2,725
Views
8
CrossRef citations to date
0
Altmetric
Review Article

Proteogenomics: advances in cancer antigen research

&
Pages 65-70 | Received 24 Apr 2019, Accepted 29 Jun 2019, Published online: 18 Jul 2019

References

  • Chen DS, Mellman I. Elements of cancer immunity and the cancer-immune set point. Nature. 2017;541:321–330.
  • Havel JJ, Chowell D, Chan TA. The evolving landscape of biomarkers for checkpoint inhibitor immunotherapy. Nat Rev Cancer. 2019;19:133.
  • Yarchoan M, Hopkins A, Jaffee EM. Tumor mutational burden and response rate to PD-1 inhibition. N Engl J Med. 2017;377:2500–2501.
  • Rock KL, Reits E, Neefjes J. Present yourself! By MHC Class I and MHC Class II molecules. Trends Immunol. 2016;37:724–737.
  • Shastri N, Schwab S, Serwold T. Producing nature's gene-chips: the generation of peptides for display by MHC class I molecules. Annu Rev Immunol. 2002;20:463–493.
  • Lundegaard C, Lamberth K, Harndahl M, et al. NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. Nucleic Acids Res. 2008;36:W509–W512.
  • Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ, et al. Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation. Mol Cell Proteomics. 2015;14:658–673.
  • Abelin JG, Keskin DB, Sarkizova S, et al. Mass spectrometry profiling of HLA-associated peptidomes in mono-allelic cells enables more accurate epitope prediction. Immunity. 2017;46:315–326.
  • Hongo A, Kanaseki T, Tokita S, et al. Upstream position of proline defines peptide-HLA Class I repertoire formation and CD8(+) T cell responses. J Immunol. 2019;202:2849–2855.
  • Creech AL, Ting YS, Goulding SP, et al. The role of mass spectrometry and proteogenomics in the advancement of HLA epitope prediction. Proteomics. 2018;18:1700259.
  • Freudenmann LK, Marcu A, Stevanovic S. Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry. Immunology. 2018;154:331–345.
  • Laumont CM, Perreault C. Exploiting non-canonical translation to identify new targets for T cell-based cancer immunotherapy. Cell Mol Life Sci. 2018;75:607–621.
  • Schumacher TN, Schreiber RD. Neoantigens in cancer immunotherapy. Science. 2015;348:69–74.
  • Vitiello A, Zanetti M. Neoantigen prediction and the need for validation. Nat Biotechnol. 2017;35:815–817.
  • McGranahan N, Rosenthal R, Hiley CT, et al. Allele-specific HLA loss and immune escape in lung cancer evolution. Cell. 2017;171:1259.
  • Shionoya Y, Kanaseki T, Miyamoto S, et al. Loss of tapasin in human lung and colon cancer cells and escape from tumor-associated antigen-specific CTL recognition. Oncoimmunology. 2017;6:e1274476.
  • EDITORIAL. The problem with neoantigen prediction. Nat Biotechnol. 2017;35:97.
  • Ott PA, Hu Z, Keskin DB, et al. An immunogenic personal neoantigen vaccine for patients with melanoma. Nature. 2017;547:217.
  • Marty R, Thompson WK, Salem RM, et al. Evolutionary pressure against MHC Class II binding cancer mutations. Cell. 2018;175:416–428.e413.
  • Yadav M, Jhunjhunwala S, Phung QT, et al. Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing. Nature. 2014;515:572–576.
  • Kochin V, Kanaseki T, Tokita S, et al. HLA-A24 ligandome analysis of colon and lung cancer cells identifies a novel cancer-testis antigen and a neoantigen that elicits specific and strong CTL responses. Oncoimmunology. 2017;6:e1293214.
  • Tran E, Ahmadzadeh M, Lu Y-C, et al. Immunogenicity of somatic mutations in human gastrointestinal cancers. Science. 2015;350:1387–1390.
  • Bassani-Sternberg M, Bräunlein E, Klar R, et al. Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry. Nat Commun. 2016;7:13404.
  • Vigneron N, Ferrari V, Stroobant V, et al. Peptide splicing by the proteasome. J Biol Chem. 2017;292:21170–21179.
  • Liepe J, Marino F, Sidney J, et al. A large fraction of HLA class I ligands are proteasome-generated spliced peptides. Science. 2016;354:354–358.
  • Faridi P, Li C, Ramarathinam SH, et al. A subset of HLA-I peptides are not genomically templated: evidence for cis- and trans-spliced peptide ligands. Sci Immunol. 2018;3:eaar3947.
  • Hanada K, Yewdell JW, Yang JC. Immune recognition of a human renal cancer antigen through post-translational protein splicing. Nature. 2004;427:252–256.
  • Djebali S, Davis CA, Merkel A, et al. Landscape of transcription in human cells. Nature. 2012;489:101–108.
  • Ingolia NT. Ribosome footprint profiling of translation throughout the genome. Cell. 2016;165:22–33.
  • Boon T, Van Pel A. T cell-recognized antigenic peptides derived from the cellular genome are not protein degradation products but can be generated directly by transcription and translation of short subgenic regions. A hypothesis. Immunogenetics. 1989;29:75–79.
  • Laumont CM, Vincent K, Hesnard L, et al. Noncoding regions are the main source of targetable tumor-specific antigens. Sci Transl Med. 2018;10:eaau5516.