IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-37440-w.html
   My bibliography  Save this article

Integrative proteogenomic characterization of early esophageal cancer

Author

Listed:
  • Lingling Li

    (Fudan University)

  • Dongxian Jiang

    (Zhongshan Hospital Fudan University)

  • Qiao Zhang

    (Fudan University)

  • Hui Liu

    (Fudan University)

  • Fujiang Xu

    (The Affiliated Hospital of Southwest Medical University)

  • Chunmei Guo

    (Fudan University)

  • Zhaoyu Qin

    (Fudan University)

  • Haixing Wang

    (Zhongshan Hospital Fudan University)

  • Jinwen Feng

    (Fudan University)

  • Yang Liu

    (Fudan University)

  • Weijie Chen

    (Zhongshan Hospital Fudan University)

  • Xue Zhang

    (Zhongshan Hospital Fudan University)

  • Lin Bai

    (Fudan University)

  • Sha Tian

    (Fudan University)

  • Subei Tan

    (Fudan University)

  • Chen Xu

    (Zhongshan Hospital Fudan University)

  • Qi Song

    (Zhongshan Hospital Fudan University)

  • Yalan Liu

    (Zhongshan Hospital Fudan University)

  • Yunshi Zhong

    (Zhongshan Hospital Fudan University)

  • Tianyin Chen

    (Zhongshan Hospital Fudan University)

  • Pinghong Zhou

    (Zhongshan Hospital Fudan University)

  • Jian-Yuan Zhao

    (Fudan University
    Xinhua Hospital, Shanghai Jiao Tong University School of Medicine
    School of Basic Medical Sciences, Zhengzhou University)

  • Yingyong Hou

    (Zhongshan Hospital Fudan University)

  • Chen Ding

    (Fudan University)

Abstract

Esophageal squamous cell carcinoma (ESCC) is malignant while the carcinogenesis is still unclear. Here, we perform a comprehensive multi-omics analysis of 786 trace-tumor-samples from 154 ESCC patients, covering 9 histopathological stages and 3 phases. Proteogenomics elucidates cancer-driving waves in ESCC progression, and reveals the molecular characterization of alcohol drinking habit associated signatures. We discover chromosome 3q gain functions in the transmit from nontumor to intraepithelial neoplasia phases, and find TP53 mutation enhances DNA replication in intraepithelial neoplasia phase. The mutations of AKAP9 and MCAF1 upregulate glycolysis and Wnt signaling, respectively, in advanced-stage ESCC phase. Six major tracks related to different clinical features during ESCC progression are identified, which is validated by an independent cohort with another 256 samples. Hyperphosphorylated phosphoglycerate kinase 1 (PGK1, S203) is considered as a drug target in ESCC progression. This study provides insight into the understanding of ESCC molecular mechanism and the development of therapeutic targets.

