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Washington University in St. Louis

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Genome Res., Dec 08 2023, | https://doi.org/10.1101/gr.277061.122 Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome

Ju Heon Maeng ^1,2, H. Josh Jang ^1,2,5, Alan Y. Du ^1,2, Shin-Cheng Tzeng ³ and Ting Wang ^1,2,4,*

¹Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
²Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
³Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
⁴McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA

^*Corresponding author: correspondence to Ting Wang

Abstract

Recent studies have shown that the noncoding genome can produce unannotated proteins as antigens that induce immune response. One major source of this activity is the aberrant epigenetic reactivation of transposable elements (TEs). In tumors, TEs often provide cryptic or alternate promoters, which can generate transcripts that encode tumor-specific unannotated proteins. Thus, TE-derived transcripts (TE transcripts) have the potential to produce tumor-specific, but recurrent, antigens shared among many tumors. Identification of TE-derived tumor antigens holds the promise to improve cancer immunotherapy approaches; however, current genomics and computational tools are not optimized for their detection. Here we combined CAGE technology with full-length long-read transcriptome sequencing (long-read CAGE, or LRCAGE) and developed a suite of computational tools to significantly improve immunopeptidome detection by incorporating TE and other tumor transcripts into the proteome database. By applying our methods to human lung cancer cell line H1299 data, we show that long-read technology significantly improves mapping of promoters with low mappability scores and that LRCAGE guarantees accurate construction of uncharacterized 5' transcript structure. Augmenting a reference proteome database with newly characterized transcripts enabled us to detect noncanonical antigens from HLA-pulldown LC-MS/MS data. Lastly, we show that epigenetic treatment increased the number of noncanonical antigens, particularly those encoded by TE transcripts, which might expand the pool of targetable antigens for cancers with low mutational burden.

논문정보

형식Research article
게재일2023년 12월 (BRIC 등록일 2023-12-13)
연구진국외 연구진
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