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Chomiak AA, Tiedemann RL, Liu Y, Kong X, Cui Y, Wiseman AK, Thurlow KE, Cornett EM, Topper MJ, Baylin SB, Rothbart SB. Select EZH2 inhibitors enhance viral mimicry effects of DNMT inhibition through a mechanism involving NFAT:AP-1 signaling. Sci Adv 2024; 10:eadk4423. [PMID: 38536911 PMCID: PMC10971413 DOI: 10.1126/sciadv.adk4423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/21/2024] [Indexed: 04/05/2024]
Abstract
DNA methyltransferase inhibitor (DNMTi) efficacy in solid tumors is limited. Colon cancer cells exposed to DNMTi accumulate lysine-27 trimethylation on histone H3 (H3K27me3). We propose this Enhancer of Zeste Homolog 2 (EZH2)-dependent repressive modification limits DNMTi efficacy. Here, we show that low-dose DNMTi treatment sensitizes colon cancer cells to select EZH2 inhibitors (EZH2is). Integrative epigenomic analysis reveals that DNMTi-induced H3K27me3 accumulates at genomic regions poised with EZH2. Notably, combined EZH2i and DNMTi alters the epigenomic landscape to transcriptionally up-regulate the calcium-induced nuclear factor of activated T cells (NFAT):activating protein 1 (AP-1) signaling pathway. Blocking this pathway limits transcriptional activating effects of these drugs, including transposable element and innate immune response gene expression involved in viral defense. Analysis of primary human colon cancer specimens reveals positive correlations between DNMTi-, innate immune response-, and calcium signaling-associated transcription profiles. Collectively, we show that compensatory EZH2 activity limits DNMTi efficacy in colon cancer and link NFAT:AP-1 signaling to epigenetic therapy-induced viral mimicry.
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Affiliation(s)
- Alison A. Chomiak
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Yanqing Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Xiangqian Kong
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ying Cui
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ashley K. Wiseman
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kate E. Thurlow
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Evan M. Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Michael J. Topper
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Stephen B. Baylin
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Scott B. Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
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3
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Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee KH, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei MS, Vander Schaaf NA, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. Cell Genom 2022; 2:100144. [PMID: 35873672 PMCID: PMC9306256 DOI: 10.1016/j.xgen.2022.100144] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 05/20/2022] [Indexed: 05/21/2023]
Abstract
We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging, and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. Apc Min/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high-sample-throughput studies in this important model organism.
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Affiliation(s)
- Wanding Zhou
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding author
| | - Toshinori Hinoue
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bret Barnes
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | - Owen Mitchell
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Waleed Iqbal
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kelly K. Foy
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kwang-Ho Lee
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ethan J. Moyer
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandra VanderArk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Julie M. Koeman
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Wubin Ding
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Manpreet Kalkat
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Nathan J. Spix
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bryn Eagleson
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Piroska E. Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Liang Kang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ashley K. Wiseman
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Peter A. Jones
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Connie M. Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Rishi Porecha
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | | | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
| | - Peter W. Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
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4
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Pappalardi MB, Keenan K, Cockerill M, Kellner WA, Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE, Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW, Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X, Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG, Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM, Waddell I, Kruger RG, McCabe MT. Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia. Nat Cancer 2021; 2:1002-1017. [PMID: 34790902 DOI: 10.1038/s43018-021-00249-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/27/2021] [Indexed: 05/22/2023]
Abstract
DNA methylation, a key epigenetic driver of transcriptional silencing, is universally dysregulated in cancer. Reversal of DNA methylation by hypomethylating agents, such as the cytidine analogs decitabine or azacytidine, has demonstrated clinical benefit in hematologic malignancies. These nucleoside analogs are incorporated into replicating DNA where they inhibit DNA cytosine methyltransferases DNMT1, DNMT3A and DNMT3B through irreversible covalent interactions. These agents induce notable toxicity to normal blood cells thus limiting their clinical doses. Herein we report the discovery of GSK3685032, a potent first-in-class DNMT1-selective inhibitor that was shown via crystallographic studies to compete with the active-site loop of DNMT1 for penetration into hemi-methylated DNA between two CpG base pairs. GSK3685032 induces robust loss of DNA methylation, transcriptional activation and cancer cell growth inhibition in vitro. Due to improved in vivo tolerability compared with decitabine, GSK3685032 yields superior tumor regression and survival mouse models of acute myeloid leukemia.
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Affiliation(s)
- Melissa B Pappalardi
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Kathryn Keenan
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Mark Cockerill
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
- These authors contributed equally: Mark Cockerill, Wendy A. Kellner
| | - Wendy A Kellner
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
- These authors contributed equally: Mark Cockerill, Wendy A. Kellner
| | - Alexandra Stowell
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Christian Sherk
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Kristen Wong
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Sarath Pathuri
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jacques Briand
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Michael Steidel
- Cellzome GmbH, Functional Genomics, GlaxoSmithKline, Heidelberg, Germany
| | - Philip Chapman
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Arthur Groy
- Future Pipeline Discovery, GlaxoSmithKline, Collegeville, PA, USA
| | - Ashley K Wiseman
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Charles F McHugh
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Nino Campobasso
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Alan P Graves
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Emma Fairweather
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Thilo Werner
- Cellzome GmbH, Functional Genomics, GlaxoSmithKline, Heidelberg, Germany
| | - Ali Raoof
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Roger J Butlin
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Lourdes Rueda
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David T Fosbenner
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Cunyu Zhang
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Jessica L Handler
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Morris Muliaditan
- Drug Metabolism and Pharmacokinetics Modelling, GlaxoSmithKline, Stevenage, UK
| | - Makda Mebrahtu
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Jon-Paul Jaworski
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Dean E McNulty
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Charlotte Burt
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - H Christian Eberl
- Cellzome GmbH, Functional Genomics, GlaxoSmithKline, Heidelberg, Germany
| | - Amy N Taylor
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Thau Ho
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Susan Merrihew
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Shawn W Foley
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Anna Rutkowska
- Cellzome GmbH, Functional Genomics, GlaxoSmithKline, Heidelberg, Germany
| | - Mei Li
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Stuart P Romeril
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Kristin Goldberg
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher S Kershaw
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Marcus Bantscheff
- Cellzome GmbH, Functional Genomics, GlaxoSmithKline, Heidelberg, Germany
| | | | - Elisabeth Minthorn
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Paola Grandi
- Cellzome GmbH, Functional Genomics, GlaxoSmithKline, Heidelberg, Germany
| | - Mehul Patel
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | | | - Helai P Mohammad
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | | | - Rab K Prinjha
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Donald Ogilvie
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | | | - Dirk Heerding
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Stephen B Baylin
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Peter A Jones
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bryan W King
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Juan I Luengo
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Allan M Jordan
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Ian Waddell
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Ryan G Kruger
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Michael T McCabe
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
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