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Oh S, Janknecht R. Versatile JMJD proteins: juggling histones and much more. Trends Biochem Sci 2024; 49:804-818. [PMID: 38926050 PMCID: PMC11380596 DOI: 10.1016/j.tibs.2024.06.009] [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: 04/27/2024] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
Jumonji C domain-containing (JMJD) proteins are found in bacteria, fungi, animals, and plants. They belong to the 2-oxoglutarate-dependent oxygenase superfamily and are endowed with various enzymatic activities, including demethylation of histones and hydroxylation of non-histone proteins. Many JMJD proteins are involved in the epigenetic control of gene expression, yet they also modulate a myriad other cellular processes. In this review we focus on the 33 human JMJD proteins and their established and controversial catalytic properties, survey their epigenetic and non-epigenetic functions, emphasize their contribution to sex-specific disease differences, and highlight how they sense metabolic changes. All this underlines not only their key roles in development and homeostasis, but also that JMJD proteins are destined to become drug targets in multiple diseases.
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Affiliation(s)
- Sangphil Oh
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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2
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Honer MA, Ferman BI, Gray ZH, Bondarenko EA, Whetstine JR. Epigenetic modulators provide a path to understanding disease and therapeutic opportunity. Genes Dev 2024; 38:473-503. [PMID: 38914477 PMCID: PMC11293403 DOI: 10.1101/gad.351444.123] [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] [Indexed: 06/26/2024]
Abstract
The discovery of epigenetic modulators (writers, erasers, readers, and remodelers) has shed light on previously underappreciated biological mechanisms that promote diseases. With these insights, novel biomarkers and innovative combination therapies can be used to address challenging and difficult to treat disease states. This review highlights key mechanisms that epigenetic writers, erasers, readers, and remodelers control, as well as their connection with disease states and recent advances in associated epigenetic therapies.
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Affiliation(s)
- Madison A Honer
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Benjamin I Ferman
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Zach H Gray
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Elena A Bondarenko
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA;
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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3
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Tsang E, Han VX, Flutter C, Alshammery S, Keating BA, Williams T, Gloss BS, Graham ME, Aryamanesh N, Pang I, Wong M, Winlaw D, Cardamone M, Mohammad S, Gold W, Patel S, Dale RC. Ketogenic diet modifies ribosomal protein dysregulation in KMT2D Kabuki syndrome. EBioMedicine 2024; 104:105156. [PMID: 38768529 PMCID: PMC11134553 DOI: 10.1016/j.ebiom.2024.105156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Kabuki syndrome (KS) is a genetic disorder caused by DNA mutations in KMT2D, a lysine methyltransferase that methylates histones and other proteins, and therefore modifies chromatin structure and subsequent gene expression. Ketones, derived from the ketogenic diet, are histone deacetylase inhibitors that can 'open' chromatin and encourage gene expression. Preclinical studies have shown that the ketogenic diet rescues hippocampal memory neurogenesis in mice with KS via the epigenetic effects of ketones. METHODS Single-cell RNA sequencing and mass spectrometry-based proteomics were used to explore molecular mechanisms of disease in individuals with KS (n = 4) versus controls (n = 4). FINDINGS Pathway enrichment analysis indicated that loss of function mutations in KMT2D are associated with ribosomal protein dysregulation at an RNA and protein level in individuals with KS (FDR <0.05). Cellular proteomics also identified immune dysregulation and increased abundance of other lysine modification and histone binding proteins, representing a potential compensatory mechanism. A 12-year-old boy with KS, suffering from recurrent episodes of cognitive decline, exhibited improved cognitive function and neuropsychological assessment performance after 12 months on the ketogenic diet, with concomitant improvement in transcriptomic ribosomal protein dysregulation. INTERPRETATION Our data reveals that lysine methyltransferase deficiency is associated with ribosomal protein dysfunction, with secondary immune dysregulation. Diet and the production of bioactive molecules such as ketone bodies serve as a significant environmental factor that can induce epigenetic changes and improve clinical outcomes. Integrating transcriptomic, proteomic, and clinical data can define mechanisms of disease and treatment effects in individuals with neurodevelopmental disorders. FUNDING This study was supported by the Dale NHMRC Investigator Grant (APP1193648) (R.D), Petre Foundation (R.D), and The Sydney Children's Hospital Foundation/Kids Research Early and Mid-Career Researcher Grant (E.T).
