Genomic and transcriptomic landscape of human gastrointestinal stromal tumors

Feifei Xie, Shuzhen Luo, Dongbing Liu, Xiaojing Lu, Ming Wang, Xiaoxiao Liu, Fujian Jia, Yuzhi Pang, Yanying Shen, Chunling Zeng, Xinli Ma, Daoqiang Tang, Lin Tu, Linxi Yang, Yumei Cheng, Yuxiang Luo, Fanfan Xie, Hao Hou, Tao Huang, Bo Ni, Chun Zhuang, Wenyi Zhao, Ke Li, Xufen Zheng, Wenbo Bi, Xiaona Jia, Yi He, Simin Wang (), Hui Cao (), Kui Wu () and Yuexiang Wang ()
Additional contact information
Feifei Xie: Chinese Academy of Sciences
Shuzhen Luo: BGI Genomics
Dongbing Liu: BGI Genomics
Xiaojing Lu: Chinese Academy of Sciences
Ming Wang: Shanghai Jiao Tong University
Xiaoxiao Liu: Chinese Academy of Sciences
Fujian Jia: BGI Research
Yuzhi Pang: Chinese Academy of Sciences
Yanying Shen: Shanghai Jiao Tong University
Chunling Zeng: Chinese Academy of Sciences
Xinli Ma: Shanghai Jiao Tong University
Daoqiang Tang: Shanghai Jiao Tong University
Lin Tu: Shanghai Jiao Tong University
Linxi Yang: Shanghai Jiao Tong University
Yumei Cheng: Chinese Academy of Sciences
Yuxiang Luo: Chinese Academy of Sciences
Fanfan Xie: BGI Research
Hao Hou: BGI Research
Tao Huang: Shanghai Institute of Nutrition and Health
Bo Ni: Shanghai Jiao Tong University
Chun Zhuang: Shanghai Jiao Tong University
Wenyi Zhao: Shanghai Jiao Tong University
Ke Li: Chinese Academy of Sciences
Xufen Zheng: Chinese Academy of Sciences
Wenbo Bi: Chinese Academy of Sciences
Xiaona Jia: Chinese Academy of Sciences
Yi He: No.1 Hospital of Jiaxing
Simin Wang: Chinese Academy of Sciences
Hui Cao: Shanghai Jiao Tong University
Kui Wu: BGI Genomics
Yuexiang Wang: Chinese Academy of Sciences

Nature Communications, 2024, vol. 15, issue 1, 1-20

Abstract: Abstract Gastrointestinal stromal tumor (GISTs) are clinically heterogenous exhibiting varying degrees of disease aggressiveness in individual patients. We comprehensively describe the genomic and transcriptomic landscape of a cohort of 117 GISTs including 31 low-risk, 18 intermediate-risk, 29 high-risk, 34 metastatic and 5 neoadjuvant GISTs from 105 patients. GISTs have notably low tumor mutation burden but widespread copy number variations. Aggressive GISTs harbor remarkably more genomic aberrations than low-/intermediate-risk GISTs. Complex genomic alterations, chromothripsis and kataegis, occur selectively in aggressive GISTs. Despite the paucity of mutations, recurrent inactivating YLPM1 mutations are identified (10.3%, 7 of 68 patients), enriched in high-risk/metastatic GIST and functional study further demonstrates YLPM1 inactivation promotes GIST proliferation, growth and oxidative phosphorylation. Spatially and temporally separated GISTs from individual patients demonstrate complex tumor heterogeneity in metastatic GISTs. Finally, four prominent subtypes are proposed with different genomic features, expression profiles, immune characteristics, clinical characteristics and subtype-specific treatment strategies. This large-scale analysis depicts the landscape and provides further insights into GIST pathogenesis and precise treatment.

Date: 2024
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DOI: 10.1038/s41467-024-53821-1

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