1. Genomic Analyses Reveal Mutational Signatures and Frequently Altered Genes in Esophageal Squamous Cell Carcinoma
- Author
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Yanbo Zhang, Chen Longyun, Xing Chen, Xuehan Zhuang, Jiansheng Guo, Jiaqian Wang, Zhi Xia, Fang Wang, Chao Chen, Jing Liu, Xiaolong Cheng, Sha Xie, Minghui He, Ruyi Shi, Qimin Zhan, Le Cheng, Xiangchun Li, Ling Zhang, Yongping Cui, Bin Li, Bin Yang, Yaoping Li, Xiaofeng Yang, Yunwei Ou, Bing Dong, Zhibo Gao, Qingshan Li, Jie Ma, Caixia Cheng, Wenliang Chen, Yanfeng Xi, Dongxin Lin, Yongjun Guo, Jinfen Wang, Mengyao Wang, Heyang Cui, Yong Zhou, Jiuzhou Zhao, Enming Li, Shengqing Wan, Xukui Yang, Lixin Liu, Jie Yang, Yingrui Li, Xuanlin Huang, Hongyi Li, Gang Chen, Guodong Li, Pengzhou Kong, Bin Song, Yin Li, Longhai Luo, Huanming Yang, Yanyan Zhang, Juan Wang, Jianfang Liang, Lin Li, Xiaoling Hu, Li-Yan Xu, Enwei Xu, Xiuqing Zhang, Zhenxiang Zhao, Yongkai Tan, Jun Wang, Yanghui Bi, Zhiwu Jia, and Yongmei Song
- Subjects
Esophageal Neoplasms ,Polycomb-Group Proteins ,Tetrazolium Salts ,Genome ,Ligases ,Phosphatidylinositol 3-Kinases ,Genetics(clinical) ,In Situ Hybridization, Fluorescence ,Genetics (clinical) ,Polycomb Repressive Complex 1 ,Genetics ,BAP1 ,LIM Domain Proteins ,CREB-Binding Protein ,Immunohistochemistry ,Hedgehog signaling pathway ,Patched-1 Receptor ,Gene Knockdown Techniques ,Carcinoma, Squamous Cell ,Esophageal Squamous Cell Carcinoma ,Erratum ,Ubiquitin Thiolesterase ,Signal Transduction ,Patched Receptors ,APOBEC ,China ,DNA Copy Number Variations ,Class I Phosphatidylinositol 3-Kinases ,APOBEC-1 Deaminase ,Ubiquitin-Protein Ligases ,Immunoblotting ,Molecular Sequence Data ,Receptors, Cell Surface ,Biology ,Real-Time Polymerase Chain Reaction ,Article ,Cell Line, Tumor ,Cytidine Deaminase ,Carcinoma ,medicine ,Humans ,Genetic Predisposition to Disease ,neoplasms ,Gene ,Analysis of Variance ,Base Sequence ,Genome, Human ,Tumor Suppressor Proteins ,Correction ,Sequence Analysis, DNA ,medicine.disease ,digestive system diseases ,Human genetics ,Thiazoles ,PTCH1 ,Mutation ,Transcription Factors - Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers worldwide and the fourth most lethal cancer in China. However, although genomic studies have identified some mutations associated with ESCC, we know little of the mutational processes responsible. To identify genome-wide mutational signatures, we performed either whole-genome sequencing (WGS) or whole-exome sequencing (WES) on 104 ESCC individuals and combined our data with those of 88 previously reported samples. An APOBEC -mediated mutational signature in 47% of 192 tumors suggests that APOBEC-catalyzed deamination provides a source of DNA damage in ESCC. Moreover, PIK3CA hotspot mutations (c.1624G>A [p.Glu542Lys] and c.1633G>A [p.Glu545Lys]) were enriched in APOBEC -signature tumors, and no smoking-associated signature was observed in ESCC. In the samples analyzed by WGS, we identified focal ( CBX4 and CBX8 . In our combined cohort, we identified frequent inactivating mutations in AJUBA , ZNF750 , and PTCH1 and the chromatin-remodeling genes CREBBP and BAP1 , in addition to known mutations. Functional analyses suggest roles for several genes ( CBX4 , CBX8 , AJUBA , and ZNF750 ) in ESCC. Notably, high activity of hedgehog signaling and the PI3K pathway in approximately 60% of 104 ESCC tumors indicates that therapies targeting these pathways might be particularly promising strategies for ESCC. Collectively, our data provide comprehensive insights into the mutational signatures of ESCC and identify markers for early diagnosis and potential therapeutic targets.
- Published
- 2020