1. Whole-genome landscape of adult T-cell leukemia/lymphoma
- Author
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Yoko Kubuki, Kengo Takeuchi, Seishi Ogawa, Yuki Tahira, Akifumi Takaori-Kondo, Kota Yoshifuji, Makoto Yoshimitsu, Kenichi Chiba, Masaaki Sekine, Ai Okada, Ana Acuna-Villaorduna, Yuichi Shiraishi, Yasushi Miyazaki, Tatsuhiro Shibata, Jun-ichirou Yasunaga, Tomonori Hidaka, Michihiro Hidaka, Mariko Tabata, Kisato Nosaka, Masao Matsuoka, Yasunori Kogure, Takuro Kameda, R. Alejandro Sica, Yuta Ito, B. Hilda Ye, Yoshitaka Imaizumi, Ayako Kamiunten, Sumito Shingaki, Keiichi Akizuki, Yuki Saito, Juan Carlos Ramos, Kazuya Shimoda, Junji Koya, Murali Janakiram, Marni B McClure, Urvi A Shah, Yasuhito Nannya, Kenji Ishitsuka, Mizuki Watanabe, Nobuaki Nakano, Satoru Miyano, Nobuyuki Kakiuchi, Atae Utsunomiya, Keisuke Kataoka, Kotaro Shide, and Akira Kitanaka
- Subjects
DNA Copy Number Variations ,Immunology ,Somatic hypermutation ,Biology ,Biochemistry ,Genome ,Adult T-cell leukemia/lymphoma ,Mice ,Exome Sequencing ,Biomarkers, Tumor ,medicine ,Animals ,Humans ,Leukemia-Lymphoma, Adult T-Cell ,IL-2 receptor ,Gene ,Ataxin-1 ,Genetics ,Genome, Human ,Germinal center ,FOXP3 ,Cell Biology ,Hematology ,Prognosis ,medicine.disease ,Proto-Oncogene Proteins c-rel ,Gene Expression Regulation, Neoplastic ,Mice, Inbred C57BL ,Repressor Proteins ,Survival Rate ,Leukemia ,Mutation ,Female - Abstract
Adult T-cell leukemia/lymphoma (ATL) is an aggressive neoplasm immunophenotypically resembling regulatory T cells, associated with human T-cell leukemia virus type-1. Here, we performed whole-genome sequencing (WGS) of 150 ATL cases to reveal the overarching landscape of genetic alterations in ATL. We discovered frequent (33%) loss-of-function alterations preferentially targeting the CIC long isoform, which were overlooked by previous exome-centric studies of various cancer types. Long but not short isoform–specific inactivation of Cic selectively increased CD4+CD25+Foxp3+ T cells in vivo. We also found recurrent (13%) 3′-truncations of REL, which induce transcriptional upregulation and generate gain-of-function proteins. More importantly, REL truncations are also common in diffuse large B-cell lymphoma, especially in germinal center B-cell–like subtype (12%). In the non-coding genome, we identified recurrent mutations in regulatory elements, particularly splice sites, of several driver genes. In addition, we characterized the different mutational processes operative in clustered hypermutation sites within and outside immunoglobulin/T-cell receptor genes and identified the mutational enrichment at the binding sites of host and viral transcription factors, suggesting their activities in ATL. By combining the analyses for coding and noncoding mutations, structural variations, and copy number alterations, we discovered 56 recurrently altered driver genes, including 11 novel ones. Finally, ATL cases were classified into 2 molecular groups with distinct clinical and genetic characteristics based on the driver alteration profile. Our findings not only help to improve diagnostic and therapeutic strategies in ATL, but also provide insights into T-cell biology and have implications for genome-wide cancer driver discovery.
- Published
- 2022
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