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Jiang W, Shaw S, Rush J, Dumont N, Kim J, Singh R, Skepner A, Khodier C, Raffier C, Yan N, Schluter C, Yu X, Szuchnicki M, Sathappa M, Kahn J, Sperling AS, McKinney DC, Gould AE, Garvie CW, Miller PG. Identification of Small Molecule Inhibitors of PPM1D Using a Novel Drug Discovery Platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.595001. [PMID: 38826457 PMCID: PMC11142126 DOI: 10.1101/2024.05.20.595001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Protein phosphatase, Mg2+/Mn2+ dependent 1D (PPM1D), is a serine/threonine phosphatase that is recurrently activated in cancer, regulates the DNA damage response (DDR), and suppresses the activation of p53. Consistent with its oncogenic properties, genetic loss or pharmacologic inhibition of PPM1D impairs tumor growth and sensitizes cancer cells to cytotoxic therapies in a wide range of preclinical models. Given the therapeutic potential of targeting PPM1D specifically and the DDR and p53 pathway more generally, we sought to deepen our biological understanding of PPM1D as a drug target and determine how PPM1D inhibition differs from other therapeutic approaches to activate the DDR. We performed a high throughput screen to identify new allosteric inhibitors of PPM1D, then generated and optimized a suite of enzymatic, cell-based, and in vivo pharmacokinetic and pharmacodynamic assays to drive medicinal chemistry efforts and to further interrogate the biology of PPM1D. Importantly, this drug discovery platform can be readily adapted to broadly study the DDR and p53. We identified compounds distinct from previously reported allosteric inhibitors and showed in vivo on-target activity. Our data suggest that the biological effects of inhibiting PPM1D are distinct from inhibitors of the MDM2-p53 interaction and standard cytotoxic chemotherapies. These differences also highlight the potential therapeutic contexts in which targeting PPM1D would be most valuable. Therefore, our studies have identified a series of new PPM1D inhibitors, generated a suite of in vitro and in vivo assays that can be broadly used to interrogate the DDR, and provided important new insights into PPM1D as a drug target.
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Affiliation(s)
- Wei Jiang
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Subrata Shaw
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Jason Rush
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Nancy Dumont
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - John Kim
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Ritu Singh
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Adam Skepner
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Carol Khodier
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Cerise Raffier
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Ni Yan
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for Cancer Research and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Cameron Schluter
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for Cancer Research and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Xiao Yu
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Mateusz Szuchnicki
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Murugappan Sathappa
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Josephine Kahn
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Adam S. Sperling
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David C. McKinney
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Alexandra E. Gould
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Colin W. Garvie
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Peter G. Miller
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Center for Cancer Research and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
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Martinikova AS, Stoyanov M, Oravetzova A, Kok YP, Yu S, Dobrovolna J, Janscak P, van Vugt M, Macurek L. PPM1D activity promotes the replication stress caused by cyclin E1 overexpression. Mol Oncol 2024; 18:6-20. [PMID: 37067201 PMCID: PMC10766204 DOI: 10.1002/1878-0261.13433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/09/2023] [Accepted: 04/13/2023] [Indexed: 04/18/2023] Open
Abstract
Oncogene-induced replication stress has been recognized as a major cause of genome instability in cancer cells. Increased expression of cyclin E1 caused by amplification of the CCNE1 gene is a common cause of replication stress in various cancers. Protein phosphatase magnesium-dependent 1 delta (PPM1D) is a negative regulator of p53 and has been implicated in termination of the cell cycle checkpoint. Amplification of the PPM1D gene or frameshift mutations in its final exon promote tumorigenesis. Here, we show that PPM1D activity further increases the replication stress caused by overexpression of cyclin E1. In particular, we demonstrate that cells expressing a truncated mutant of PPM1D progress faster from G1 to S phase and fail to complete licensing of the replication origins. In addition, we show that transcription-replication collisions and replication fork slowing caused by CCNE1 overexpression are exaggerated in cells expressing the truncated PPM1D. Finally, replication speed and accumulation of focal DNA copy number alterations caused by induction of CCNE1 expression was rescued by pharmacological inhibition of PPM1D. We propose that increased activity of PPM1D suppresses the checkpoint function of p53 and thus promotes genome instability in cells expressing the CCNE1 oncogene.
