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The landscape of chimeric RNAs in non-diseased tissues and cells

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Title The landscape of chimeric RNAs in non-diseased tissues and cells
 
Creator Singh, Sandeep
Qin, Fujun
Kumar, Shailesh
Elfman, Justin
Lin, Emily
Pham, Lam-Phong
Yang, Amy
Li, Hui
 
Subject chimeric RNAs
non-diseased tissues and cells
 
Description Accepted date: January 20, 2020
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.
NCI Grant [CA190713]; NIGMS Grant [GM132138]; St.
Baldrick’s V Scholarship (to H.L.). Funding for open access
charge: NIGMS [GM132138]. High-performance computing systems and services were
provided by the Data Science Institute and the other Computation and Data Resource Exchange (CADRE) partner
organizations at the University of Virginia. We thank the
Biorepository and Tissue Research Facility (BTRF) at the University of Virginia for providing the clinical samples. We
thank Dr Roger Abounader for providing the immortalized
astrocyte cell line.
 
Date 2020-01-24T09:34:34Z
2020-01-24T09:34:34Z
2020
 
Type Article
 
Identifier Nucleic Acids Research, 48(4): 1764-1778
1362-4962
https://doi.org/10.1093/nar/gkz1223
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz1223/5713453
http://223.31.159.10:8080/jspui/handle/123456789/1034
 
Language en_US
 
Format application/pdf
 
Publisher Oxford University Press