Whole-exome and targeted gene sequencing of gallbladder carcinoma identifies recurrent mutations in the ErbB pathway (original) (raw)

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Acknowledgements

This study was supported by the National Natural Science Foundation of China (81172026, 81272402, 81301816, 81172029, 81370728, 81125020, 81328022 and 81302507), the National High-Technology Research and Development Program (863 Program, 2012AA022606; 2012BAK01B00), the Foundation for Interdisciplinary Research of Shanghai Jiao Tong University (YG2011ZD07), the Shanghai Science and Technology Commission Intergovernmental International Cooperation Project (12410705900), the Shanghai Science and Technology Commission Medical-Guiding Project (12401905800), the China Postdoctoral Science Foundation (2013M541513), the Program for Changjiang Scholars and the Leading Talent program of Shanghai.

Author information

Author notes

  1. Maolan Li, Zhou Zhang and Xiaoguang Li: These authors contributed equally to this work.
  2. Hui Wang, Yun Liu and Yingbin Liu: These authors jointly directed this work.

Authors and Affiliations

  1. Department of General Surgery, Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
    Maolan Li, Zhou Zhang, Xiangsong Wu, Zhujun Tan, Xu-An Wang, Wenguang Wu, Qichen Ding, Hao Weng, Qian Ding, Jiasheng Mu, Yijun Shu, Runfa Bao, Yang Cao, Tianyu Liu, Lin Jiang, Yunping Hu, Ping Dong, Jun Gu, Wei Lu, Weibin Shi, Jianhua Lu, Wei Gong, Zhaohui Tang, Yong Zhang, Xuefeng Wang & Yingbin Liu
  2. Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
    Maolan Li, Zhou Zhang, Xiangsong Wu, Zhujun Tan, Xu-An Wang, Wenguang Wu, Qichen Ding, Hao Weng, Qian Ding, Jiasheng Mu, Yijun Shu, Runfa Bao, Yang Cao, Tianyu Liu, Lin Jiang, Yunping Hu, Ping Dong, Jun Gu, Wei Lu, Weibin Shi, Jianhua Lu, Wei Gong, Zhaohui Tang, Yong Zhang, Xuefeng Wang & Yingbin Liu
  3. Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Center, Shanghai Jiao Tong University, Shanghai, China
    Zhou Zhang, Daizhan Zhou, Di Zhang, Ting Wang & Lin He
  4. Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
    Xiaoguang Li, Peizhan Chen & Hui Wang
  5. Institutes of Biomedical Sciences, Fudan University, Shanghai, China
    Junyi Ye, Xiaoling Weng, Hong Zhang, Lin He & Yun Liu
  6. Department of Hepatobiliary Surgery, The First Affiliated Hospital of Medical College, Xi′an Jiaotong University, Xi'an, China
    Chang Liu & Kai Qu
  7. Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
    Baiyong Shen & Bingya Liu
  8. Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Y Eugene Chin
  9. Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA
    Wei Tang
  10. Department of Medicine, The University of Chicago, Chicago, Illinois, USA
    Yonglan Zheng
  11. Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
    Lin He
  12. Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing, China
    Hui Wang

Authors

  1. Maolan Li
  2. Zhou Zhang
  3. Xiaoguang Li
  4. Junyi Ye
  5. Xiangsong Wu
  6. Zhujun Tan
  7. Chang Liu
  8. Baiyong Shen
  9. Xu-An Wang
  10. Wenguang Wu
  11. Daizhan Zhou
  12. Di Zhang
  13. Ting Wang
  14. Bingya Liu
  15. Kai Qu
  16. Qichen Ding
  17. Hao Weng
  18. Qian Ding
  19. Jiasheng Mu
  20. Yijun Shu
  21. Runfa Bao
  22. Yang Cao
  23. Peizhan Chen
  24. Tianyu Liu
  25. Lin Jiang
  26. Yunping Hu
  27. Ping Dong
  28. Jun Gu
  29. Wei Lu
  30. Weibin Shi
  31. Jianhua Lu
  32. Wei Gong
  33. Zhaohui Tang
  34. Yong Zhang
  35. Xuefeng Wang
  36. Y Eugene Chin
  37. Xiaoling Weng
  38. Hong Zhang
  39. Wei Tang
  40. Yonglan Zheng
  41. Lin He
  42. Hui Wang
  43. Yun Liu
  44. Yingbin Liu

