Small genomic insertions form enhancers that misregulate oncogenes

• Published in: Nature communications Vol. 8; no. 1; p. 14385
• Main Authors: Abraham, Brian J., Hnisz, Denes, Weintraub, Abraham S., Kwiatkowski, Nicholas, Li, Charles H., Li, Zhaodong, Weichert-Leahey, Nina, Rahman, Sunniyat, Liu, Yu, Etchin, Julia, Li, Benshang, Shen, Shuhong, Lee, Tong Ihn, Zhang, Jinghui, Look, A. Thomas, Mansour, Marc R., Young, Richard A.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 09.02.2017; Nature Publishing Group; Nature Portfolio
• Subjects: 13/106; 38/35; 38/91; 631/114/2785; 631/67/69; Adolescent; Adult; Base Sequence; Biology; Cancer; Cell Line, Tumor; Child; Child, Preschool; Enhancer Elements, Genetic; Gene Expression Regulation, Leukemic; Genome, Human; Genomes; Hematology; Humanities and Social Sciences; Humans; Infant; Leukemia-Lymphoma, Adult T-Cell - genetics; multidisciplinary; Mutagenesis, Insertional - genetics; Mutation; Oncogenes; Oncology; Pediatrics; Reproducibility of Results; Science; Science (multidisciplinary); Young Adult; United States > US; China; Massachusetts
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms14385

The non-coding regions of tumour cell genomes harbour a considerable fraction of total DNA sequence variation, but the functional contribution of these variants to tumorigenesis is ill-defined. Among these non-coding variants, somatic insertions are among the least well characterized due to challenges with interpreting short-read DNA sequences. Here, using a combination of Chip-seq to enrich enhancer DNA and a computational approach with multiple DNA alignment procedures, we identify enhancer-associated small insertion variants. Among the 102 tumour cell genomes we analyse, small insertions are frequently observed in enhancer DNA sequences near known oncogenes. Further study of one insertion, somatically acquired in primary leukaemia tumour genomes, reveals that it nucleates formation of an active enhancer that drives expression of the LMO2 oncogene. The approach described here to identify enhancer-associated small insertion variants provides a foundation for further study of these abnormalities across human cancers. Sequencing initiatives have detected multiple types of mutations in cancer. Here the authors, analysing enhancer-targeting sequence data, show that small insertions in transcriptional enhancers are frequently found near oncogenes, and demonstrate how one mutation deregulates expression of LMO2 in leukemia cells.