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Machine learning of genomic features in organotropic metastases stratifies progression risk of primary tumors

Author

Listed:
  • Biaobin Jiang

    (The Hong Kong University of Science and Technology
    Tencent AI Lab)

  • Quanhua Mu

    (The Hong Kong University of Science and Technology)

  • Fufang Qiu

    (The Hong Kong University of Science and Technology)

  • Xuefeng Li

    (The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital
    Guangzhou Medical University
    The University of Texas MD Anderson Cancer Center)

  • Weiqi Xu

    (Fudan University Shanghai Cancer Center
    Fudan University)

  • Jun Yu

    (The Chinese University of Hong Kong
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong
    The Chinese University of Hong Kong)

  • Weilun Fu

    (Capital Medical University)

  • Yong Cao

    (Capital Medical University)

  • Jiguang Wang

    (The Hong Kong University of Science and Technology
    The Hong Kong University of Science and Technology
    The Hong Kong University of Science and Technology
    Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park)

Abstract

Metastatic cancer is associated with poor patient prognosis but its spatiotemporal behavior remains unpredictable at early stage. Here we develop MetaNet, a computational framework that integrates clinical and sequencing data from 32,176 primary and metastatic cancer cases, to assess metastatic risks of primary tumors. MetaNet achieves high accuracy in distinguishing the metastasis from the primary in breast and prostate cancers. From the prediction, we identify Metastasis-Featuring Primary (MFP) tumors, a subset of primary tumors with genomic features enriched in metastasis and demonstrate their higher metastatic risk and shorter disease-free survival. In addition, we identify genomic alterations associated with organ-specific metastases and employ them to stratify patients into various risk groups with propensities toward different metastatic organs. This organotropic stratification method achieves better prognostic value than the standard histological grading system in prostate cancer, especially in the identification of Bone-MFP and Liver-MFP subtypes, with potential in informing organ-specific examinations in follow-ups.

Suggested Citation

  • Biaobin Jiang & Quanhua Mu & Fufang Qiu & Xuefeng Li & Weiqi Xu & Jun Yu & Weilun Fu & Yong Cao & Jiguang Wang, 2021. "Machine learning of genomic features in organotropic metastases stratifies progression risk of primary tumors," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-27017-w
    DOI: 10.1038/s41467-021-27017-w
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    References listed on IDEAS

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    1. Hongbin Ji & Matthew R. Ramsey & D. Neil Hayes & Cheng Fan & Kate McNamara & Piotr Kozlowski & Chad Torrice & Michael C. Wu & Takeshi Shimamura & Samanthi A. Perera & Mei-Chih Liang & Dongpo Cai & Geo, 2007. "LKB1 modulates lung cancer differentiation and metastasis," Nature, Nature, vol. 448(7155), pages 807-810, August.
    2. Ayuko Hoshino & Bruno Costa-Silva & Tang-Long Shen & Goncalo Rodrigues & Ayako Hashimoto & Milica Tesic Mark & Henrik Molina & Shinji Kohsaka & Angela Di Giannatale & Sophia Ceder & Swarnima Singh & C, 2015. "Tumour exosome integrins determine organotropic metastasis," Nature, Nature, vol. 527(7578), pages 329-335, November.
    3. Dan R. Robinson & Yi-Mi Wu & Robert J. Lonigro & Pankaj Vats & Erin Cobain & Jessica Everett & Xuhong Cao & Erica Rabban & Chandan Kumar-Sinha & Victoria Raymond & Scott Schuetze & Ajjai Alva & Javed , 2017. "Integrative clinical genomics of metastatic cancer," Nature, Nature, vol. 548(7667), pages 297-303, August.
    4. Samuel F. Bakhoum & Bryan Ngo & Ashley M. Laughney & Julie-Ann Cavallo & Charles J. Murphy & Peter Ly & Pragya Shah & Roshan K. Sriram & Thomas B. K. Watkins & Neil K. Taunk & Mercedes Duran & Chantal, 2018. "Chromosomal instability drives metastasis through a cytosolic DNA response," Nature, Nature, vol. 553(7689), pages 467-472, January.
    5. Paul T E Cusack, 2020. "The Human Brain," Biomedical Journal of Scientific & Technical Research, Biomedical Research Network+, LLC, vol. 31(3), pages 24261-24266, October.
    6. Ron Firestein & Adam J. Bass & So Young Kim & Ian F. Dunn & Serena J. Silver & Isil Guney & Ellen Freed & Azra H. Ligon & Natalie Vena & Shuji Ogino & Milan G. Chheda & Pablo Tamayo & Stephen Finn & Y, 2008. "CDK8 is a colorectal cancer oncogene that regulates β-catenin activity," Nature, Nature, vol. 455(7212), pages 547-551, September.
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