Suggested Citation

  • Lingling Li & Dongxian Jiang & Qiao Zhang & Hui Liu & Fujiang Xu & Chunmei Guo & Zhaoyu Qin & Haixing Wang & Jinwen Feng & Yang Liu & Weijie Chen & Xue Zhang & Lin Bai & Sha Tian & Subei Tan & Chen Xu, 2023. "Integrative proteogenomic characterization of early esophageal cancer," Nature Communications, Nature, vol. 14(1), pages 1-28, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37440-w
    DOI: 10.1038/s41467-023-37440-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-37440-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-37440-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Sai Ge & Xia Xia & Chen Ding & Bei Zhen & Quan Zhou & Jinwen Feng & Jiajia Yuan & Rui Chen & Yumei Li & Zhongqi Ge & Jiafu Ji & Lianhai Zhang & Jiayuan Wang & Zhongwu Li & Yumei Lai & Ying Hu & Yanyan, 2018. "A proteomic landscape of diffuse-type gastric cancer," Nature Communications, Nature, vol. 9(1), pages 1-16, December.
    2. Bradley A. Webb & Farhad Forouhar & Fu-En Szu & Jayaraman Seetharaman & Liang Tong & Diane L. Barber, 2015. "Structures of human phosphofructokinase-1 and atomic basis of cancer-associated mutations," Nature, Nature, vol. 523(7558), pages 111-114, July.
    3. Daniel D. Lee & H. Sebastian Seung, 1999. "Learning the parts of objects by non-negative matrix factorization," Nature, Nature, vol. 401(6755), pages 788-791, October.
    4. Helgo Schmidt & Ruta Zalyte & Linas Urnavicius & Andrew P. Carter, 2015. "Structure of human cytoplasmic dynein-2 primed for its power stroke," Nature, Nature, vol. 518(7539), pages 435-438, February.
    5. Sai Ge & Xia Xia & Chen Ding & Bei Zhen & Quan Zhou & Jinwen Feng & Jiajia Yuan & Rui Chen & Yumei Li & Zhongqi Ge & Jiafu Ji & Lianhai Zhang & Jiayuan Wang & Zhongwu Li & Yumei Lai & Ying Hu & Yanyan, 2018. "Author Correction: A proteomic landscape of diffuse-type gastric cancer," Nature Communications, Nature, vol. 9(1), pages 1-1, December.
    6. Björn Schwanhäusser & Dorothea Busse & Na Li & Gunnar Dittmar & Johannes Schuchhardt & Jana Wolf & Wei Chen & Matthias Selbach, 2011. "Global quantification of mammalian gene expression control," Nature, Nature, vol. 473(7347), pages 337-342, May.
    7. Xiaotian Ni & Zhaoli Tan & Chen Ding & Chunchao Zhang & Lan Song & Shuai Yang & Mingwei Liu & Ru Jia & Chuanhua Zhao & Lei Song & Wanlin Liu & Quan Zhou & Tongqing Gong & Xianju Li & Yanhong Tai & Wei, 2019. "A region-resolved mucosa proteome of the human stomach," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Lingling Li & Dongxian Jiang & Hui Liu & Chunmei Guo & Rui Zhao & Qiao Zhang & Chen Xu & Zhaoyu Qin & Jinwen Feng & Yang Liu & Haixing Wang & Weijie Chen & Xue Zhang & Bin Li & Lin Bai & Sha Tian & Su, 2023. "Comprehensive proteogenomic characterization of early duodenal cancer reveals the carcinogenesis tracks of different subtypes," Nature Communications, Nature, vol. 14(1), pages 1-24, December.
    2. Yan Li & Chen Xu & Bing Wang & Fujiang Xu & Fahan Ma & Yuanyuan Qu & Dongxian Jiang & Kai Li & Jinwen Feng & Sha Tian & Xiaohui Wu & Yunzhi Wang & Yang Liu & Zhaoyu Qin & Yalan Liu & Jing Qin & Qi Son, 2022. "Proteomic characterization of gastric cancer response to chemotherapy and targeted therapy reveals potential therapeutic strategies," Nature Communications, Nature, vol. 13(1), pages 1-26, December.
    3. Yan Li & Bing Wang & Wentao Yang & Fahan Ma & Jianling Zou & Kai Li & Subei Tan & Jinwen Feng & Yunzhi Wang & Zhaoyu Qin & Zhiyu Chen & Chen Ding, 2024. "Longitudinal plasma proteome profiling reveals the diversity of biomarkers for diagnosis and cetuximab therapy response of colorectal cancer," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    4. Wenhao Shi & Yushen Wang & Chen Xu & Yan Li & Sai Ge & Bin Bai & Kecheng Zhang & Yunzhi Wang & Nairen Zheng & Juan Wang & Shiqi Wang & Gang Ji & Jipeng Li & Yongzhan Nie & Wenquan Liang & Xiaosong Wu , 2023. "Multilevel proteomic analyses reveal molecular diversity between diffuse-type and intestinal-type gastric cancer," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    5. Shengli Li & Li Yuan & Zhi-Yuan Xu & Jing-Li Xu & Gui-Ping Chen & Xiaoqing Guan & Guang-Zhao Pan & Can Hu & Jinyun Dong & Yi-An Du & Li-Tao Yang & Mao-Wei Ni & Rui-Bin Jiang & Xiu Zhu & Hang Lv & Han-, 2023. "Integrative proteomic characterization of adenocarcinoma of esophagogastric junction," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    6. Zhenmei Yao & Ning Xu & Guoguo Shang & Haixing Wang & Hui Tao & Yunzhi Wang & Zhaoyu Qin & Subei Tan & Jinwen Feng & Jiajun Zhu & Fahan Ma & Sha Tian & Qiao Zhang & Yuanyuan Qu & Jun Hou & Jianming Gu, 2023. "Proteogenomics of different urothelial bladder cancer stages reveals distinct molecular features for papillary cancer and carcinoma in situ," Nature Communications, Nature, vol. 14(1), pages 1-25, December.
