas P (2019) Chapter 20: Cancer stem cells. In: Pezzella F, Tavassoli M, Kerr DJ (eds) Oxford textbook of cancer biology. Oxford University Press, Oxford, pp 283–299

    Google Scholar 

  • Tay RE, Richardson EK, Toh HC (2021) Revisiting the role of CD4+ T cells in cancer immunotherapy – new insights into old paradigms. Cancer Gene Ther 28:5–17

    Google Scholar 

  • Tedeschi V, Paldino G, Paladini F, Mattorre B, Tuosto L, Sorrentino R et al (2020) The impact of the ‘Mis-Peptidome’ on HLA class I-mediated diseases: contribution of ERAP1 and ERAP2 and effects on the immune response. Int J Mol Sci 21:9608

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tellam J, Connolly G, Green KJ, Miles JJ, Moss DJ, Burrows SR et al (2004) Endogenous presentation of CD8+ T cell epitopes from Epstein-Barr virusencoded nuclear antigen 1. J Exp Med 199:1421–1431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ternette N, Block PD, Sanchez-Bernabeu A, Borthwick N, Pappalardo E, Abdul-Jawad S et al (2015) Early kinetics of the HLA Class I-associated Peptidome of MVA.HIVconsv-infected cells. J Virol 89:5760–5771

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Theodossis A, Guillonneau C, Welland A, Ely LK, Clements CS, Williamson NA et al (2010) Constraints within major histocompatibility complex class I restricted peptides: presentation and consequences for T-cell recognition. Proc Natl Acad Sci U S A 107:5534–5539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thomas C, Tampe R (2017) Structure of the TAPBPR-MHC I complex defines the mechanism of peptide loading and editing. Science 358:1060–1064

    Article  CAS  PubMed  Google Scholar 

  • Thomas C, Tampe R (2019) MHC I chaperone complexes shaping immunity. Curr Opin Immunol 58:9–15

    Article  CAS  PubMed  Google Scholar 

  • Tomko RJ Jr, Hochstrasser M (2013) Molecular architecture and assembly of the eukaryotic proteasome. Annu Rev Biochem 82:415–445

    Article  CAS  PubMed  Google Scholar 

  • Townsend A, Ohlén C, Bastin J, Ljunggren HG, Foster L, Kärre K (1989) Association of class I major histocompatibility heavy and light chains induced by viral peptides. Nature 340:443–448

    Google Scholar 

  • Tran E, Ahmadzadeh M, Lu YC, Gros A, Turcotte S, Robbins PF et al (2015) Immunogenicity of somatic mutations in human gastrointestinal cancers. Science 350:1387–1390

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tsao H, Millman P, Linette GP, Hodi FS, Sober AJ, Goldberg MA et al (2002) Hypopigmentation associated with an adenovirus-mediated gp100/MART-1- transduced dendritic cell vaccine for metastatic melanoma. Arch Dermatol 138:799–802

    Article  PubMed  Google Scholar 

  • van Baren N, Coulie PG (2022) Chapter 4: Human tumor antigens recognized by T lymphocytes. In: Butterfield LH, Kaufman HL, Marincola FM (eds) Cancer immunotherapy: principles and practice. Springer Publishing Company, LLC, New York, pp 31–40

    Google Scholar 

  • Van Bleek GM, Nathenson SG (1990) Isolation of an endogenously processed immunodominant viral peptide from the class I H-2Kb molecule. Nature 348:213–216

    Article  PubMed  Google Scholar 

  • Van den Eynde B, Hainaut P, Herin M, Knuth A, Lemoine C, Weynants P et al (1989) Presence on a human melanoma of multiple antigens recognized by autologous CTL. Int J Cancer 44:634–640

    Article  PubMed  Google Scholar 

  • Van Kaer L, Ashton-Rickardt PG, Ploegh HL, Tonegawa S (1992) TAP1 mutant mice are deficient in antigen presentation, surface class I molecules, and CD4-8+ T cells. Cell 71: 1205–1214

    Google Scholar 

  • Vance RE, Kraft JR, Altman JD, Jensen PE, Raulet DH (1998) Mouse CD94/NKG2A is a natural killer cell receptor for the nonclassical major histocompatibility complex (MHC) class I molecule Qa-1(b). J Exp Med 188:1841–1848

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vassilakos A, Cohen-Doyle MF, Peterson PA, Jackson MR, Williams DB (1996) The molecular chaperone calnexin facilitates folding and assembly of class I histocompatibility molecules. EMBO J 15:1495–1506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vigneron N, Stroobant V, Chapiro J, Ooms A, Degiovanni G, Morel S et al (2004) An antigenic peptide produced by peptide splicing in the proteasome. Science 304:587–590

