Multi-region sequencing unveils novel actionable targets and spatial heterogeneity in esophageal squamous cell carcinoma
Authors: Dan Su
Yan Wang
Huijuan Liu
Yong Zhou
Shiping Guo
Yiqian Liu
Ruifang Sun
Yikun Cheng
Heyang Cui
Fang Wang
Ting Yan
Caixia Cheng
Jiayi Li
Yingchun Zhang
Yongping Cui
Ling Zhang
Xuefeng Liu
Jing Liu
Zhihua Liu
Hongyi Li
Bin Wang
Yaoping Li
Yu Qian
Enwei Xu
Yanchun Ma
Pengzhou Kong
Xiaolong Cheng
Ling Chen
Jian Yang
Bin Yang
Qimin Zhan
Shixing Guo
Xiaofei Zhuang
Journal: Nature Communications (2019)
Discipline: Multidisciplinary
Keywords: Esophageal squamous cell carcinoma; ERBB4 mutations; BRCA1/2 variants; signature 3; cisplatin sensitivity
Affiliations: Shenzhen Peking University-The Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Peking University Shenzhen Hospital, 518035, Shenzhen, PR China., Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, 030001, Taiyuan, PR China., Department of Tumor Surgery, Shanxi Cancer Hospital, 030013, Taiyuan, PR China., College of Information and Computer, Taiyuan University of Technology, 030001, Taiyuan, PR China., College of Letter & Science, University of California Berkeley, Berkeley, CA, 94704, USA., Anglo-Chinese School (Independent), Singapore, 139650, Singapore., Department of Pathology, Shanxi Cancer Hospital, 030013, Taiyuan, PR China., Department of Pathology, the First Hospital, Shanxi Medical University, 030001, Taiyuan, PR China., Department of Pathology, Tianjin Central Hospital of Gynecology Obstetrics, Nankai University Gynecology Obstetrics Hospital, 300052, Tianjin, PR China., Department of General Surgery, the First Hospital, Shanxi Medical University, 030001, Taiyuan, PR China., Department of Pathology, Zhejiang Cancer Hospital, 310022, Hangzhou, PR China., Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, 100191, Beijing, PR China., Tumor Biobank, Shanxi Cancer Hospital, 030013, Taiyuan, PR China., Department of Colorectal & Anal Surgery, Affiliated Provincial Hospital of Shanxi Medical University, 030001, Taiyuan, PR China., State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, PR China., Shenzhen Peking University-The Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Peking University Shenzhen Hospital, 518035, Shenzhen, PR China. ., Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, 100191, Beijing, PR China. ., Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, 030001, Taiyuan, PR China. .

Abstract:  Esophageal squamous cell carcinoma (ESCC) ranks fourth among cancer-related deaths in China due to the lack of actionable molecules. We performed whole-exome and T-cell receptor (TCR) repertoire sequencing on multi-regional tumors, normal tissues and blood samples from 39 ESCC patients. The data revealed 12.8% of ERBB4 mutations at patient level and functional study supported its oncogenic role. 18% of patients with early BRCA1/2 variants were associated with high-level contribution of signature 3, which was validated in an independent large cohort (n = 508). Furthermore, knockdown of BRCA1/2 dramatically increased sensitivity to cisplatin in ESCC cells. 5% of patients harbored focal high-level amplification of CD274 that led to massive expression of PD-L1, and might be more sensitive to immune checkpoint blockade. Finally, we found a tight correlation between genomic and TCR repertoire intra-tumor heterogeneity (ITH). Collectively, we reveal high-level ITH in ESCC, identify several potential actionable targets and may provide novel insight into ESCC treatment. 

