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Wang TY, Liu Q, Ren Y, Alam SK, Wang L, Zhu Z, Hoeppner LH, Dehm SM, Cao Q, Yang R. A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes. Mol Cell 2021; 81:2246-2260.e12. [PMID: 33861991 DOI: 10.1016/j.molcel.2021.03.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 01/02/2021] [Accepted: 03/17/2021] [Indexed: 12/20/2022]
Abstract
Exitron splicing (EIS) creates a cryptic intron (called an exitron) within a protein-coding exon to increase proteome diversity. EIS is poorly characterized, but emerging evidence suggests a role for EIS in cancer. Through a systematic investigation of EIS across 33 cancers from 9,599 tumor transcriptomes, we discovered that EIS affected 63% of human coding genes and that 95% of those events were tumor specific. Notably, we observed a mutually exclusive pattern between EIS and somatic mutations in their affected genes. Functionally, we discovered that EIS altered known and novel cancer driver genes for causing gain- or loss-of-function, which promotes tumor progression. Importantly, we identified EIS-derived neoepitopes that bind to major histocompatibility complex (MHC) class I or II. Analysis of clinical data from a clear cell renal cell carcinoma cohort revealed an association between EIS-derived neoantigen load and checkpoint inhibitor response. Our findings establish the importance of considering EIS alterations when nominating cancer driver events and neoantigens.
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Affiliation(s)
- Ting-You Wang
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Qi Liu
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yanan Ren
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Sk Kayum Alam
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Li Wang
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Zhu Zhu
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Luke H Hoeppner
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Departments of Laboratory Medicine and Pathology and Urology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Qi Cao
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
| | - Rendong Yang
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
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