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Exome sequencing of esophageal cancer

Xi Liu, Min Zhang, Songmin Ying, Chong Zhang, Runhua Lin, Jiaxuan Zheng, Guohong Zhang, Dongping Tian, Yi Guo, Caiwen Du, Yuping Chen, Shaobin Chen, Xue Su, Juan Ji, Wanting Deng, Xiang Li, Shiyue Qiu, Ruijing Yan, Zexin Xu, Yuan Wang, Yuanning Guo, Jiancheng Cui, Shanshan Zhuang, Huan Yu, Qi Zheng, Moshe Marom, Sitong Sheng, Guoqiang Zhang, Songnian Hu, Ruiqiang Li, Min Su
BACKGROUND & AIMS: Esophageal squamous cell carcinoma (ESCC) is most common subtype of esophageal cancer. Little is known about the genetic changes that occur in esophageal cells during development of ESCC. We performed next-generation sequence analyses of esophageal non-tumor, intraepithelial neoplasia (IEN), and ESCC tissues from the same patients to track genetic changes during tumor development. METHODS: We performed whole-genome, exome, or targeted sequence analyses of 227 esophageal tissue samples from 70 patients with ESCC undergoing resection at Shantou University Medical College in China from 2012 through 2015 (no patients had received chemotherapy or radiation therapy); we analyzed normal tissue, tissue with simple hyperplasia, dysplastic tissue (intraepithelial neoplasia, IEN), and ESCC tissues collected from different regions of the esophagus at the same time...
March 29, 2017: Gastroenterology
Iikki Donner, Riku Katainen, Tomas Tanskanen, Eevi Kaasinen, Mervi Aavikko, Kristian Ovaska, Miia Artama, Eero Pukkala, Lauri A Aaltonen
Esophageal cancer is common worldwide, and often fatal. The major histological subtype is esophageal squamous cell carcinoma (ESCC). ESCC shows familial aggregation and high heritability. Mutations in RHBDF2 cause tylosis, a very rare disorder characterized by high life-time risk of ESCC, but no other well-established predisposition genes have been identified. To identify candidate susceptibility variants for ESCC we utilized the Population Information System and the Finnish cancer registry to find study materials by clustering ESCC patients by family name at birth and municipality at birth...
February 6, 2017: Genes, Chromosomes & Cancer
Wenjin Liu, Jeff M Snell, William R Jeck, Katherine A Hoadley, Matthew D Wilkerson, Joel S Parker, Nirali Patel, Yohannie B Mlombe, Gift Mulima, N George Liomba, Lindsey L Wolf, Carol G Shores, Satish Gopal, Norman E Sharpless
Esophageal squamous cell carcinoma (ESCC) is endemic in regions of sub-Saharan Africa (SSA), where it is the third most common cancer. Here, we describe whole-exome tumor/normal sequencing and RNA transcriptomic analysis of 59 patients with ESCC in Malawi. We observed similar genetic aberrations as reported in Asian and North American cohorts, including mutations of TP53, CDKN2A, NFE2L2, CHEK2, NOTCH1, FAT1, and FBXW7. Analyses for nonhuman sequences did not reveal evidence for infection with HPV or other occult pathogens...
October 6, 2016: JCI Insight
Victoria E Wang, Jennifer R Grandis, Andrew H Ko
Esophageal cancer remains a highly lethal malignancy in which relatively modest therapeutic advances have been made over the past several decades. Cytotoxic therapy remains the mainstay of treatment for both advanced esophageal adenocarcinoma and squamous cell carcinoma (SCC), with incremental benefit conferred by antibodies targeting HER2 and VEGFR in selected patients. However, intrinsic or acquired resistance in this disease almost invariably occurs and remains a major challenge. Moreover, although large-scale exome and whole-genome sequencing efforts have identified a variety of somatic mutations and copy number variations, particularly amplifications, in esophageal cancer, the ability to translate these findings successfully into actionable therapeutic approaches has been elusive...
