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Integrated cohort of esophageal squamous cell cancer reveals genomic features underlying clinical characteristics

Author

Listed:
  • Minghao Li

    (Shandong University)

  • Zicheng Zhang

    (The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine
    Shandong First Medical University and Shandong Academy of Medical Sciences)

  • Qianrong Wang

    (The Third Affiliated Hospital of Shandong First Medical University)

  • Yan Yi

    (Shandong First Medical University and Shandong Academy of Medical Sciences)

  • Baosheng Li

    (Shandong University
    Shandong First Medical University and Shandong Academy of Medical Sciences)

Abstract

Esophageal squamous cell cancer (ESCC) is the major pathologic type of esophageal cancer in Asian population. To systematically evaluate the mutational features underlying clinical characteristics, we establish the integrated dataset of ESCC-META that consists of 1930 ESCC genomes from 33 datasets. The data process pipelines lead to well homogeneity of this integrated cohort for further analysis. We identified 11 mutational signatures in ESCC, some of which are related to clinical features, and firstly detect the significant mutated hotspots in TGFBR2 and IRF2BPL. We screen the survival related mutational features and found some genes had different prognostic impacts between early and late stage, such as PIK3CA and NFE2L2. Based on the results, an applicable approach of mutational score is proposed and validated to predict prognosis in ESCC. As an open-sourced, quality-controlled and updating mutational landscape, the ESCC-META dataset could facilitate further genomic and translational study in this field.

Suggested Citation

  • Minghao Li & Zicheng Zhang & Qianrong Wang & Yan Yi & Baosheng Li, 2022. "Integrated cohort of esophageal squamous cell cancer reveals genomic features underlying clinical characteristics," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32962-1
    DOI: 10.1038/s41467-022-32962-1
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    as
    1. Karthik Devarajan, 2008. "Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology," PLOS Computational Biology, Public Library of Science, vol. 4(7), pages 1-12, July.
    2. Michael S. Lawrence & Petar Stojanov & Paz Polak & Gregory V. Kryukov & Kristian Cibulskis & Andrey Sivachenko & Scott L. Carter & Chip Stewart & Craig H. Mermel & Steven A. Roberts & Adam Kiezun & Pe, 2013. "Mutational heterogeneity in cancer and the search for new cancer-associated genes," Nature, Nature, vol. 499(7457), pages 214-218, July.
    3. Jiaying Deng & Hu Chen & Daizhan Zhou & Junhua Zhang & Yun Chen & Qi Liu & Dashan Ai & Hanting Zhu & Li Chu & Wenjia Ren & Xiaofei Zhang & Yi Xia & Menghong Sun & Huiwen Zhang & Jun Li & Xinxin Peng &, 2017. "Comparative genomic analysis of esophageal squamous cell carcinoma between Asian and Caucasian patient populations," Nature Communications, Nature, vol. 8(1), pages 1-9, December.
    4. Akira Yokoyama & Nobuyuki Kakiuchi & Tetsuichi Yoshizato & Yasuhito Nannya & Hiromichi Suzuki & Yasuhide Takeuchi & Yusuke Shiozawa & Yusuke Sato & Kosuke Aoki & Soo Ki Kim & Yoichi Fujii & Kenichi Yo, 2019. "Age-related remodelling of oesophageal epithelia by mutated cancer drivers," Nature, Nature, vol. 565(7739), pages 312-317, January.
    5. Jiang Chang & Wenle Tan & Zhiqiang Ling & Ruibin Xi & Mingming Shao & Mengjie Chen & Yingying Luo & Yanjie Zhao & Yun Liu & Xiancong Huang & Yuchao Xia & Jinlin Hu & Joel S. Parker & David Marron & Qi, 2017. "Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations," Nature Communications, Nature, vol. 8(1), pages 1-11, August.
    6. Ludmil B. Alexandrov & Jaegil Kim & Nicholas J. Haradhvala & Mi Ni Huang & Alvin Wei Tian Ng & Yang Wu & Arnoud Boot & Kyle R. Covington & Dmitry A. Gordenin & Erik N. Bergstrom & S. M. Ashiqul Islam , 2020. "The repertoire of mutational signatures in human cancer," Nature, Nature, vol. 578(7793), pages 94-101, February.
    7. Ruoyan Li & Lin Di & Jie Li & Wenyi Fan & Yachen Liu & Wenjia Guo & Weiling Liu & Lu Liu & Qiong Li & Liping Chen & Yamei Chen & Chuanwang Miao & Hongjin Liu & Yuqian Wang & Yuling Ma & Deshu Xu & Don, 2021. "A body map of somatic mutagenesis in morphologically normal human tissues," Nature, Nature, vol. 597(7876), pages 398-403, September.
    8. 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 & Liji, 2014. "Identification of genomic alterations in oesophageal squamous cell cancer," Nature, Nature, vol. 509(7498), pages 91-95, May.
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    Cited by:

    1. De-Chen Lin, 2023. "Large-scale genomic analyses reveal alterations and mechanisms underlying clonal evolution and immune evasion in esophageal cancer," Nature Communications, Nature, vol. 14(1), pages 1-3, December.

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