Contributions

H. Wang, Yun Liu and Yingbin Liu conceived the study. C.L., B.S., B.L., Y.E.C., L.H., H. Wang, Yun Liu and Yingbin Liu directed the study. M.L., Z.Z., X.L., H. Wang, Yun Liu and Yingbin Liu contributed to the project design. M.L., X.L., D. Zhou, T.W., X. Wu, X.-A.W. and Qichen Ding performed experiments. Z.Z., J.Y., D. Zhang, X. Weng and H.Z. performed bioinformatics data analysis. W.W., K.Q., H. Weng, Qian Ding, P.C., T.L., Y.H. and W.L. contributed samples, data and comments on the manuscript. M.L., Z.Z., X.L., Z. Tan, J.M., W.G., W.T. and Y. Zheng analyzed and interpreted data. Y.S., R.B., Y.C., L.J., P.D., J.G., W.S., J.L., Z. Tang, Y. Zhang and X. Wang contributed reagents, materials and/or analysis tools. M.L., Z.Z. and X.L. wrote the manuscript.

Corresponding authors

Correspondence toHui Wang, Yun Liu or Yingbin Liu.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Research strategy of this study.

Whole-exome sequencing was performed for 32 GBC pairs, and ultra-deep targeted gene sequencing was performed for 51 GBC pairs. The recurrently mutated genes, as determined from the exome data, were included in the targeted gene panels. Recurrently mutated genes and pathways were evaluated for the two data sets. By combining the 2 data sets, 21 of 57 GBC patients carrying non-silent somatic mutation(s) of ErbB pathways were identified. Oncology studies of the ErbB family on GBC cell lines were conducted, and associations between ErbB pathway mutations and prognosis were assessed.

Supplementary Figure 2 Comparison between exome and targeted sequencing.

(a) The samples included in the exome and targeted sequencing are shown in a Venn diagram. In total, 57 samples were utilized in this study, 26 of which were processed with both exome and targeted sequencing. (b) In the 26 overlapped samples, somatic non-silent mutations found in the shared coding region of exome and targeted sequencing are compared and shown in a Venn diagram. Seventy-one somatic mutations were identified by both methods; 22 and 96 were discovered only by exome or targeted sequencing, respectively.

Supplementary Figure 3 Schematic diagram of TP53 and KRAS somatic mutations.

(a,b) The relative positions of somatic mutations in TP53 and KRAS are shown with the gene structure. An orange box indicates a non-silent mutation, and a blue box indicates a mutation in an intron or UTR.

Supplementary Figure 4 The oncogenic effect of ERBB3 mutants in OCUG-1 cells.

OCUG-1 cells were transiently transfected with vector expressing ERBB3-WT or mutants, and cell viability was determined by MTT assay. Data represent the means ± s.e.m. of three independent experiments (*P < 0.05, **P < 0.01 compared to cells transfected with the control vector; §P < 0.05, §§P < 0.01 compared to cells expressing ERBB3 WT).

Supplementary Figure 5 The efficacies of RNA interference against ERBB1, ERBB2 and ERBB3 in GBC cells as determined by RT-PCR.

(a–d) GBC cells were respectively transfected with RNAi against two independent regions of ERBB1, ERBB2 and ERBB3, and the mRNA expressions of these genes was determined with real-time quantitative PCR 48 h later. β-actin was used as an internal control.

Supplementary Figure 6 Analysis of cell viability of GBC cells after knocking down ERBB1, ERBB2 and ERBB3.

(a–d) GBC cells were transfected with two siRNAs against ERBB1, ERBB2 and ERBB3, and cell viability was determined at days 0, 2, 4 and 6. The data shown are representative of values from three independent experiments (mean ± s.e.m.; *P < 0.05, **P < 0.01 versus the control siRNA group).

Supplementary Figure 7 Knocking down of ERBB3 and ERBB2 impaired GBC cell migration.

The effect of ERBB3 and ERBB2 on cell migration was determined for NOZ and OCUG-1 cells using RNAi. Representative images indicate three independent experiments with similar results.

Supplementary information

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Li, M., Zhang, Z., Li, X. et al. Whole-exome and targeted gene sequencing of gallbladder carcinoma identifies recurrent mutations in the ErbB pathway.Nat Genet 46, 872–876 (2014). https://doi.org/10.1038/ng.3030

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