1
|
Chi P, 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, Fletcher J, Scandura JM, Koche R, Glass JL, Antonescu CR, Zheng D, Chen Y. Abstract PR005: PRC2 inactivating mutations amplify cell death in response to DNMT1-targeted therapy through enhanced viral mimicry in malignant peripheral nerve sheath tumor. Clin Cancer Res 2022. [DOI: 10.1158/1557-3265.sarcomas22-pr005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Polycomb Repressive Complex 2 (PRC2) establishes and maintains di- and tri-methylation at histone 3 at lysine 27 (H3K27me2/3) in the genome and plays oncogenic and tumor suppressor roles in context-dependent cancer pathogenesis. While there is clinical success of therapeutically targeting PRC2 core component, EZH2, in PRC2-dependent cancers (e.g., follicular lymphoma, epithelioid sarcoma), it remains an unmet therapeutic bottleneck in PRC2-inactivated cancer. Biallelic inactivating mutations in PRC2 core components are a hallmark feature of high-grade malignant peripheral nerve sheath tumor (MPNST), an aggressive subtype of sarcoma with poor prognosis and no effective targeted therapeutics. Using a custom RNAi-based drop out screen, we observed that PRC2-inactivation is synthetic lethal with DNA methyltransferase 1 (DNMT1) downregulation; we further observed that small molecule DNMT inhibitors (DNMTis) resulted in enhanced cytotoxicity and anti-tumor responses in PRC2-loss cancer context in vitro and in vivo. Mechanistically, DNMTi-mediated de-repression of retrotransposons (e.g., endogenous retroviral elements) and gene targets is partly restricted by PRC2, which potentially contributes to limited therapeutic activity in PRC2-wild-type (wt) cancer context. In contrast, DNMTi treatment synergizes with PRC2 inactivation and cooperatively amplifies the expression of retrotransposons, and subsequent viral mimicry response that promotes robust cell death in part through PKR-dependent double stranded-RNA (dsRNA) sensing. Collectively, our observations posit DNA methylation as a safeguard against anti-tumorigenic cell fate decisions in the context of PRC2-inactivation to promote cancer pathogenesis, identify DNMT1-targeted therapy as novel therapeutic strategy for PRC2-inactivated MPNST, and merit further preclinical and clinical investigation of this strategy in other PRC2-inactivated cancers.
Citation Format: Ping Chi, Amish J. Patel, Sarah Warda, Jesper L.V. Maag, Rohan Misra, Miguel A. Miranda-Román, Mohini R. Pachai, Cindy J. Lee, Dan Li, Naitao Wang, Gabriella Bayshtok, Eve Fishinevich, Yinuo Meng, Elissa W.P. Wong, Juan Yan, Emily Giff, Jonathan Fletcher, Joseph M. Scandura, Richard Koche, Jacob L. Glass, Cristina R. Antonescu, Deyou Zheng, Yu Chen. PRC2 inactivating mutations amplify cell death in response to DNMT1-targeted therapy through enhanced viral mimicry in malignant peripheral nerve sheath tumor [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr PR005.
