Intron retention is a source of neoepitopes in cancer
Alicia C Smart, Claire A Margolis, Harold Pimentel, Meng Xiao He, Diana Miao, Dennis Adeegbe, Tim Fugmann, Kwok-Kin Wong, Eliezer M Van Allen, Alicia C Smart, Claire A Margolis, Harold Pimentel, Meng Xiao He, Diana Miao, Dennis Adeegbe, Tim Fugmann, Kwok-Kin Wong, Eliezer M Van Allen
Abstract
We present an in silico approach to identifying neoepitopes derived from intron retention events in tumor transcriptomes. Using mass spectrometry immunopeptidome analysis, we show that retained intron neoepitopes are processed and presented on MHC I on the surface of cancer cell lines. RNA-derived neoepitopes should be considered for prospective personalized cancer vaccine development.
Conflict of interest statement
Disclosure of Potential Conflicts of Interest
EMV holds consulting roles with Tango Therapeutics, Invitae, and Genome Medical and receives research support from Bristol-Myers Squibb and Novartis.
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References
- Ott PA et al. Nature 547, 217–221 (2017).
- Sahin U et al. Nature 547, 222–226 (2017).
- Carreno BM et al. Science 348, 803–808 (2015).
- Hunder NN et al. N Engl J Med 358, 2698–2703 (2008).
- Robbins PF et al. Clin Cancer Res 21, 1019–1027 (2015).
- Dvinge H & Bradley RK Genome Med 7, 45 (2015).
- Jung H et al. Nat Genet 47, 1242–1248 (2015).
- Apcher S et al. Proc Natl Acad Sci U S A 108, 11572–11577 (2011).
- Rock KL, Farfan-Arribas DJ & Shen L J Immunol 184, 9–15 (2010).
- Pearson H et al. J Clin Invest 126, 4690–4701 (2016).
- Hugo W et al. Cell 165, 35–44 (2016).
- Snyder A et al. N Engl J Med 371, 2189–2199 (2014).
- Li S et al. Nat Biotechnol 32, 888–895 (2014).
- Van Allen EM et al. Science 350, 207–211 (2015).
- Rooney MS, Shukla SA, Wu CJ, Getz G & Hacohen N Cell 160, 48–61 (2015).
- Middleton R et al. Genome Biol 18, 51 (2017).
- Dominguez D et al. Elife 5 (2016).
- Deng J et al. Cancer Discov 8, 216–233 (2018).
- Schaer DA et al. Cell Rep 22, 2978–2994 (2018).
- Goel S et al. Nature 548, 471–475 (2017).
- Lupetti R et al. J Exp Med 188, 1005–1016 (1998).
- Andersen RS et al. Oncoimmunology 2, e25374 (2013).
- Nathanson T et al. Cancer Immunol Res 5, 84–91 (2017).
- Harrow J et al. Genome Res 22, 1760–1774 (2012).
- Bray NL, Pimentel H, Melsted P & Pachter L Nat Biotechnol 34, 525–527 (2016).
- Pimentel H et al. Nucleic Acids Res 44, 838–851 (2016).
- Karolchik D et al. Nucleic Acids Res 32, D493–496 (2004).
- Shukla SA et al. Nat Biotechnol 33, 1152–1158 (2015).
- Nielsen M & Andreatta M Genome Med 8, 33 (2016).
- The UniProt C Nucleic Acids Res 45, D158–D169 (2017).
- Robinson JT et al. Nat Biotechnol 29, 24–26 (2011).
- Cibulskis K et al. Nat Biotechnol 31, 213–219 (2013).
- Saunders CT et al. Bioinformatics 28, 1811–1817 (2012).
- Ritz D et al. Proteomics 16, 1570–1580 (2016).
- Barretina J et al. Nature 483, 603–607 (2012).
- Subramanian A et al. Proc Natl Acad Sci U S A 102, 15545–15550 (2005).
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