Abstract 2115: An atlas of transposable element derived alternative splicing in cancer

Abstract

Transposable element (TE) derived sequences comprise more than half of the human genome, and their presence has been documented to alter gene expression in a number of different ways, including the generation of alternatively spliced transcript isoforms. Alternative splicing has been associated with tumorigenesis for a number of different cancers. The objective of this study was to broadly characterize the role of human TEs in generating alternatively spliced transcript isoforms in cancer. To do so, we screened for the presence of TE-derived sequences co-located with alternative splice sites that are differentially utilized in normal versus cancer tissues. We analyzed a comprehensive set of alternative splice variants characterized for 614 matched normal-tumor tissue pairs across 13 cancer types, resulting in the discovery of 4,820 TE-generated alternative splice events distributed among 723 cancer-associated genes. SINEs (Alu) and LINEs (L1) were found to contribute the majority of TE-generated alternative splice sites in cancer genes. A number of cancer-associated genes - including MYH11, WHSC1, and CANT1 - were shown to have overexpressed TE-derived isoforms across a range of cancer types. TE-derived isoforms were also linked to cancer-specific fusion transcripts, suggesting a novel mechanism for the generation of transcriptome diversity via trans-splicing mediated by dispersed TE repeats. Citation Format: Evan A. Clayton, Lavanya Rishishwar, Tzu-Chuan Huang, Saurabh Gulati, Dongjo Ban, John F. McDonald, I. King Jordan. An atlas of transposable element derived alternative splicing in cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2115.

A genomic portrait of zebrafish transposable elements and their spatiotemporal embryonic expression

“…2E); we find that LTR elements and LINEs are located significantly further away from genes on the same strand than those on the opposite strand (Wilcoxon rank-sum tests: p=3e-16 and p=6e-26, respectively). Autonomous retroelements often encode strong cis-regulatory sequences capable of affecting nearby gene expression, including promoters, splice sites, and polyadenylation signals (Clayton et al, 2020;Ishiuchi et al, 2015;Ng et al, 2020). Thus, there may be stronger selection against zebrafish LTR elements and LINEs when they insert on the same strand as a nearby gene, similar to what has been observed in mammalian genomes (Medstrand et al, 2002).…”