September 1, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Yasushi Sasaki, Miyuki Tamura, Ryota Koyama, Takafumi Nakagaki, Yasushi Adachi, Takashi Tokino
Two major types of cancer occur in the esophagus: squamous cell carcinoma, which is associated with chronic smoking and alcohol consumption, and adenocarcinoma, which typically arises in gastric reflux-associated Barrett's esophagus. Although there is increasing incidence of esophageal adenocarcinoma in Western counties, esophageal squamous cell carcinoma (ESCC) accounts for most esophageal malignancies in East Asia, including China and Japan. Technological advances allowing for massively parallel, high-throughput next-generation sequencing (NGS) of DNA have enabled comprehensive characterization of somatic mutations in large numbers of tumor samples...
February 21, 2016: World Journal of Gastroenterology: WJG
Honglei Luo, Hong Li, Zhaoyang Hu, Hongjin Wu, Chenglin Liu, Ying Li, Xiaoyan Zhang, Ping Lin, Qiang Hou, Guohui Ding, Yan Wang, Shuang Li, Dongkai Wei, Feng Qiu, Yixue Li, Shixiu Wu
Circulating tumor DNA (ctDNA) is becoming an important biomarker in noninvasive diagnosis and monitoring of tumor dynamics. This study tested the feasibility of plasma ctDNA for the non-invasive analysis of tumor mutations in esophageal squamous cell carcinoma (ESCC) by sequencing of tumor, tumor-adjacent, and normal tissue, as well as pre-surgery and post-surgery plasma. Exome sequencing of eight patients identified between 29 and 134 somatic mutations in ESCCs, many of which were also determined in ctDNA...
March 18, 2016: Biochemical and Biophysical Research Communications
Genta Sawada, Atsushi Niida, Ryutaro Uchi, Hidenari Hirata, Teppei Shimamura, Yutaka Suzuki, Yuichi Shiraishi, Kenichi Chiba, Seiya Imoto, Yusuke Takahashi, Takeshi Iwaya, Tomoya Sudo, Tomoatsu Hayashi, Hiroki Takai, Yoshihiro Kawasaki, Takashi Matsukawa, Hidetoshi Eguchi, Keishi Sugimachi, Fumiaki Tanaka, Hiromichi Suzuki, Ken Yamamoto, Hideshi Ishii, Makiko Shimizu, Hiroshi Yamazaki, Makoto Yamazaki, Yuji Tachimori, Yoshiaki Kajiyama, Shoji Natsugoe, Hiromasa Fujita, Kenichi Mafune, Yoichi Tanaka, David P Kelsell, Claire A Scott, Shoji Tsuji, Shinichi Yachida, Tatsuhiro Shibata, Sumio Sugano, Yuichiro Doki, Tetsu Akiyama, Hiroyuki Aburatani, Seishi Ogawa, Satoru Miyano, Masaki Mori, Koshi Mimori
BACKGROUND & AIMS: Esophageal squamous cell carcinoma (ESCC) is the predominant form of esophageal cancer in Japan. Smoking and drinking alcohol are environmental risk factors for ESCC, whereas single nucleotide polymorphisms in ADH1B and ALDH2, which increase harmful intermediates produced by drinking alcohol, are genetic risk factors. We conducted a large-scale genomic analysis of ESCCs from patients in Japan to determine the mutational landscape of this cancer. METHODS: We performed whole-exome sequence analysis of tumor and nontumor esophageal tissues collected from 144 patients with ESCC who underwent surgery at 5 hospitals in Japan...
May 2016: Gastroenterology
Ashley M Burris, Bari J Ballew, Joshua B Kentosh, Clesson E Turner, Scott A Norton, Neelam Giri, Blanche P Alter, Anandani Nellan, Christopher Gamper, Kip R Hartman, Sharon A Savage
BACKGROUND: Hoyeraal-Hreidarsson syndrome is a dyskeratosis congenita-related telomere biology disorder that presents in infancy with intrauterine growth retardation, immunodeficiency, and cerebellar hypoplasia in addition to the triad of nail dysplasia, skin pigmentation, and oral leukoplakia. Individuals with Hoyeraal-Hreidarsson syndrome often develop bone marrow failure in early childhood. Germline mutations in DKC1, TERT, TINF2, RTEL1, ACD, or PARN cause about 60% of individuals with Hoyeraal-Hreidarsson syndrome...