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Affiliation(s)
- Erica Tsang
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Velda X Han
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chloe Flutter
- The Kabuki Syndrome Foundation - Volunteer, Northbrook, IL, USA
| | - Sarah Alshammery
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Brooke A Keating
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Tracey Williams
- Kids Rehab, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Brian S Gloss
- Westmead Research Hub, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Mark E Graham
- Biomedical Proteomics, Children's Medical Research Institute, The University of Sydney, Australia
| | - Nader Aryamanesh
- Bioinformatics Group, Children's Medical Research Institute, Westmead, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Ignatius Pang
- Bioinformatics Group, Children's Medical Research Institute, Westmead, Sydney, NSW, Australia
| | - Melanie Wong
- The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - David Winlaw
- Heart Centre, Ann and Robert H. Lurie Children's Hospital of Chicago and Feinberg School of Medicine, Northwestern University, USA
| | - Michael Cardamone
- Sydney Children's Hospital, Randwick, NSW, Australia; School of Clinical Medicine, University of New South Wales, NSW, Australia
| | - Shekeeb Mohammad
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Wendy Gold
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia; Molecular Neurobiology Research Laboratory, Kids Research, The Children's Hospital at Westmead & the Children's Medical Research Institute, NSW, Australia
| | - Shrujna Patel
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Russell C Dale
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; The Brain and Mind Centre, The University of Sydney, Sydney, NSW, Australia.
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4
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Pichavaram P, Jablonowski CM, Fang J, Fleming AM, Gil HJ, Boghossian AS, Rees MG, Ronan MM, Roth JA, Morton CL, Zambetti GP, Davidoff AM, Yang J, Murphy AJ. Oncogenic Cells of Renal Embryonic Lineage Sensitive to the Small-Molecule Inhibitor QC6352 Display Depletion of KDM4 Levels and Disruption of Ribosome Biogenesis. Mol Cancer Ther 2024; 23:478-491. [PMID: 37988559 PMCID: PMC10987284 DOI: 10.1158/1535-7163.mct-23-0312] [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: 05/22/2023] [Revised: 10/23/2023] [Accepted: 11/08/2023] [Indexed: 11/23/2023]
Abstract
The histone lysine demethylases KDM4A-C are involved in physiologic processes including stem cell identity and self-renewal during development, DNA damage repair, and cell-cycle progression. KDM4A-C are overexpressed and associated with malignant cell behavior in multiple human cancers and are therefore potential therapeutic targets. Given the role of KDM4A-C in development and cancer, we aimed to test the potent, selective KDM4A-C inhibitor QC6352 on oncogenic cells of renal embryonic lineage. The anaplastic Wilms tumor cell line WiT49 and the tumor-forming human embryonic kidney cell line HEK293 demonstrated low nanomolar QC6352 sensitivity. The cytostatic response to QC6352 in WiT49 and HEK293 cells was marked by induction of DNA damage, a DNA repair-associated protein checkpoint response, S-phase cell-cycle arrest, profound reduction of ribosomal protein gene and rRNA transcription, and blockade of newly synthesized proteins. QC6352 caused reduction of KDM4A-C levels by a proteasome-associated mechanism. The cellular phenotype caused by QC6352 treatment of reduced migration, proliferation, tumor spheroid growth, DNA damage, and S-phase cell-cycle arrest was most closely mirrored by knockdown of KDM4A as determined by siRNA knockdown of KDM4A-C. QC6352 sensitivity correlated with high basal levels of ribosomal gene transcription in more than 900 human cancer cell lines. Targeting KDM4A may be of future therapeutic interest in oncogenic cells of embryonic renal lineage or cells with high basal expression of ribosomal protein genes.