    Article  CAS  PubMed  Google Scholar 

  • Vigneron N, Stroobant V, Ferrari V, Abi Habib J, Van den Eynde BJ (2019) Production of spliced peptides by the proteasome. Mol Immunol 113:93–102

    Article  CAS  PubMed  Google Scholar 

  • Vinitsky A, Anton LC, Snyder HL, Orlowski M, Bennink JR, Yewdell JW (1997) The generation of MHC class I-associated peptides is only partially inhibited by proteasome inhibitors: involvement of nonproteasomal cytosolic proteases in antigen processing? J Immunol 159:554–564

    Article  CAS  PubMed  Google Scholar 

  • Vlachos A (2017) Acquired ribosomopathies in leukemia and solid tumors. Hematology Am Soc Hematol Educ Program 2017:716–719

    Article  PubMed  PubMed Central  Google Scholar 

  • Voo KS, Fu T, Wang HY, Tellam J, Heslop HE, Brenner MK et al (2004) Evidence for the presentation of major histocompatibility complex class I-restricted Epstein- Barr virus nuclear antigen 1 peptides to CD8+ T lymphocytes. J Exp Med 199:459–470

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wahl A, Schafer F, Bardet W, Hildebrand WH (2010) HLA class I molecules reflect an altered host proteome after influenza virus infection. Hum Immunol 71:14–22

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wan X, Vomund AN, Peterson OJ, Chervonsky AV, Lichti CF, Unanue ER (2020) The MHC-II peptidome of pancreatic islets identifies key features of autoimmune peptides. Nat Immunol 21:455–463

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Sosinowski T, Novikov A, Crawford F, Neau DB, Yang J et al (2018) Cterminal modification of the insulin B:11-23 peptide creates superagonists in mouse and human type 1 diabetes. Proc Natl Acad Sci U S A 115:162–167

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Sosinowski T, Novikov A, Crawford F, White J, Jin N et al (2019) How Cterminal additions to insulin B-chain fragments create superagonists for T cells in mouse and human type 1 diabetes. Sci Immunol 4:eaav7517

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang TY, Liu Q, Ren Y, Alam SK, Wang L, Zhu Z et al (2021) A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes. Mol Cell 81:2246–2260 e2212

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Warren EH, Vigneron NJ, Gavin MA, Coulie PG, Stroobant V, Dalet A et al (2006) An antigen produced by splicing of noncontiguous peptides in the reverse order. Science 313:1444–1447

    Article  CAS  PubMed  Google Scholar 

  • Watson J, Baker T, Bell S, Gann A, Levine M, Losick R (2013) Molecular biology of the. Gene Chapter 15:912

    Google Scholar 

  • Wearsch PA, Cresswell P (2007) Selective loading of high-affinity peptides onto major histocompatibility complex class I molecules by the tapasin-ERp57 heterodimer. Nat Immunol 8:873–881

    Article  CAS  PubMed  Google Scholar 

  • Wei J, Yewdell JW (2019) Immunoribosomes: Where’s there’s fire, there’s fire. Mol Immunol 113:38–42

    Article  CAS  PubMed  Google Scholar 

  • Wei J, Zanker D, Di Carluccio AR, Smelkinson MG, Takeda K, Seedhom MO et al (2017) Varied role of Ubiquitylation in generating MHC class I peptide ligands. J Immunol 198:3835–3845

    Article  CAS  PubMed  Google Scholar 

  • Wei J, Kishton RJ, Angel M, Conn CS, Dalla-Venezia N, Marcel V et al (2019) Ribosomal proteins regulate MHC Class I peptide generation for Immunosurveillance. Mol Cell 73:1162–1173 e1165

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Williams AP, Peh CA, Purcell AW, McCluskey J, Elliott T (2002) Optimization of the MHC class I peptide cargo is dependent on tapasin. Immunity 16:509–520

    Article  CAS  PubMed  Google Scholar 

  • Wooldridge L, Ekeruche-Makinde J, van den Berg HA, Skowera A, Miles JJ, Tan MP et al (2012) A single autoimmune T cell receptor recognizes more than a million different peptides. J Biol Chem 287:1168–1177

    Article  CAS  PubMed  Google Scholar 

  • Yaciuk JC, Skaley M, Bardet W, Schafer F, Mojsilovic D, Cate S et al (2014) Direct interrogation of viral peptides presented by the class I HLA of HIV-infected T cells. J Virol 88:12992–13004

