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Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer

Author

Listed:
  • Zhe Jiang

    (Toronto General Research Institute - University Health Network)

  • YoungJun Ju

    (Toronto General Research Institute - University Health Network)

  • Amjad Ali

    (Toronto General Research Institute - University Health Network)

  • Philip E. D. Chung

    (Toronto General Research Institute - University Health Network
    University of Toronto)

  • Patryk Skowron

    (University of Toronto
    The Hospital for Sick Children
    The Hospital for Sick Children)

  • Dong-Yu Wang

    (Toronto General Research Institute - University Health Network)

  • Mariusz Shrestha

    (Toronto General Research Institute - University Health Network
    University of Toronto)

  • Huiqin Li

    (Toronto General Research Institute - University Health Network)

  • Jeff C. Liu

    (University of Toronto)

  • Ioulia Vorobieva

    (Toronto General Research Institute - University Health Network
    University of Toronto)

  • Ronak Ghanbari-Azarnier

    (Toronto General Research Institute - University Health Network
    University of Toronto)

  • Ethel Mwewa

    (Toronto General Research Institute - University Health Network)

  • Marianne Koritzinsky

    (University Health Network)

  • Yaacov Ben-David

    (The Key laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences
    Guizhou Medical University)

  • James R. Woodgett

    (Sinai Health System)

  • Charles M. Perou

    (University of North Carolina)

  • Adam Dupuy

    (The University of Iowa)

  • Gary D. Bader

    (University of Toronto
    University of Toronto)

  • Sean E. Egan

    (The Hospital for Sick Children
    University of Toronto)

  • Michael D. Taylor

    (University of Toronto
    The Hospital for Sick Children
    The Hospital for Sick Children)

  • Eldad Zacksenhaus

    (Toronto General Research Institute - University Health Network
    University of Toronto
    University of Toronto)

Abstract

Metastatic breast-cancer is a major cause of death in women worldwide, yet the relationship between oncogenic drivers that promote metastatic versus primary cancer is still contentious. To elucidate this relationship in treatment-naive animals, we hereby describe mammary-specific transposon-mutagenesis screens in female mice together with loss-of-function Rb, which is frequently inactivated in breast-cancer. We report gene-centric common insertion-sites (gCIS) that are enriched in primary-tumors, in metastases or shared by both compartments. Shared-gCIS comprise a major MET-RAS network, whereas metastasis-gCIS form three additional hubs: Rho-signaling, Ubiquitination and RNA-processing. Pathway analysis of four clinical cohorts with paired primary-tumors and metastases reveals similar organization in human breast-cancer with subtype-specific shared-drivers (e.g. RB1-loss, TP53-loss, high MET, RAS, ER), primary-enriched (EGFR, TGFβ and STAT3) and metastasis-enriched (RHO, PI3K) oncogenic signaling. Inhibitors of RB1-deficiency or MET plus RHO-signaling cooperate to block cell migration and drive tumor cell-death. Thus, targeting shared- and metastasis- but not primary-enriched derivers offers a rational avenue to prevent metastatic breast-cancer.