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Affiliation(s)
| | | | - Jie Fang
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Andrew M. Fleming
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Hyea Jin Gil
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - Matthew G. Rees
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Melissa M. Ronan
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Jennifer A. Roth
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Christopher L. Morton
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Gerard P. Zambetti
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Andrew M. Davidoff
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jun Yang
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Andrew J. Murphy
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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5
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Abu-Zaid A, Fang J, Jin H, Singh S, Pichavaram P, Wu Q, Tillman H, Janke L, Rosikiewicz W, Xu B, Van De Velde LA, Guo Y, Li Y, Shendy NAM, Delahunty IM, Rankovic Z, Chen T, Chen X, Freeman KW, Hatley ME, Durbin AD, Murray PJ, Murphy AJ, Thomas PG, Davidoff AM, Yang J. Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma. Cell Rep Med 2024; 5:101468. [PMID: 38508144 PMCID: PMC10983111 DOI: 10.1016/j.xcrm.2024.101468] [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: 08/22/2022] [Revised: 12/21/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Neuroblastoma with MYCN amplification (MNA) is a high-risk disease that has a poor survival rate. Neuroblastoma displays cellular heterogeneity, including more differentiated (adrenergic) and more primitive (mesenchymal) cellular states. Here, we demonstrate that MYCN oncoprotein promotes a cellular state switch in mesenchymal cells to an adrenergic state, accompanied by induction of histone lysine demethylase 4 family members (KDM4A-C) that act in concert to control the expression of MYCN and adrenergic core regulatory circulatory (CRC) transcription factors. Pharmacologic inhibition of KDM4 blocks expression of MYCN and the adrenergic CRC transcriptome with genome-wide induction of transcriptionally repressive H3K9me3, resulting in potent anticancer activity against neuroblastomas with MNA by inducing neuroblastic differentiation and apoptosis. Furthermore, a short-term KDM4 inhibition in combination with conventional, cytotoxic chemotherapy results in complete tumor responses of xenografts with MNA. Thus, KDM4 blockade may serve as a transformative strategy to target the adrenergic CRC dependencies in MNA neuroblastomas.
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Affiliation(s)
- Ahmed Abu-Zaid
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA; College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jie Fang
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shivendra Singh
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Qiong Wu
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Heather Tillman
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laura Janke
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lee-Ann Van De Velde
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yian Guo
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yimei Li
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Noha A M Shendy
- Department of Molecular Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ian M Delahunty
- Department of Molecular Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiang Chen
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kevin W Freeman
- Genetics, Genomics & Informatics, The University of Tennessee Health Science Center, Memphis, TN 38103, USA
| | - Mark E Hatley
- Department of Molecular Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Adam D Durbin
- Department of Molecular Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter J Murray
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Andrew J Murphy
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Division of Pediatric Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrew M Davidoff
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Division of Pediatric Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, TN 38105, USA; St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Avenue, Suite 500, Memphis, TN 38163, USA
| | - Jun Yang
- Department of Surgery, St Jude Children's Research Hospital, Memphis, TN 38105, USA; St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Avenue, Suite 500, Memphis, TN 38163, USA; College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA.
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6
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Chowdhury P, Wang X, Love JF, Vargas-Hernandez S, Nakatani Y, Grimm SL, Mezquita D, Mason FM, Martinez ED, Coarfa C, Walker CL, Gustavsson AK, Dere R. Lysine Demethylase 4A is a Centrosome Associated Protein Required for Centrosome Integrity and Genomic Stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.20.581246. [PMID: 38464252 PMCID: PMC10925129 DOI: 10.1101/2024.02.20.581246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Centrosomes play a fundamental role in nucleating and organizing microtubules in the cell and are vital for faithful chromosome segregation and maintenance of genomic stability. Loss of structural or functional integrity of centrosomes causes genomic instability and is a driver of oncogenesis. The lysine demethylase 4A (KDM4A) is an epigenetic 'eraser' of chromatin methyl marks, which we show also localizes to the centrosome with single molecule resolution. We additionally discovered KDM4A demethylase enzymatic activity is required to maintain centrosome homeostasis, and is required for centrosome integrity, a new functionality unlinked to altered expression of genes regulating centrosome number. We find rather, that KDM4A interacts with both mother and daughter centriolar proteins to localize to the centrosome in all stages of mitosis. Loss of KDM4A results in supernumerary centrosomes and accrual of chromosome segregation errors including chromatin bridges and micronuclei, markers of genomic instability. In summary, these data highlight a novel role for an epigenetic 'eraser' regulating centrosome integrity, mitotic fidelity, and genomic stability at the centrosome.