Retracted: No

PubPeer comments:
 sFig.4d: Formation assay image in ErbB4-WT group reappeared in ErbB4-E57K. Could authors give an explanation? ![file] , 
 #1 to overlay the two images with 50% transparency of the top layer, they do look like identical except that there s a 7-ish deg rotation and a slight vertical compression of the E57K image. ![] , 
 ![file] Fig.1e: Could the authors provide the uncropped images? It seems that the blots on the left and right are not from the same gel. , 
 #1 We thank Dr. Cicindela Chrysippe so much for pointing out the mistake in Supplementary Figure 4D. We do deepest apologize to all readers for the mistake we made. Supplementary Figure 4D shows colony formation results of ErbB4 wild-type and mutants in KYSE180 cell line. Sadly, we put the same picture for ErbB4-WT and ErbB4-E57K by mistake. We went back to the initial images of colony formation experiments and checked, we find that this picture is acturally for ErbB4-WT, namely, we didnu2019t include the correct image for ErbB4-E57K. We have corrected the Supplementary Figure 4D in the following figure, we also provided the initial images for this experiment in the end. We are contacting the editor office of Nature Communications to make correction of this figure. Thank you again. We are really appreciated for your comment. ![file] ![file] , 
 #2 We thank Dr. Oeneis Buddha so much for pointing out the mistake in Supplementary Figure 4D. We do deepest apologize to all readers for the mistake we made. Supplementary Figure 4D shows colony formation results of ErbB4 wild-type and mutants in KYSE180 cell line. Sadly, we put the same picture for ErbB4-WT and ErbB4-E57K by mistake. We went back to the initial images of colony formation experiments and checked, we find that this picture is acturally for ErbB4-WT, namely, we didnu2019t include the correct image for ErbB4-E57K. We have corrected the Supplementary Figure 4D in the following figure, we also provided the initial images for this experiment in the end. We are contacting the editor office of Nature Communications to make correction of this figure. Thank you again. We are really appreciated for your comment. ![file] ![file] , 
 Could the authors provide the uncropped images for Fig.1e? , 
 #6 We thank Dr. Anomoporia Flavissima so much for the kindly comment. The left part of Figure 1e shows western blotting results of phosphorylated ErbB4 of wild-type and mutants in KYSE150 cell line with or without NRG-1 addition. In our lab, we used 10-well comb for gel casting. However, we designed 10 samples and 1 protein markers to load in the gel for this result. So, we decided to load two groups (4 samples) in another gel rather than one sample or one group. We provided the initial images for this experiment and these images are also available in the article page on Nature Communications. Thank you again. We are really appreciated for your comment. ![file] , 
 #6 We thank so much for the kindly comment. The left part of Figure 1e shows western blotting results of phosphorylated ErbB4 of wild-type and mutants in KYSE150 cell line with or without NRG-1 addition. In our lab, we used 10-well comb for gel casting. However, we designed 10 samples and 1 protein markers to load in the gel for this result. So, we decided to load two groups (4 samples) in another gel rather than one sample or one group. We provided the initial images for this experiment and these images are also available in the article page on Nature Communications. Thank you again. We are really appreciated for your comment. ![file] , 
 The author said: ![file] *All data files supporting the conclusions of this project are going to be uploaded to Sequence Read Archive (SRA) under accession code PRJNA511368.* But up to now, one year past and the PRJNA511368 still not be public. ![file] Could the author provide an access to download your raw sequence data? , 
 #5 Thank you for the response. If I understand you correctly, you re saying the transwell pic of ErbB4-WT, after being used the first time correctly, was somehow accidentally rotated CW for a few deg and vertically compressed slightly, before finally being inadvertently used again for ErbB4-E57K. Is that right? , 
 #10 We do apologize that we didnu2019t make this clear. During this experiment, we manually took several photos for every plate using camera, that may cause different direction of photos but not artificially adjusting. We then chose one photo for each plate in the final figure. Sadly, we picked another WT-photo for E57K by mistake. , 
 We do apologize that we didnu2019t make this clear. During this experiment, we manually took several photos for every plate using camera, that may cause different direction of photos but not artificially adjusting. We then chose one photo for each plate in the final figure. Sadly, we picked another WT-photo for E57K by mistake. Please check the following images. ![file] , 
 #9 We thank you so much for your comment. We do apologize that the raw data cannot be accessed by public. Due to the restriction policy in our country, we are transferring our raw data to Genome Sequence Archive (GSA) in BIG Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, and that will be publicly accessible once we finish transfer. We are contacting the editor office of Nature Communications to make a clarification statement. , 
 12 November 2020 Correction to: Nature Communications https: doi.org 10.1038 s41467-019-09255-1, published online 11 April 2019. This Article contained errors in Fig. 1 and Supplementary Fig. 4. In Fig. 1. and Supplementary Fig. 4d the gels were inappropriately spliced together. For each experiment, multiple gels were prepared and the gels were probed in parallel. The figure legends have been updated to describe the parallel processing of the blots. Additionally, in Supplementary Fig. 4d the colony formation image for ErbB4-E57K of the KYSE180 cells was inadvertently duplicated from the ErbB4-WT image. The image has now been replaced, while the experiment was repeated three times, images are only available from one experiment. Finally, the original manuscript was published without the Source data for the histograms and gels. The Source data file now contains all the Source data supporting the study. These errors have been corrected in the Pdf and HTML versions of the Article. Author notes These authors contributed equally: Ting Yan, Heyang Cui, Yong Zhou, Bin Yang, Pengzhou Kong, Yingchun Zhang. ,