March 2016: Pediatric Neurology
Carolyn A Paisie, Morgan S Schrock, Jenna R Karras, Jie Zhang, Satoshi Miuma, Iman M Ouda, Catherine E Waters, Joshua C Saldivar, Teresa Druck, Kay Huebner
Loss of expression of Fhit, a tumor suppressor and genome caretaker, occurs in preneoplastic lesions during development of many human cancers. Furthermore, Fhit-deficient mouse models are exquisitely susceptible to carcinogen induction of cancers of the lung and forestomach. Due to absence of Fhit genome caretaker function, cultured cells and tissues of the constitutive Fhit knockout strain develop chromosome aneuploidy and allele copy number gains and losses and we hypothesized that Fhit-deficient cells would also develop point mutations...
April 2016: Cancer Science
W Cao, W Wu, M Yan, F Tian, C Ma, Q Zhang, X Li, P Han, Z Liu, J Gu, F G Biddle
Cancer is a disease of genome instability and genomic alterations; now, genomic heterogeneity is rapidly emerging as a defining feature of cancer, both within and between tumors. Motivation for our pilot study of tumor heterogeneity in esophageal squamous cell carcinoma (ESCC) is that it is not well studied, but the highest incidences of esophageal cancers are found in China and ESCC is the most common type. We profiled the mutations and changes in copy number that were identified by whole-exome sequencing and array-based comparative genomic hybridization in multiple regions within an ESCC from two patients...
2015: Oncogenesis
Qiyan Wang, Jian Bai, Amir Abliz, Ying Liu, Kenan Gong, Jingjing Li, Wenjie Shi, Yaqi Pan, Fangfang Liu, Shujuan Lai, Haijun Yang, Changdong Lu, Lixin Zhang, Wei Chen, Ruiping Xu, Hong Cai, Yang Ke, Changqing Zeng
Esophageal squamous cell carcinoma (ESCC) has a high mortality rate. To determine the molecular basis of ESCC development, this study sought to identify characteristic genome-wide alterations in ESCC, including exonic mutations and structural alterations. The clinical implications of these genetic alterations were also analyzed. Exome sequencing and verification were performed for nine pairs of ESCC and the matched blood samples, followed by validation with additional samples using Sanger sequencing. Whole-genome SNP arrays were employed to detect copy number alteration (CNA) and loss of heterozygosity (LOH) in 55 cases, including the nine ESCC samples subjected to exome sequencing...
August 2015: Genomics, Proteomics & Bioinformatics
Shinya Ohashi, Shin'ichi Miyamoto, Osamu Kikuchi, Tomoyuki Goto, Yusuke Amanuma, Manabu Muto
Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive squamous cell carcinomas and is highly prevalent in Asia. Alcohol and its metabolite, acetaldehyde, are considered definite carcinogens for the esophagus. Polymorphisms in the aldehyde dehydrogenase 2 gene, which encodes an enzyme that eliminates acetaldehyde, have been associated with esophageal carcinogenesis. Studies of the mutagenic and carcinogenic effects of acetaldehyde support this observation. Several recent large-scale comprehensive analyses of the genomic alterations in ESCC have shown a high frequency of mutations in genes such as TP53 and others that regulate the cell cycle or cell differentiation...
December 2015: Gastroenterology
Xiaoyu Wang, Xiaohong Li, Yichen Cheng, Xin Sun, Xibin Sun, Steve Self, Charles Kooperberg, James Y Dai
BACKGROUND: Esophageal adenocarcinoma (EA) is among the leading causes of cancer mortality, especially in developed countries. A high level of somatic copy number alterations (CNAs) accumulates over the decades in the progression from Barrett's esophagus, the precursor lesion, to EA. Accurate identification of somatic CNAs is essential to understand cancer development. Many studies have been conducted for the detection of CNA in EA using microarrays. Next-generation sequencing (NGS) technologies are believed to have advantages in sensitivity and accuracy to detect CNA, yet no NGS-based CNA detection in EA has been reported...