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7
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Gu R, Kim TD, Song H, Sui Y, Shin S, Oh S, Janknecht R. SET7/9-mediated methylation affects oncogenic functions of histone demethylase JMJD2A. JCI Insight 2023; 8:e164990. [PMID: 37870957 PMCID: PMC10619491 DOI: 10.1172/jci.insight.164990] [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: 08/30/2022] [Accepted: 09/05/2023] [Indexed: 10/25/2023] Open
Abstract
The histone demethylase JMJD2A/KDM4A facilitates prostate cancer development, yet how JMJD2A function is regulated has remained elusive. Here, we demonstrate that SET7/9-mediated methylation on 6 lysine residues modulated JMJD2A. Joint mutation of these lysine residues suppressed JMJD2A's ability to stimulate the MMP1 matrix metallopeptidase promoter upon recruitment by the ETV1 transcription factor. Mutation of just 3 methylation sites (K505, K506, and K507) to arginine residues (3xR mutation) was sufficient to maximally reduce JMJD2A transcriptional activity and also decreased its binding to ETV1. Introduction of the 3xR mutation into DU145 prostate cancer cells reduced in vitro growth and invasion and also severely compromised tumorigenesis. Consistently, the 3xR genotype caused transcriptome changes related to cell proliferation and invasion pathways, including downregulation of MMP1 and the NPM3 nucleophosmin/nucleoplasmin gene. NPM3 downregulation phenocopied and its overexpression rescued, to a large degree, the 3xR mutation in DU145 cells, suggesting that NPM3 was a seminal downstream effector of methylated JMJD2A. Moreover, we found that NPM3 was overexpressed in prostate cancer and might be indicative of disease aggressiveness. SET7/9-mediated lysine methylation of JMJD2A may aggravate prostate tumorigenesis in a manner dependent on NPM3, implying that the SET7/9→JMJD2A→NPM3 axis could be targeted for therapy.
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Affiliation(s)
| | | | | | | | - Sook Shin
- Department of Cell Biology
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Sangphil Oh
- Department of Cell Biology
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Ralf Janknecht
- Department of Cell Biology
- Department of Pathology, and
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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8
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Kuwik J, Hinkelman K, Waldman M, Stepler KE, Wagner S, Arora S, Chernenkoff S, Cabalteja C, Sidoli S, Robinson RAS, Islam K. Activity Guided Azide-methyllysine Photo-trapping for Substrate Profiling of Lysine Demethylases. J Am Chem Soc 2023; 145:21066-21076. [PMID: 37703462 PMCID: PMC10540216 DOI: 10.1021/jacs.3c07299] [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: 07/10/2023] [Indexed: 09/15/2023]
Abstract
Reversible post-translational modifications (PTMs) are key to establishing protein-protein and protein-nucleic acid interactions that govern a majority of the signaling pathways in cells. Sequence-specific PTMs are catalyzed by transferases, and their removal is carried out by a class of reverse-acting enzymes termed "detransferases". Currently available chemoproteomic approaches have been valuable in characterizing substrates of transferases. However, proteome-wide cataloging of the substrates of detransferases is challenging, mostly due to the loss of the epitope, rendering immunoprecipitation and activity-based methods ineffective. Herein, we develop a general chemoproteomic strategy called crosslinking-assisted substrate identification (CASI) for systematic characterization of cellular targets of detransferases and successfully apply it to lysine demethylases (KDMs) which catalyze the removal of methyl groups from lysine sidechain in histones to modulate gene transcription. By setting up a targeted azido-methylamino photo-reaction deep inside the active site of KDM4, engineered to carry p-azido phenylalanine, we reveal a novel "demethylome" that has escaped the traditional methods. The proteomic survey led to the identification of a battery of nonhistone substrates of KDM4, extending the biological footprint of KDM4 beyond its canonical functions in gene transcription. A notable finding of KDM4A-mediated demethylation of an evolutionarily conserved lysine residue in eukaryotic translational initiation factor argues for a much broader role of KDM4A in ribosomal processes. CASI, representing a substantive departure from earlier approaches by shifting focus from simple peptide-based probes to employing full-length photo-activatable demethylases, is poised to be applied to >400 human detransferases, many of which have remained poorly understood due to the lack of knowledge about their cellular targets.
