The landscape of chimeric RNAs in non-diseased tissues and cells. Issue 4 (22nd January 2020)

• Record Type: Journal Article
• Authors: Singh, Sandeep; Qin, Fujun; Kumar, Shailesh; Elfman, Justin; Lin, Emily; Pham, Lam-Phong; Yang, Amy; Li, Hui
• Is Part Of: Nucleic acids research. Volume 48:Issue 4(2020)
• Page Start: 1764
• Page End: 1778
• Publication Date: 2020-01-22
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkz1223
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Chimeric RNAs and their encoded proteins have been traditionally viewed as unique features of neoplasia, and have been used as biomarkers and therapeutic targets for multiple cancers. Recent studies have demonstrated that chimeric RNAs also exist in non-cancerous cells and tissues, although large-scale, genome-wide studies of chimeric RNAs in non-diseased tissues have been scarce. Here, we explored the landscape of chimeric RNAs in 9495 non-diseased human tissue samples of 53 different tissues from the GTEx project. Further, we established means for classifying chimeric RNAs, and observed enrichment for particular classifications as more stringent filters are applied. We experimentally validated a subset of chimeric RNAs from each classification and demonstrated functional relevance of two chimeric RNAs in non-cancerous cells. Importantly, our list of chimeric RNAs in non-diseased tissues overlaps with some entries in several cancer fusion databases, raising concerns for some annotations. The data from this study provides a large repository of chimeric RNAs present in non-diseased tissues, which can be used as a control dataset to facilitate the identification of true cancer-specific chimeras.