Genomic and molecular characterization of esophageal squamous cell carcinoma
Authors: Liang Xu
Jia-Jie Hao
Xin Xu
Ling-Wen Ding
De-Chen Lin
Yasunobu Nagata
Ting Gong
Dong Yin
Yusuke Sato
Li Shang
Ming-Rong Wang
Xuan Meng
Manoj Garg
Ana Maria Varela
Henry Yang
Yusuke Okuno
Zhi-Zhou Shi
Seishi Ogawa
Sharon Shacham
Ori Kalid
Yan-Yi Jiang
H Phillip Koeffler
Wen-Yue Gu
Li-Zhen Liu
Yu Zhang
Journal: Nature Genetics (2014)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Esophageal squamous cell carcinoma; whole-exome sequencing; somatic copy number variations; mutated genes; functional relevance
Affiliations: 1] Cedars-Sinai Medical Center, Division of Hematology/Oncology, University of California Los Angeles School of Medicine, Los Angeles, California, USA. [2] Cancer Science Institute of Singapore, National University of Singapore, Singapore. [3]., 1] State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China. [2]., 1] Cancer Genomics Project, Graduate School of Medicine, University of Tokyo, Tokyo, Japan. [2]., 1] Cancer Science Institute of Singapore, National University of Singapore, Singapore. [2]., State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China., Cancer Science Institute of Singapore, National University of Singapore, Singapore., Cancer Genomics Project, Graduate School of Medicine, University of Tokyo, Tokyo, Japan., Medical Research Center, Sun Yat-Sen Memorial Hospital, Guangzhou, China., Karyopharm Therapeutics, Natick, Massachusetts, USA., 1] Cedars-Sinai Medical Center, Division of Hematology/Oncology, University of California Los Angeles School of Medicine, Los Angeles, California, USA. [2] Cancer Science Institute of Singapore, National University of Singapore, Singapore. [3] National University Cancer Institute, National University Hospital Singapore, Singapore.

Abstract:  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. Notably, RTK-MAPK-PI3K pathways, cell cycle and epigenetic regulation are frequently dysregulated by multiple molecular mechanisms in this cancer. Our approaches also uncovered many druggable candidates, and XPO1 was further explored as a therapeutic target because it showed both gene mutation and protein overexpression. Our integrated study unmasks a number of novel genetic lesions in ESCC and provides an important molecular foundation for understanding esophageal tumors and developing therapeutic targets. 

Retracted: No

PubPeer comments:
 This paper appears to be one of a set of at least 2 papers by the same research group that both appear to share the same photo. In both papers, this photo is used as a zoomed-in inset representing the high-resolution transmission electron microscopy (HRTEM) analysis of the  atomic lattice fringe and particle size of the nanoparticles. Of concern, the same photo, which I have called  Inset 6 , is used to represent a different type of nanoparticle in each of these papers. The two papers using the  Inset 6 photo are: * Handan Pamuk et al. - DOI: 10.1039 C5RA06441D - Pt NPs@GO * Yasar Karatas et al. - DOI: 10.1038 s41598-020-64046-9 - ptRu@Vc Here is a comparison of both figures that contain the  Inset 6 photo: ![file] ![file] Here is a close-up view of both inset photos: ![file] Of note, this is a different set of papers than the 30 papers by the same group that all appear to use another HRTEM image called  Inset 1 . For an example of that photo and the list of those 30 papers, see DOI 10.1016 j.ijhydene.2018.03.175 https: pubpeer.com publications 8AD71F4A32472314CCE9983D47E36F It is also a different set of papers than the 14 papers by the same group that all appear to use another HRTEM image called  Inset 2 . For an example of that photo and the list of those 14 papers, see DOI: 10.1016 j.ijhydene.2017.05.113 https: pubpeer.com publications CAD2F16435F6C639F5DE6851A2E61D , 
 Figure 3. XRD patterns of Pt@VC and PtRu@VC nanocatalysts. Two XRD patterns are different only in the region of one peak. ![file] ,