Comprehensive profiling of 1015 patients’ exomes reveals genomic-clinical associations in colorectal cancer

Qi Zhao, Feng Wang (), Yan-Xing Chen, Shifu Chen, Yi-Chen Yao, Zhao-Lei Zeng, Teng-Jia Jiang, Ying-Nan Wang, Chen-Yi Wu, Ying Jing, You-Sheng Huang, Jing Zhang, Zi-Xian Wang, Ming-Ming He, Heng-Ying Pu, Zong-Jiong Mai, Qi-Nian Wu, Renwen Long, Xiaoni Zhang, Tanxiao Huang, Mingyan Xu, Miao-Zheng Qiu, Hui-Yan Luo, Yu-Hong Li, Dong-Shen Zhang, Wei-Hua Jia, Gong Chen, Pei-Rong Ding, Li-Ren Li, Zheng-Hai Lu, Zhi-Zhong Pan and Rui-Hua Xu ()
Additional contact information
Qi Zhao: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Feng Wang: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Yan-Xing Chen: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Shifu Chen: HaploX Biotechnology, Co., Ltd., 8th floor, Auto Electric Power Building
Yi-Chen Yao: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Zhao-Lei Zeng: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Teng-Jia Jiang: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Ying-Nan Wang: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Chen-Yi Wu: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Ying Jing: Sun Yat-sen University Cancer Center, Sun Yat-sen University
You-Sheng Huang: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Jing Zhang: HaploX Biotechnology, Co., Ltd., 8th floor, Auto Electric Power Building
Zi-Xian Wang: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Ming-Ming He: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Heng-Ying Pu: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Zong-Jiong Mai: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Qi-Nian Wu: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Renwen Long: HaploX Biotechnology, Co., Ltd., 8th floor, Auto Electric Power Building
Xiaoni Zhang: HaploX Biotechnology, Co., Ltd., 8th floor, Auto Electric Power Building
Tanxiao Huang: HaploX Biotechnology, Co., Ltd., 8th floor, Auto Electric Power Building
Mingyan Xu: HaploX Biotechnology, Co., Ltd., 8th floor, Auto Electric Power Building
Miao-Zheng Qiu: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Hui-Yan Luo: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Yu-Hong Li: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Dong-Shen Zhang: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Wei-Hua Jia: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Gong Chen: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Pei-Rong Ding: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Li-Ren Li: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Zheng-Hai Lu: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Zhi-Zhong Pan: Sun Yat-sen University Cancer Center, Sun Yat-sen University
Rui-Hua Xu: Sun Yat-sen University Cancer Center, Sun Yat-sen University

Nature Communications, 2022, vol. 13, issue 1, 1-17

Abstract: Abstract The genetic basis of colorectal cancer (CRC) and its clinical associations remain poorly understood due to limited samples or targeted genes in current studies. Here, we perform ultradeep whole-exome sequencing on 1015 patients with CRC as part of the ChangKang Project. We identify 46 high-confident significantly mutated genes, 8 of which mutate in 14.9% of patients: LYST, DAPK1, CR2, KIF16B, NPIPB15, SYTL2, ZNF91, and KIAA0586. With an unsupervised clustering algorithm, we propose a subtyping strategy that classisfies CRC patients into four genomic subtypes with distinct clinical characteristics, including hypermutated, chromosome instability with high risk, chromosome instability with low risk, and genome stability. Analysis of immunogenicity uncover the association of immunogenicity reduction with genomic subtypes and poor prognosis in CRC. Moreover, we find that mitochondrial DNA copy number is an independent factor for predicting the survival outcome of CRCs. Overall, our results provide CRC-related molecular features for clinical practice and a valuable resource for translational research.

Date: 2022
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DOI: 10.1038/s41467-022-30062-8

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