    7. Yunzhi Wang & Rongkui Luo & Xuan Zhang & Hang Xiang & Bing Yang & Jinwen Feng & Mengjie Deng & Peng Ran & Akesu Sujie & Fan Zhang & Jiajun Zhu & Subei Tan & Tao Xie & Pin Chen & Zixiang Yu & Yan Li & , 2023. "Proteogenomics of diffuse gliomas reveal molecular subtypes associated with specific therapeutic targets and immune-evasion mechanisms," Nature Communications, Nature, vol. 14(1), pages 1-32, December.
    8. Del Corso, Gianna M. & Romani, Francesco, 2019. "Adaptive nonnegative matrix factorization and measure comparisons for recommender systems," Applied Mathematics and Computation, Elsevier, vol. 354(C), pages 164-179.
    9. P Fogel & C Geissler & P Cotte & G Luta, 2022. "Applying separative non-negative matrix factorization to extra-financial data," Working Papers hal-03689774, HAL.
    10. Spelta, A. & Pecora, N. & Rovira Kaltwasser, P., 2019. "Identifying Systemically Important Banks: A temporal approach for macroprudential policies," Journal of Policy Modeling, Elsevier, vol. 41(1), pages 197-218.
    11. Paul Fogel & Yann Gaston-Mathé & Douglas Hawkins & Fajwel Fogel & George Luta & S. Stanley Young, 2016. "Applications of a Novel Clustering Approach Using Non-Negative Matrix Factorization to Environmental Research in Public Health," IJERPH, MDPI, vol. 13(5), pages 1-14, May.
    12. Le Thi Khanh Hien & Duy Nhat Phan & Nicolas Gillis, 2022. "Inertial alternating direction method of multipliers for non-convex non-smooth optimization," Computational Optimization and Applications, Springer, vol. 83(1), pages 247-285, September.
    13. Yuping Chen & Jo-Hsi Huang & Connie Phong & James E. Ferrell, 2024. "Viscosity-dependent control of protein synthesis and degradation," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    14. Jingfeng Guo & Chao Zheng & Shanshan Li & Yutong Jia & Bin Liu, 2022. "BiInfGCN: Bilateral Information Augmentation of Graph Convolutional Networks for Recommendation," Mathematics, MDPI, vol. 10(17), pages 1-16, August.
    15. Jianfei Cao & Han Yang & Jianshu Lv & Quanyuan Wu & Baolei Zhang, 2023. "Estimating Soil Salinity with Different Levels of Vegetation Cover by Using Hyperspectral and Non-Negative Matrix Factorization Algorithm," IJERPH, MDPI, vol. 20(4), pages 1-15, February.
    16. Zhang, Lifeng & Chao, Xiangrui & Qian, Qian & Jing, Fuying, 2022. "Credit evaluation solutions for social groups with poor services in financial inclusion: A technical forecasting method," Technological Forecasting and Social Change, Elsevier, vol. 183(C).
    17. Wentao Qu & Xianchao Xiu & Huangyue Chen & Lingchen Kong, 2023. "A Survey on High-Dimensional Subspace Clustering," Mathematics, MDPI, vol. 11(2), pages 1-39, January.
    18. Gábor Csárdi & Alexander Franks & David S Choi & Edoardo M Airoldi & D Allan Drummond, 2015. "Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast," PLOS Genetics, Public Library of Science, vol. 11(5), pages 1-32, May.
    19. Anna Luiza Silva Almeida Vicente & Alexei Novoloaca & Vincent Cahais & Zainab Awada & Cyrille Cuenin & Natália Spitz & André Lopes Carvalho & Adriane Feijó Evangelista & Camila Souza Crovador & Rui Ma, 2022. "Cutaneous and acral melanoma cross-OMICs reveals prognostic cancer drivers associated with pathobiology and ultraviolet exposure," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    20. Takehiro Sano & Tsuyoshi Migita & Norikazu Takahashi, 2022. "A novel update rule of HALS algorithm for nonnegative matrix factorization and Zangwill’s global convergence," Journal of Global Optimization, Springer, vol. 84(3), pages 755-781, November.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37440-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.