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Affiliation(s)
- Jordan Kuwik
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kathryn Hinkelman
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Megan Waldman
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kaitlyn E. Stepler
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Shana Wagner
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Simran Arora
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sasha Chernenkoff
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chino Cabalteja
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Simone Sidoli
- Albert
Einstein College of Medicine, Bronx, New York 10461, United States
| | - Renã AS Robinson
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Kabirul Islam
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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9
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Song YQ, Yang GJ, Ma DL, Wang W, Leung CH. The role and prospect of lysine-specific demethylases in cancer chemoresistance. Med Res Rev 2023; 43:1438-1469. [PMID: 37012609 DOI: 10.1002/med.21955] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 02/08/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023]
Abstract
Histone methylation plays a key function in modulating gene expression, and preserving genome integrity and epigenetic inheritance. However, aberrations of histone methylation are commonly observed in human diseases, especially cancer. Lysine methylation mediated by histone methyltransferases can be reversed by lysine demethylases (KDMs), which remove methyl marks from histone lysine residues. Currently, drug resistance is a main impediment for cancer therapy. KDMs have been found to mediate drug tolerance of many cancers via altering the metabolic profile of cancer cells, upregulating the ratio of cancer stem cells and drug-tolerant genes, and promoting the epithelial-mesenchymal transition and metastatic ability. Moreover, different cancers show distinct oncogenic addictions for KDMs. The abnormal activation or overexpression of KDMs can alter gene expression signatures to enhance cell survival and drug resistance in cancer cells. In this review, we describe the structural features and functions of KDMs, the KDMs preferences of different cancers, and the mechanisms of drug resistance resulting from KDMs. We then survey KDM inhibitors that have been used for combating drug resistance in cancer, and discuss the opportunities and challenges of KDMs as therapeutic targets for cancer drug resistance.
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Affiliation(s)
- Ying-Qi Song
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Guan-Jun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao, China
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10
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Terzo E, Apte SA, Padhye S, Rashed S, Austin W, Caponegro M, Reddy A, Shi S, Wang C, Clark RB, Sidransky D, Modur V, Badarinarayana V. A Novel Class of Ribosome Modulating Agents Exploits Cancer Ribosome Heterogeneity to Selectively Target the CMS2 Subtype of Colorectal Cancer. CANCER RESEARCH COMMUNICATIONS 2023; 3:969-979. [PMID: 37377612 PMCID: PMC10241187 DOI: 10.1158/2767-9764.crc-22-0469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/01/2023] [Accepted: 05/05/2023] [Indexed: 06/29/2023]
Abstract
Ribosomes in cancer cells accumulate numerous patient-specific structural and functional modifications that facilitate tumor progression by modifying protein translation. We have taken a unique synthetic chemistry approach to generate novel macrolides, Ribosome modulating agents (RMA), that are proposed to act distal to catalytic sites and exploit cancer ribosome heterogeneity. The RMA ZKN-157 shows two levels of selectivity: (i) selective translation inhibition of a subset of proteins enriched for components of the ribosome and protein translation machinery that are upregulated by MYC; and (ii) selective inhibition of proliferation of a subset of colorectal cancer cell lines. Mechanistically, the selective ribosome targeting in sensitive cells triggered cell-cycle arrest and apoptosis. Consequently, in colorectal cancer, sensitivity to ZKN-157 in cell lines and patient-derived organoids was restricted to the consensus molecular subtype 2 (CMS2) subtype that is distinguished by high MYC and WNT pathway activity. ZKN-157 showed efficacy as single agent and, the potency and efficacy of ZKN-157 synergized with clinically approved DNA-intercalating agents which have previously been shown to inhibit ribogenesis as well. ZKN-157 thus represents a new class of ribosome modulators that display cancer selectivity through specific ribosome inhibition in the CMS2 subtype of colorectal cancer potentially targeting MYC-driven addiction to high protein translation. Significance This study demonstrates that ribosome heterogeneity in cancer can be exploited to develop selective ribogenesis inhibitors. The colorectal cancer CMS2 subtype, with a high unmet need for therapeutics, shows vulnerability to our novel selective ribosome modulator. The mechanism suggests that other cancer subtypes with high MYC activation could also be targeted.