Collapse
Affiliation(s)
- Ping Chi
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | - Sarah Warda
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | - Rohan Misra
- 2Albert Einstein College of Medicine, Bronx, NY,
| | | | | | - Cindy J. Lee
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Dan Li
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Naitao Wang
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | - Yinuo Meng
- 3Weill Cornell Graduate School of Medical Sciences, New York, NY,
| | | | - Juan Yan
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Emily Giff
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Jonathan Fletcher
- 4Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | | | - Richard Koche
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | - Deyou Zheng
- 2Albert Einstein College of Medicine, Bronx, NY,
| | - Yu Chen
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Yan J, Chen Y, Patel AJ, Warda S, Lee CJ, Nixon BG, Wong EW, Miranda-Román MA, Yang N, Wang Y, Pachai MR, Sher J, Giff E, Tang F, Khurana E, Singer S, Liu Y, Galbo PM, Maag JL, Koche RP, Zheng D, Antonescu CR, Deng L, Li MO, Chen Y, Chi P. Tumor-intrinsic PRC2 inactivation drives a context-dependent immune-desert microenvironment and is sensitized by immunogenic viruses. J Clin Invest 2022; 132:e153437. [PMID: 35852856 PMCID: PMC9433107 DOI: 10.1172/jci153437] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 07/14/2022] [Indexed: 02/01/2023] Open
Abstract
Immune checkpoint blockade (ICB) has demonstrated clinical success in "inflamed" tumors with substantial T cell infiltrates, but tumors with an immune-desert tumor microenvironment (TME) fail to benefit. The tumor cell-intrinsic molecular mechanisms of the immune-desert phenotype remain poorly understood. Here, we demonstrated that inactivation of the polycomb-repressive complex 2 (PRC2) core components embryonic ectoderm development (EED) or suppressor of zeste 12 homolog (SUZ12), a prevalent genetic event in malignant peripheral nerve sheath tumors (MPNSTs) and sporadically in other cancers, drove a context-dependent immune-desert TME. PRC2 inactivation reprogramed the chromatin landscape that led to a cell-autonomous shift from primed baseline signaling-dependent cellular responses (e.g., IFN-γ signaling) to PRC2-regulated developmental and cellular differentiation transcriptional programs. Further, PRC2 inactivation led to diminished tumor immune infiltrates through reduced chemokine production and impaired antigen presentation and T cell priming, resulting in primary resistance to ICB. Intratumoral delivery of inactivated modified vaccinia virus Ankara (MVA) enhanced tumor immune infiltrates and sensitized PRC2-loss tumors to ICB. Our results identify molecular mechanisms of PRC2 inactivation-mediated, context-dependent epigenetic reprogramming that underline the immune-desert phenotype in cancer. Our studies also point to intratumoral delivery of immunogenic viruses as an initial therapeutic strategy to modulate the immune-desert TME and capitalize on the clinical benefit of ICB.
Collapse
Affiliation(s)
- Juan Yan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Yuedan Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
| | - Amish J. Patel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Sarah Warda
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Cindy J. Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Briana G. Nixon
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
- Immunology Program, Sloan Kettering Institute
| | - Elissa W.P. Wong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Miguel A. Miranda-Román
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, and
| | - Ning Yang
- Dermatology Service, Department of Medicine, MSK Cancer Center, New York, New York, USA
| | - Yi Wang
- Dermatology Service, Department of Medicine, MSK Cancer Center, New York, New York, USA
| | - Mohini R. Pachai
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Jessica Sher
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Emily Giff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
| | - Fanying Tang
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
- Institute for Computational Biomedicine
- Meyer Cancer Center, and
| | - Ekta Khurana
- Institute for Computational Biomedicine
- Meyer Cancer Center, and
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Sam Singer
- Department of Surgery, MSK Cancer Center, New York, New York, USA
| | - Yang Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Phillip M. Galbo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jesper L.V. Maag
- Center for Epigenetics Research, MSK Cancer Center, New York, New York, USA
| | - Richard P. Koche
- Center for Epigenetics Research, MSK Cancer Center, New York, New York, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Neurology, and
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Liang Deng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
- Dermatology Service, Department of Medicine, MSK Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Ming O. Li
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
- Immunology Program, Sloan Kettering Institute
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, and
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
- Department of Medicine, MSK Cancer Center, New York, New York, USA
| | - Ping Chi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering (MSK) Cancer Center, New York, New York, USA
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
- Department of Medicine, MSK Cancer Center, New York, New York, USA
| |
Collapse
|
4
|
Suan D, Kräutler NJ, Maag JL, Butt D, Bourne K, Hermes JR, Avery DT, Young C, Statham A, Elliott M, Dinger ME, Basten A, Tangye SG, Brink R. CCR6 Defines Memory B Cell Precursors in Mouse and Human Germinal Centers, Revealing Light-Zone Location and Predominant Low Antigen Affinity. Immunity 2017; 47:1142-1153.e4. [DOI: 10.1016/j.immuni.2017.11.022] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 08/29/2017] [Accepted: 11/28/2017] [Indexed: 11/28/2022]
|