September 15, 2015: Human Genomics
Yelena Y Janjigian, Efsevia Vakiani, Geoffrey Y Ku, Jessica M Herrera, Laura H Tang, Nancy Bouvier, Agnès Viale, Nicholas D Socci, Marinela Capanu, Michael Berger, David H Ilson
PURPOSE: Vascular endothelial growth factor receptor (VEGFR2) directed therapies result in a modest survival benefit for patients with advanced esophageal and gastroesophageal (GE) junction cancer. Platelet-derived growth factor receptor (PDGFR) may contribute to escape from VEGFR2 inhibition. We evaluated the efficacy of sorafenib, a broad spectrum tyrosine kinase inhibitor targeting VEGFR2 and PDGFR as well as RET and RAF1, in patients with metastatic chemotherapy refractory esophageal and GE junction cancer...
2015: PloS One
Ling Zhang, Yong Zhou, Caixia Cheng, Heyang Cui, Le Cheng, Pengzhou Kong, Jiaqian Wang, Yin Li, Wenliang Chen, Bin Song, Fang Wang, Zhiwu Jia, Lin Li, Yaoping Li, Bin Yang, Jing Liu, Ruyi Shi, Yanghui Bi, Yanyan Zhang, Juan Wang, Zhenxiang Zhao, Xiaoling Hu, Jie Yang, Hongyi Li, Zhibo Gao, Gang Chen, Xuanlin Huang, Xukui Yang, Shengqing Wan, Chao Chen, Bin Li, Yongkai Tan, Longyun Chen, Minghui He, Sha Xie, Xiangchun Li, Xuehan Zhuang, Mengyao Wang, Zhi Xia, Longhai Luo, Jie Ma, Bing Dong, Jiuzhou Zhao, Yongmei Song, Yunwei Ou, Enming Li, Liyan Xu, Jinfen Wang, Yanfeng Xi, Guodong Li, Enwei Xu, Jianfang Liang, Xiaofeng Yang, Jiansheng Guo, Xing Chen, Yanbo Zhang, Qingshan Li, Lixin Liu, Yingrui Li, Xiuqing Zhang, Huanming Yang, Dongxin Lin, Xiaolong Cheng, Yongjun Guo, Jun Wang, Qimin Zhan, Yongping Cui
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...
April 2, 2015: American Journal of Human Genetics
Scott K Sherman, Jessica E Maxwell, Qining Qian, Andrew M Bellizzi, Terry A Braun, Mark D Iannettoni, Benjamin W Darbro, James R Howe
Germline mutations in the PTEN tumor-suppressor gene cause autosomal-dominant conditions such as Cowden and Bannayan-Riley-Ruvalcaba syndromes with variable presentations, including hamartomatous gastrointestinal tumors, dermatologic abnormalities, neurologic symptoms, and elevated cancer risk. We describe a father and son with extensive hamartomatous gastrointestinal polyposis who both developed early-onset esophageal cancer. Exome sequencing identified a novel germline PTEN frameshift mutation (c.568_569insC, p...
January 2015: Cancer Genetics
Yi-Bo Gao, Zhao-Li Chen, Jia-Gen Li, Xue-Da Hu, Xue-Jiao Shi, Zeng-Miao Sun, Fan Zhang, Zi-Ran Zhao, Zi-Tong Li, Zi-Yuan Liu, Yu-Da Zhao, Jian Sun, Cheng-Cheng Zhou, Ran Yao, Su-Ya Wang, Pan Wang, Nan Sun, Bai-Hua Zhang, Jing-Si Dong, Yue Yu, Mei Luo, Xiao-Li Feng, Su-Sheng Shi, Fang Zhou, Feng-Wei Tan, Bin Qiu, Ning Li, Kang Shao, Li-Jian Zhang, Lan-Jun Zhang, Qi Xue, Shu-Geng Gao, Jie He
Esophageal squamous cell carcinoma (ESCC) is one of the deadliest cancers. 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 alterations of TP53 (93%), CCND1 (33%), CDKN2A (20%), NFE2L2 (10%) and RB1 (9%)...
