Oncogenic structural aberration landscape in gastric cancer genomes.

Autor: Saito-Adachi M; Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan., Hama N; Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan., Totoki Y; Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.; Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan., Nakamura H; Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan., Arai Y; Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan., Hosoda F; Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan., Rokutan H; Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan., Yachida S; Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.; Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan., Kato M; Division of Bioinformatics, National Cancer Center Research Institute, Tokyo, Japan., Fukagawa A; Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan., Shibata T; Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan. tashibat@ncc.go.jp.; Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. tashibat@ncc.go.jp.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2023 Jun 22; Vol. 14 (1), pp. 3688. Date of Electronic Publication: 2023 Jun 22.
DOI: 10.1038/s41467-023-39263-1
Abstrakt: Structural variants (SVs) are responsible for driver events in gastric cancer (GC); however, their patterns and processes remain poorly understood. Here, we examine 170 GC whole genomes to unravel the oncogenic structural aberration landscape in GC genomes and identify six rearrangement signatures (RSs). Non-random combinations of RSs elucidate distinctive GC subtypes comprising one or a few dominant RS that are associated with specific driver events (BRCA1/2 defects, mismatch repair deficiency, and TP53 mutation) and epidemiological backgrounds. Twenty-seven SV hotspots are identified as GC driver candidates. SV hotspots frequently constitute complexly clustered SVs involved in driver gene amplification, such as ERBB2, CCNE1, and FGFR2. Further deconstruction of the locally clustered SVs uncovers amplicon-generating profiles characterized by super-large SVs and intensive segmental amplifications, contributing to the extensive amplification of GC oncogenes. Comprehensive analyses using adjusted SV allele frequencies indicate the significant involvement of extra-chromosomal DNA in processes linked to specific RSs.
(© 2023. The Author(s).)
Databáze: MEDLINE
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