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Affiliation(s)
- Andra S. Martinikova
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
| | - Miroslav Stoyanov
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
| | - Anna Oravetzova
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
| | - Yannick P. Kok
- Department of Medical Oncology, University Medical Center GroningenUniversity of GroningenThe Netherlands
| | - Shibo Yu
- Department of Pathology and Medical Biology, University Medical Center GroningenUniversity of GroningenThe Netherlands
| | - Jana Dobrovolna
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
| | - Pavel Janscak
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
- Institute of Molecular Cancer ResearchUniversity of ZurichSwitzerland
| | - Marcel van Vugt
- Department of Medical Oncology, University Medical Center GroningenUniversity of GroningenThe Netherlands
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
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Burocziova M, Danek P, Oravetzova A, Chalupova Z, Alberich-Jorda M, Macurek L. Ppm1d truncating mutations promote the development of genotoxic stress-induced AML. Leukemia 2023; 37:2209-2220. [PMID: 37709843 PMCID: PMC10624630 DOI: 10.1038/s41375-023-02030-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
Hematopoietic stem cells (HSCs) ensure blood cell production during the life-time of an organism, and to do so they need to balance self-renewal, proliferation, differentiation, and migration in a steady state as well as in response to stress or injury. Importantly, aberrant proliferation of HSCs leads to hematological malignancies, and thus, tight regulation by various tumor suppressor pathways, including p53, is essential. Protein phosphatase magnesium-dependent 1 delta (PPM1D) is a negative regulator of p53 and promotes cell survival upon induction of genotoxic stress. Truncating mutations in the last exon of PPM1D lead to the production of a stable, enzymatically active protein and are commonly associated with clonal hematopoiesis. Using a transgenic mouse model, we demonstrate that truncated PPM1D reduces self-renewal of HSCs in basal conditions but promotes the development of aggressive AML after exposure to ionizing radiation. Inhibition of PPM1D suppressed the colony growth of leukemic stem and progenitor cells carrying the truncated PPM1D, and remarkably, it provided protection against irradiation-induced cell growth. Altogether, we demonstrate that truncated PPM1D affects HSC maintenance, disrupts normal hematopoiesis, and that its inhibition could be beneficial in the context of therapy-induced AML.
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Affiliation(s)
- Monika Burocziova
- Department Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic
- Department of Hemato-oncology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic
| | - Petr Danek
- Department of Hemato-oncology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic
| | - Anna Oravetzova
- Department Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic
| | - Zuzana Chalupova
- Department Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic
| | - Meritxell Alberich-Jorda
- Department of Hemato-oncology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic.
- Childhood Leukaemia Investigation Prague, Department of Pediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University in Prague, University Hospital Motol, V Uvalu 84, Praha, 150 06, Czech Republic.
| | - Libor Macurek
- Department Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Prague, Czech Republic.
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Franch-Expósito S, Mehine M, Ptashkin RN, Bolton KL, Bandlamudi C, Srinivasan P, Zhang L, Goodell MA, Gedvilaite E, Menghrajani K, Sánchez-Vela P, Mandelker D, Comen E, Norton L, Benayed R, Gao T, Papaemmanuil E, Taylor B, Levine R, Offit K, Stadler Z, Berger MF, Zehir A. Associations Between Cancer Predisposition Mutations and Clonal Hematopoiesis in Patients With Solid Tumors. JCO Precis Oncol 2023; 7:e2300070. [PMID: 37561983 PMCID: PMC10581611 DOI: 10.1200/po.23.00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/31/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
PURPOSE Clonal hematopoiesis (CH), the expansion of clones in the hematopoietic system, has been linked to different internal and external features such as aging, genetic ancestry, smoking, and oncologic treatment. However, the interplay between mutations in known cancer predisposition genes and CH has not been thoroughly examined in patients with solid tumors. METHODS We used prospective tumor-blood paired sequencing data from 46,906 patients who underwent Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) testing to interrogate the associations between CH and rare pathogenic or likely pathogenic (P/LP) germline variants. RESULTS We observed an enrichment of CH-positive patients among those carrying P/LP germline mutations and identified a significant association between P/LP germline variants in ATM and CH. Germline and CH comutation patterns in ATM, TP53, and CHEK2 suggested biallelic inactivation as a potential mediator of clonal expansion. Moreover, we observed that CH-PPM1D mutations, similar to somatic tumor-associated PPM1D mutations, were depleted in patients with P/LP germline mutations in the DNA damage response (DDR) genes ATM, CHEK2, and TP53. Patients with solid tumors and harboring P/LP germline mutations, CH mutations, and mosaicism chromosomal alterations might be at an increased risk of developing secondary leukemia while germline variants in TP53 were identified as an independent risk factor (hazard ratio, 36; P < .001) for secondary leukemias. CONCLUSION Our results suggest a close relationship between inherited variants and CH mutations within the DDR genes in patients with solid tumors. Associations identified in this study might translate into enhanced clinical surveillance for CH and associated comorbidities in patients with cancer harboring these germline mutations.
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Affiliation(s)
- Sebastià Franch-Expósito
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Miika Mehine
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan N. Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- C2i Genomics, New York, NY
| | - Kelly L. Bolton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Preethi Srinivasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Natera Inc, San Carlos, CA
| | - Linda Zhang
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Margaret A. Goodell
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Erika Gedvilaite
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kamal Menghrajani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pablo Sánchez-Vela
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth Comen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Precision Medicine and Biosamples, AstraZeneca, New York, NY
| | - Teng Gao
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Elli Papaemmanuil
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Barry Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Precision Medicine and Biosamples, AstraZeneca, New York, NY
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