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Patel AJ, Warda S, Maag JL, Misra R, Miranda-Román MA, Pachai MR, Lee CJ, Li D, Wang N, Bayshtok G, Fishinevich E, Meng Y, Wong EW, Yan J, Giff E, Pappalardi MB, McCabe MT, Fletcher JA, Rudin CM, Chandarlapaty S, Scandura JM, Koche RP, Glass JL, Antonescu CR, Zheng D, Chen Y, Chi P. PRC2-Inactivating Mutations in Cancer Enhance Cytotoxic Response to DNMT1-Targeted Therapy via Enhanced Viral Mimicry. Cancer Discov 2022; 12:2120-2139. [PMID: 35789380 PMCID: PMC9437570 DOI: 10.1158/2159-8290.cd-21-1671] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/19/2022] [Accepted: 06/29/2022] [Indexed: 02/01/2023]
Abstract
Polycomb repressive complex 2 (PRC2) has oncogenic and tumor-suppressive roles in cancer. There is clinical success of targeting this complex in PRC2-dependent cancers, but an unmet therapeutic need exists in PRC2-loss cancer. PRC2-inactivating mutations are a hallmark feature of high-grade malignant peripheral nerve sheath tumor (MPNST), an aggressive sarcoma with poor prognosis and no effective targeted therapy. Through RNAi screening in MPNST, we found that PRC2 inactivation increases sensitivity to genetic or small-molecule inhibition of DNA methyltransferase 1 (DNMT1), which results in enhanced cytotoxicity and antitumor response. Mechanistically, PRC2 inactivation amplifies DNMT inhibitor-mediated expression of retrotransposons, subsequent viral mimicry response, and robust cell death in part through a protein kinase R (PKR)-dependent double-stranded RNA sensor. Collectively, our observations posit DNA methylation as a safeguard against antitumorigenic cell-fate decisions in PRC2-loss cancer to promote cancer pathogenesis, which can be therapeutically exploited by DNMT1-targeted therapy. SIGNIFICANCE PRC2 inactivation drives oncogenesis in various cancers, but therapeutically targeting PRC2 loss has remained challenging. Here we show that PRC2-inactivating mutations set up a tumor context-specific liability for therapeutic intervention via DNMT1 inhibitors, which leads to innate immune signaling mediated by sensing of derepressed retrotransposons and accompanied by enhanced cytotoxicity. See related commentary by Guil and Esteller, p. 2020. This article is highlighted in the In This Issue feature, p. 2007.
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Affiliation(s)
- Amish J. Patel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sarah Warda
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jesper L.V. Maag
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rohan Misra
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Miguel A. Miranda-Román
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mohini R. Pachai
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cindy J. Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dan Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Naitao Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gabriella Bayshtok
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eve Fishinevich
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yinuo Meng
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York
| | - Elissa W.P. Wong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Juan Yan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Giff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Melissa B. Pappalardi
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Michael T. McCabe
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Jonathan A. Fletcher
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Charles M. Rudin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Joseph M. Scandura
- Laboratory of Molecular Hematopoiesis, Hematology and Oncology, Weill Cornell Medicine, New York, New York
- Richard T. Silver MD Myeloproliferative Neoplasm Center, Weill Cornell Medicine, New York, New York
- Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jacob L. Glass
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Deyou Zheng
- The Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, New York
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Ping Chi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
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