Genetic landscape of esophageal squamous cell carcinoma

© 2014 Nature America, Inc. All rights reserved.

Yi-Bo Gao1, Zhao-Li Chen1, Jia-Gen Li1, Xue-Da Hu1, Xue-Jiao Shi1, Zeng-Miao Sun1, Fan Zhang1, Zi-Ran Zhao2, Zi-Tong Li2, Zi-Yuan Liu1, Yu-Da Zhao1, Jian Sun1, Cheng-Cheng Zhou1, Ran Yao1, Su-Ya Wang1, Pan Wang2, Nan Sun1, Bai-Hua Zhang1, Jing-Si Dong1, Yue Yu1, Mei Luo1, Xiao-Li Feng3, Su-Sheng Shi3, Fang Zhou1, Feng-Wei Tan1, Bin Qiu1, Ning Li1, Kang Shao1, Li-Jian Zhang4, Lan-Jun Zhang5, Qi Xue1, Shu-Geng Gao1 & Jie He1 Esophageal squamous cell carcinoma (ESCC) is one of the deadliest cancers1. We performed exome sequencing on 113 tumor-normal pairs, yielding a mean of 82 non-silent mutations per tumor, and 8 cell lines. The mutational profile of ESCC closely resembles those of squamous cell carcinomas of other tissues but differs from that of esophageal adenocarcinoma. Genes involved in cell cycle and apoptosis regulation were mutated in 99% of cases by somatic alternations of TP53 (93%),  CCND1 (33%), CDKN2A (20%), NFE2L2 (10%) and RB1 (9%). Histone modifier genes were frequently mutated, including KMT2D (also called MLL2; 19%), KMT2C (MLL3; 6%),  KDM6A (7%), EP300 (10%) and CREBBP (6%). EP300 mutations were associated with poor survival. The Hippo and Notch pathways were dysregulated by mutations in FAT1, FAT2, FAT3 or FAT4 (27%) or AJUBA (JUB; 7%) and NOTCH1, NOTCH2 or NOTCH3 (22%) or FBXW7 (5%), respectively. These results define the mutational landscape of ESCC and highlight mutations in epigenetic modulators with prognostic and potentially therapeutic implications. Esophageal cancer is the eighth most common cancer in the world, with more than 480,000 new cases and 400,000 deaths each year, half of which occur in China2,3. Although ESCC remains the dominant histological type of esophageal cancer incidence both in China and worldwide, the application of targeted therapy is mostly limited to esophageal adenocarcinoma (EAC)4. Global risk factors such as cigarette smoking and alcohol consumption account for more than 90% of population-attributable risks in the United States 5, but these factors only account for 46% of ESCC incidence and mortality in China 6. Additional regional or population-specific factors have therefore been proposed to contribute to ESCC etiology in China7–11. Sequencing of ESCC samples from US cases and from cases in southern China has pinpointed several recurrently mutated ESCC-relevant genes12,13 and led to the suggestion that ESCC cases from different geographic regions might differ genetically. We sought to define the mutational landscape of ESCC in a larger cohort of northern Chinese cases to

identify additional significantly mutated genes and potential prognostic markers for ESCC and to comprehensively genetically characterize cell line models of ESCC for functional and therapeutic studies. We performed exome sequencing on 113 pairs of tumor and normal DNA samples collected from well-characterized individuals of Chinese ancestry with treatment-naive primary ESCC (Supplementary Tables 1 and 2), along with 8 cell lines, including 7 from the KYSE series ESCC cell lines14 and 1 immortalized esophageal squamous epithelial cell line, Het-1A15. On average, each library yielded 18.8 Gb of sequence, with 92% of the targeted regions represented by at least ten high-quality reads. Tumor and normal exome sequences were covered by a mean of 122× and 134× distinct high-quality reads, respectively (Supplementary Table 3). In paired clinical samples, we identified a total of 9,197 non-silent mutations and 2,825 silent mutations, corresponding to 81 non-silent mutations per tumor (range of 5–216) or 2.9 (0.18–7.7) non-silent mutations per megabase (Fig. 1a, Supplementary Fig. 1 and Supplementary Table 4). Thus, the mutation frequency for ESCC is substantially lower than for ultraviolet light–exposed melanomas and smoking-related lung tumors, which contain ~200 nonsynonymous mutations per tumor, but is relatively high among adult solid tumors in the absence of potent mutagens or DNA repair defects16,17. Sanger sequencing validated 98% of the 686 mutations selected, including 74 insertions or deletions (indels) and 85 synonymous mutations, located in 150 genes comprising both consensus cancer genes and new recurrently mutated genes in ESCC (Supplementary Table 5). We also detected somatic copy number alterations (SCNAs) in 72% of cases (n = 81; Supplementary Fig. 2 and Supplementary Table 6) with a validation rate of 98% by quantitative PCR (Supplementary Table 7). The most common type of mutation in the exomic region was C>T transition, with a marked preference for this transition among all alterations at CpG dinucleotides (constituting up to 85% of CpG dinucleotide alterations; Supplementary Fig. 3a and Supplementary Tables 8 and 9). This predominance of C>T transitions is consistent with spontaneous cytosine deamination18 being a major mutagenic process in ESCC, as previously observed in ESCC12,13 and EAC19.


of Thoracic Surgery, Cancer Institute and Hospital Chinese Academy of Medical Sciences, Beijing, China. 2Department of Clinical Medicine, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China. 3Department of Pathology, Cancer Institute and Hospital Chinese Academy of Medical Sciences, Beijing, China. 4Department of Thoracic Surgery, Peking University Cancer Hospital, Beijing, China. 5Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China. Correspondence should be addressed to J.H. ([email protected]). Received 25 March; accepted 31 July; published online 24 August 2014; doi:10.1038/ng.3076



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Genetic landscape of esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) is one of the deadliest cancers. We performed exome sequencing on 113 tumor-normal pairs, yielding a mean of...
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