    Article  PubMed  PubMed Central  Google Scholar 

  • Yadav R, Yoshimura Y, Boesteanu A, Christianson GJ, Ajayi WU, Shashidharamurthy R et al (2003) The H4b minor histocompatibility antigen is caused by a combination of genetically determined and posttranslational modifications. J Immunol 170:5133–5142

    Article  CAS  PubMed  Google Scholar 

  • Yadav M, Jhunjhunwala S, Phung QT, Lupardus P, Tanguay J, Bumbaca S et al (2014) Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing. Nature 515:572–576

    Article  CAS  PubMed  Google Scholar 

  • Yamamoto TN, Kishton RJ, Restifo NP (2019) Developing neoantigen-targeted T cell-based treatments for solid tumors. Nat Med 25:1488–1499

    Article  CAS  PubMed  Google Scholar 

  • Yamauchi T, Hoki T, Oba T, Kajihara R, Attwood K, Cao X et al (2021) CD40 and CD80/86 signaling in cDC1s mediate effective neoantigen vaccination and generation of antigen-specific CX3CR1(+) CD8(+) T cells. Cancer Immunol Immunother. https://doi.org/10.1007/s00262-021-02969-6

  • Yan J, Parekh VV, Mendez-Fernandez Y, Olivares-Villagomez D, Dragovic S, Hill T et al (2006) In vivo role of ER-associated peptidase activity in tailoring peptides for presentation by MHC class Ia and class Ib molecules. J Exp Med 203:647–659

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang N, Gibbs JS, Hickman HD, Reynoso GV, Ghosh AK, Bennink JR et al (2016) Defining viral defective ribosomal products: standard and alternative translation initiation events generate a common peptide from influenza a virus M2 and M1 mRNAs. J Immunol 196:3608–3617

    Article  CAS  PubMed  Google Scholar 

  • Yao Y, Liu N, Zhou Z, Shi L (2019) Influence of ERAP1 and ERAP2 gene polymorphisms on disease susceptibility in different populations. Hum Immunol 80:325–334

    Article  CAS  PubMed  Google Scholar 

  • Yewdell JW, Holly J (2020) DRiPs get molecular. Curr Opin Immunol 64:130–136

    Article  CAS  PubMed  Google Scholar 

  • Yewdell JW, Nicchitta CV (2006) The DRiP hypothesis decennial: support, controversy, refinement and extension. Trends Immunol 27:368–373

    Article  CAS  PubMed  Google Scholar 

  • Yewdell JW, Dersh D, Fahraeus R (2019) Peptide channeling: the key to MHC Class I Immunosurveillance? Trends Cell Biol 29:929–939

    Article  CAS  PubMed  Google Scholar 

  • York IA, Chang SC, Saric T, Keys JA, Favreau JM, Goldberg AL et al (2002) The ER aminopeptidase ERAP1 enhances or limits antigen presentation by trimming epitopes to 8-9 residues. Nat Immunol 3:1177–1184

    Article  CAS  PubMed  Google Scholar 

  • Young AC, Zhang W, Sacchettini JC, Nathenson SG (1994) The three-dimensional structure of H-2Db at 2.4 A resolution: implications for antigen-determinant selection. Cell 76:39–50

    Article  CAS  PubMed  Google Scholar 

  • Zarling AL, Ficarro SB, White FM, Shabanowitz J, Hunt DF, Engelhard VH (2000) Phosphorylated peptides are naturally processed and presented by major histocompatibility complex class I molecules in vivo. J Exp Med 192:1755–1762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zarling AL, Polefrone JM, Evans AM, Mikesh LM, Shabanowitz J, Lewis ST et al (2006) Identification of class I MHC-associated phosphopeptides as targets for cancer immunotherapy. Proc Natl Acad Sci U S A 103:14889–14894

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang W, Young AC, Imarai M, Nathenson SG, Sacchettini JC (1992) Crystal structure of the major histocompatibility complex class I H-2Kb molecule containing a single viral peptide: implications for peptide binding and T-cell receptor recognition. Proc Natl Acad Sci U S A 89:8403–8407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Q, Ji SY, Busayavalasa K, Shao J, Yu C (2019) Meiosis I progression in spermatogenesis requires a type of testis-specific 20S core proteasome. Nat Commun 10:3387

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

Supported by a Research Career Scientist (IK6 BX004595) & Merit (I01 BX001444 & BX001610) Awards from the VA and by NIH grants (R01 AI137082 & DE027749).

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Joyce, S. (2023). Cancer Antigens: Sources, Generation, and Presentation. In: Rezaei, N. (eds) Handbook of Cancer and Immunology. Springer, Cham. https://doi.org/10.1007/978-3-030-80962-1_38-1

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