October 2014: Nature Genetics
De-Chen Lin, Jia-Jie Hao, Yasunobu Nagata, Liang Xu, Li Shang, Xuan Meng, Yusuke Sato, Yusuke Okuno, Ana Maria Varela, Ling-Wen Ding, Manoj Garg, Li-Zhen Liu, Henry Yang, Dong Yin, Zhi-Zhou Shi, Yan-Yi Jiang, Wen-Yue Gu, Ting Gong, Yu Zhang, Xin Xu, Ori Kalid, Sharon Shacham, Seishi Ogawa, Ming-Rong Wang, H Phillip Koeffler
Esophageal squamous cell carcinoma (ESCC) is prevalent worldwide and particularly common in certain regions of Asia. Here we report the whole-exome or targeted deep sequencing of 139 paired ESCC cases, and analysis of somatic copy number variations (SCNV) of over 180 ESCCs. We identified previously uncharacterized mutated genes such as FAT1, FAT2, ZNF750 and KMT2D, in addition to those already known (TP53, PIK3CA and NOTCH1). Further SCNV evaluation, immunohistochemistry and biological analysis suggested their functional relevance in ESCC...
May 2014: Nature Genetics
Yongmei Song, Lin Li, Yunwei Ou, Zhibo Gao, Enmin Li, Xiangchun Li, Weimin Zhang, Jiaqian Wang, Liyan Xu, Yong Zhou, Xiaojuan Ma, Lingyan Liu, Zitong Zhao, Xuanlin Huang, Jing Fan, Lijia Dong, Gang Chen, Liying Ma, Jie Yang, Longyun Chen, Minghui He, Miao Li, Xuehan Zhuang, Kai Huang, Kunlong Qiu, Guangliang Yin, Guangwu Guo, Qiang Feng, Peishan Chen, Zhiyong Wu, Jianyi Wu, Ling Ma, Jinyang Zhao, Longhai Luo, Ming Fu, Bainan Xu, Bo Chen, Yingrui Li, Tong Tong, Mingrong Wang, Zhihua Liu, Dongxin Lin, Xiuqing Zhang, Huanming Yang, Jun Wang, Qimin Zhan
Oesophageal cancer is one of the most aggressive cancers and is the sixth leading cause of cancer death worldwide. Approximately 70% of global oesophageal cancer cases occur in China, with oesophageal squamous cell carcinoma (ESCC) being the histopathological form in the vast majority of cases (>90%). Currently, there are limited clinical approaches for the early diagnosis and treatment of ESCC, resulting in a 10% five-year survival rate for patients. However, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear...
May 1, 2014: Nature
Irene Y Chong, David Cunningham, Louise J Barber, James Campbell, Lina Chen, Iwanka Kozarewa, Kerry Fenwick, Ioannis Assiotis, Sebastian Guettler, Isaac Garcia-Murillas, Saima Awan, Maryou Lambros, Naureen Starling, Andrew Wotherspoon, Gordon Stamp, David Gonzalez-de-Castro, Martin Benson, Ian Chau, Sanna Hulkki, Mahrokh Nohadani, Zakaria Eltahir, Alina Lemnrau, Nicholas Orr, Sheela Rao, Christopher J Lord, Alan Ashworth
The incidence of oesophagogastric junctional (OGJ) adenocarcinoma is rising rapidly in western countries, in contrast to the declining frequency of distal gastric carcinoma. Treatment options for adenocarcinomas involving the oesophagogastric junction are limited and the overall prognosis is extremely poor. To determine the genomic landscape of OGJ adenocarcinoma, exomes of eight tumours and matched germline DNA were subjected to massively parallel DNA sequencing. Microsatellite instability was observed in three tumours which coincided with an elevated number of somatic mutations...
November 2013: Journal of Pathology
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