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Genome-wide functional screening identifies CDC37 as a crucial HSP90-cofactor for KIT oncogenic expression in gastrointestinal stromal tumors

Oncogene volume 33, pages 1872–1876 (2014)Cite this article

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Abstract

Most gastrointestinal stromal tumors (GISTs) contain KIT or PDGFRA kinase gain-of-function mutations, and therefore respond clinically to imatinib and other tyrosine kinase inhibitor (TKI) therapies. However, clinical progression subsequently results from selection of TKI-resistant clones, typically containing secondary mutations in the KIT kinase domain, which can be heterogeneous between and within GIST metastases in a given patient. TKI-resistant KIT oncoproteins require HSP90 chaperoning and are potently inactivated by HSP90 inhibitors, but clinical applications in GIST patients are constrained by the toxicity resulting from concomitant inactivation of various other HSP90 client proteins, beyond KIT and PDGFRA. To identify novel targets responsible for KIT oncoprotein function, we performed parallel genome-scale short hairpin RNA (shRNA)-mediated gene knockdowns in KIT-mutant GIST-T1 and GIST882. GIST cells were infected with a lentiviral shRNA pooled library targeting 11 194 human genes, and allowed to proliferate for 5–7 weeks, at which point assessment of relative hairpin abundance identified the HSP90 cofactor, CDC37, as one of the top six GIST-specific essential genes. Validations in treatment-naive (GIST-T1, GIST882) vs imatinib-resistant GISTs (GIST48, GIST430) demonstrated that: (1) CDC37 interacts with oncogenic KIT; (2) CDC37 regulates expression and activation of KIT and downstream signaling intermediates in GIST; and (3) unlike direct HSP90 inhibition, CDC37 knockdown accomplishes prolonged KIT inhibition (>20 days) in GIST. These studies highlight CDC37 as a key biologic vulnerability in both imatinib-sensitive and imatinib-resistant GIST. CDC37 targeting is expected to be selective for KIT/PDGFRA and a subset of other HSP90 clients, and thereby represents a promising strategy for inactivating the myriad KIT/PDGFRA oncoproteins in TKI-resistant GIST patients.

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Acknowledgements

Adrián Mariño-Enríquez, Wen-Bin Ou, Yuexiang Wang, Jonathan A Fletcher and George D Demetri, are supported by the GI SPORE 1P50CA12703-05, Virginia and Daniel K Ludwig Trust for Cancer Research, Paul’s Posse and Team Cesarini of the Pan Mass Challenge, LifeRaft Group and the GIST Cancer Research Fund. Adrián Mariño-Enríquez is also supported by a Sarcoma Alliance for Research Through Collaboration (SARC) Career Development Award. Wen-Bin Ou is also supported by Qianjiang Talents Project of Zhejiang (2012R10079), a grant from the Science and Technology Bureau of Jiaxing, Zhejiang (2012AY1039) and the Major Science and Technology Special Project of Zhejiang Province (2012C03007-4). The RNAi Consortium (TRC) supported the development of pooled screening methods used for these screens.

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Authors and Affiliations

  1. Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA

    A Mariño-Enríquez, W-B Ou, A H Jonker, M Mayeda, G Eilers, Y Wang & J A Fletcher

  2. Departamento de Anatomía Patológica, Hospital Universitario La Paz, Fundación para la Investigación Biomédica FIBHULP, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain

    A Mariño-Enríquez

  3. Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang, China

    W-B Ou

  4. RNAi Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA

    G Cowley, B Luo, M Okamoto & D E Root

  5. Center for Molecular Oncologic Pathology, Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA

    J T Czaplinski & E Sicinska

  6. Department of Human Health and Medical Science, Graduate School of Kuroshio Science, Kochi University, Nankoku, Kochi, Japan

    T Taguchi

  7. Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA

    G D Demetri

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  1. A Mariño-Enríquez
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  13. G D Demetri
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Correspondence to A Mariño-Enríquez or J A Fletcher.

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Competing interests

Dr George D Demetri serves as consultant for Novartis, Pfizer, Sanofi-Aventis, Glaxo-Smith-Kline, Johnson & Johnson, Merrimack Pharma, Foundation Medicine, Merck, ZioPharm, N-of-One, Champions Biotechnology, Blueprint Medicines; he is a member of the Scientific Advisory Boards of ZioPharm, Kolltan Pharmaceuticals, N-of-One, and Blueprint Medicines; and he holds minor equity stakes at N-of-One, Champions Biotechnology, Kolltan Pharmaceuticals and Blueprint Medicines. Novartis, Pfizer, Sanofi-Aventis, Glaxo-Smith-Kline, Johnson & Johnson, Merck, and Amgen support clinical trials in the Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute. Dr Jonathan A Fletcher has consulting arrangements with Novartis, Pfizer and Deciphera Pharmaceuticals. None of these relationships constitute a conflict of interest for this work. The remaining authors declare no conflict of interest.

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Mariño-Enríquez, A., Ou, WB., Cowley, G. et al. Genome-wide functional screening identifies CDC37 as a crucial HSP90-cofactor for KIT oncogenic expression in gastrointestinal stromal tumors. Oncogene 33, 1872–1876 (2014). https://doi.org/10.1038/onc.2013.127

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