Suggested Citation

  • Zhe Jiang & YoungJun Ju & Amjad Ali & Philip E. D. Chung & Patryk Skowron & Dong-Yu Wang & Mariusz Shrestha & Huiqin Li & Jeff C. Liu & Ioulia Vorobieva & Ronak Ghanbari-Azarnier & Ethel Mwewa & Maria, 2023. "Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39935-y
    DOI: 10.1038/s41467-023-39935-y
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    as
    1. Sohrab P. Shah & Andrew Roth & Rodrigo Goya & Arusha Oloumi & Gavin Ha & Yongjun Zhao & Gulisa Turashvili & Jiarui Ding & Kane Tse & Gholamreza Haffari & Ali Bashashati & Leah M. Prentice & Jaswinder , 2012. "The clonal and mutational evolution spectrum of primary triple-negative breast cancers," Nature, Nature, vol. 486(7403), pages 395-399, June.
    2. René Bernards & Robert A. Weinberg, 2002. "Metastasis genes: A progression puzzle," Nature, Nature, vol. 418(6900), pages 823-823, August.
    3. Matthew J. Ellis & Li Ding & Dong Shen & Jingqin Luo & Vera J. Suman & John W. Wallis & Brian A. Van Tine & Jeremy Hoog & Reece J. Goiffon & Theodore C. Goldstein & Sam Ng & Li Lin & Robert Crowder & , 2012. "Whole-genome analysis informs breast cancer response to aromatase inhibition," Nature, Nature, vol. 486(7403), pages 353-360, June.
    4. Philip J. Stephens & Patrick S. Tarpey & Helen Davies & Peter Van Loo & Chris Greenman & David C. Wedge & Serena Nik-Zainal & Sancha Martin & Ignacio Varela & Graham R. Bignell & Lucy R. Yates & Elli , 2012. "The landscape of cancer genes and mutational processes in breast cancer," Nature, Nature, vol. 486(7403), pages 400-404, June.
    5. Nicola Cosgrove & Damir Varešlija & Stephen Keelan & Ashuvinee Elangovan & Jennifer M. Atkinson & Sinéad Cocchiglia & Fiona T. Bane & Vikrant Singh & Simon Furney & Chunling Hu & Jodi M. Carter & Stev, 2022. "Mapping molecular subtype specific alterations in breast cancer brain metastases identifies clinically relevant vulnerabilities," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    6. Christina Curtis & Sohrab P. Shah & Suet-Feung Chin & Gulisa Turashvili & Oscar M. Rueda & Mark J. Dunning & Doug Speed & Andy G. Lynch & Shamith Samarajiwa & Yinyin Yuan & Stefan Gräf & Gavin Ha & Gh, 2012. "The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups," Nature, Nature, vol. 486(7403), pages 346-352, June.
    7. Xiaochong Wu & Paul A. Northcott & Adrian Dubuc & Adam J. Dupuy & David J. H. Shih & Hendrik Witt & Sidney Croul & Eric Bouffet & Daniel W. Fults & Charles G. Eberhart & Livia Garzia & Timothy Van Met, 2012. "Clonal selection drives genetic divergence of metastatic medulloblastoma," Nature, Nature, vol. 482(7386), pages 529-533, February.
    8. Mahmoud Ghandi & Franklin W. Huang & Judit Jané-Valbuena & Gregory V. Kryukov & Christopher C. Lo & E. Robert McDonald & Jordi Barretina & Ellen T. Gelfand & Craig M. Bielski & Haoxin Li & Kevin Hu & , 2019. "Next-generation characterization of the Cancer Cell Line Encyclopedia," Nature, Nature, vol. 569(7757), pages 503-508, May.
    9. Peter Priestley & Jonathan Baber & Martijn P. Lolkema & Neeltje Steeghs & Ewart Bruijn & Charles Shale & Korneel Duyvesteyn & Susan Haidari & Arne Hoeck & Wendy Onstenk & Paul Roepman & Mircea Voda & , 2019. "Pan-cancer whole-genome analyses of metastatic solid tumours," Nature, Nature, vol. 575(7781), pages 210-216, November.
    10. Naveed Ishaque & Mohammed L. Abba & Christine Hauser & Nitin Patil & Nagarajan Paramasivam & Daniel Huebschmann & Jörg Hendrik Leupold & Gnana Prakash Balasubramanian & Kortine Kleinheinz & Umut H. To, 2018. "Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
    11. Serena Nik-Zainal & Helen Davies & Johan Staaf & Manasa Ramakrishna & Dominik Glodzik & Xueqing Zou & Inigo Martincorena & Ludmil B. Alexandrov & Sancha Martin & David C. Wedge & Peter Van Loo & Young, 2016. "Landscape of somatic mutations in 560 breast cancer whole-genome sequences," Nature, Nature, vol. 534(7605), pages 47-54, June.
    12. 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.
    13. Nathan F. Schachter & Jessica R. Adams & Patryk Skowron & Katelyn. J. Kozma & Christian A. Lee & Nandini Raghuram & Joanna Yang & Amanda J. Loch & Wei Wang & Aaron Kucharczuk & Katherine L. Wright & R, 2021. "Single allele loss-of-function mutations select and sculpt conditional cooperative networks in breast cancer," Nature Communications, Nature, vol. 12(1), pages 1-19, December.
    14. Lisanne F. Dessel & Job Riet & Minke Smits & Yanyun Zhu & Paul Hamberg & Michiel S. Heijden & Andries M. Bergman & Inge M. Oort & Ronald Wit & Emile E. Voest & Neeltje Steeghs & Takafumi N. Yamaguchi , 2019. "The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    15. Michael S. Lawrence & Petar Stojanov & Craig H. Mermel & James T. Robinson & Levi A. Garraway & Todd R. Golub & Matthew Meyerson & Stacey B. Gabriel & Eric S. Lander & Gad Getz, 2014. "Discovery and saturation analysis of cancer genes across 21 tumour types," Nature, Nature, vol. 505(7484), pages 495-501, January.
    16. Adam J. Dupuy & Keiko Akagi & David A. Largaespada & Neal G. Copeland & Nancy A. Jenkins, 2005. "Mammalian mutagenesis using a highly mobile somatic Sleeping Beauty transposon system," Nature, Nature, vol. 436(7048), pages 221-226, July.
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