Abstract Chromosomal instability (CIN) is the leading cause of the cell genome instability and is a common trait of more than 70% of human cancers, therefore is implicated as an initiator of tumorigenesis. More importantly, CIN may facilitate the adaptation of tumors to environmental or stromal stress and is implicated in determining tumor progression and associated with poor outcome, tumor relapse, and multi-drug resistance across a range of cancer types. The latest studies suggest that cancer is the result of micro-evolution altermate with macro-evolution. That means the cells get mutations through micro-evolution and expansion by the mutational accumulation; the cells begin to undergo macro-evolution instead of micro-evolution when encounter tumorigenic factors, and CIN will be the main driver for tumor evolution. However, studies focus on genomic signatures, especially for macro-evolutionary events, in esophageal squamous cell carcinoma (ESCC) are limited. We integrated 31 whole genomic sequencing data of ESCC samples from China to investigate underlying evolutionary characteristics in ESCC. We combined copy number profiles of 1660 cancer specimens from 5 types of gestrointestinal tumors. Different from colorectal carcinoma, liver hepatocellular carcinoma, pancreatic adenocarcinoma and stomach adenocarcinoma, ESCC possesses largely copy number alterations, and frequent copy-number changes were not clustered in specific chromosome. In our cohort, we found whole genome doubling (WGD) that acts as one of mechanisms for polyploidy was predicted as a late event in the majority of ESCC genome. Moreover, loss of heterozygosity events was more likely to occur in chromosomes harboring tumor suppressor genes in ESCC. The 40% of neutral loss of heterozygosity events was not a result of genome doubling suggesting an alternative mechanism for neutral loss of heterozygosity formation. Importantly, deconstruction of copy number alterations extending to telomere revealed that telomere-bounded copy number alterations play a critical role for amplification/deletion of oncogenes/suppressor genes. For well-known genes SOX2, PIK3CA and TERT, almost all of their amplifications were telomere bounded, which was further confirmed in a Japanese ESCC cohort. Furthermore, we provide evidence that karyotype evolution was mostly punctuated in ESCC. Collectively, our data reveal the potential biological role of whole genome doubling, neutral loss of heterozygosity and telomere-bounded copy number alterations, and highlight macro-evolution in ESCC tumorigenesis. Citation Format: Ting Yan, Xiaolong Cheng, Yongping Cui. The chromosomal instability in tumorigenesis of esophageal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3375.
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