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Affiliation(s)
| | | | | | | | | | | | - Anupama Reddy
- Vindhya Data Science, Data Science, Morrisville, North Carolina
| | - Shuhao Shi
- Eloxx Pharmaceuticals, Watertown, New York
| | | | | | - David Sidransky
- Johns Hopkins University School of Medicine, The Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
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11
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Wright GM, Menzel J, Tatman PD, Black JC. Transition from Transient DNA Rereplication to Inherited Gene Amplification Following Prolonged Environmental Stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539886. [PMID: 37214911 PMCID: PMC10197558 DOI: 10.1101/2023.05.08.539886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cells require the ability to adapt to changing environmental conditions, however, it is unclear how these changes elicit stable permanent changes in genomes. We demonstrate that, in response to environmental metal exposure, the metallothionein (MT) locus undergoes DNA rereplication generating transient site-specific gene amplifications (TSSGs). Chronic metal exposure allows transition from MT TSSG to inherited MT gene amplification through homologous recombination within and outside of the MT locus. DNA rereplication of the MT locus is suppressed by H3K27me3 and EZH2. Long-term ablation of EZH2 activity eventually leads to integration and inheritance of MT gene amplifications without the selective pressure of metal exposure. The rereplication and inheritance of MT gene amplification is an evolutionarily conserved response to environmental metal from yeast to human. Our results describe a new paradigm for adaptation to environmental stress where targeted, transient DNA rereplication precedes stable inherited gene amplification.
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12
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Inchakalody VP, Hydrose SP, Krishnankutty R, Merhi M, Therachiyil L, Sasidharan Nair V, Elashi AA, Khan AQ, Taleb S, Raza A, Yoosuf ZSKM, Fernandes Q, Al-Zaidan L, Mestiri S, Taib N, Bedhiafi T, Moustafa D, Assami L, Maalej KM, Elkord E, Uddin S, Al Homsi U, Dermime S. The molecular mechanisms of apoptosis accompanied with the epigenetic regulation of the NY-ESO-1 antigen in non-small lung cancer cells treated with decitabine (5-aza-CdR). Eur J Pharmacol 2023; 945:175612. [PMID: 36822455 DOI: 10.1016/j.ejphar.2023.175612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/23/2023]
Abstract
Dysregulated epigenetic modifications are common in lung cancer but have been reversed using demethylating agent like 5-Aza-CdR. 5-Aza-CdR induces/upregulates the NY-ESO-1 antigen in lung cancer. Therefore, we investigated the molecular mechanisms accompanied with the epigenetic regulation of NY-ESO-1 in 5-Aza-CdR-treated NCI-H1975 cell line. We showed significant induction of the NY-ESO-1 protein (**p < 0.0097) using Cellular ELISA. Bisulfite-sequencing demonstrated 45.6% demethylation efficiency at the NY-ESO-1 gene promoter region and RT-qPCR analysis confirmed the significant induction of NY-ESO-1 at mRNA level (128-fold increase, *p < 0.050). We then investigated the mechanism by which 5-Aza-CdR inhibits cell proliferation in the NCI-H1975 cell line. Upregulation of the death receptors TRAIL (2.04-fold *p < 0.011) and FAS (2.1-fold *p < 0.011) indicate activation of the extrinsic apoptotic pathway. The upregulation of Voltage-dependent anion-selective channel protein 1 (1.9-fold), Major vault protein (1.8-fold), Bax (1.16-fold), and Cytochrome C (1.39-fold) indicate the activation of the intrinsic pathway. We also observed the differential expression of protein Complement C3 (3.3-fold), Destrin (-5.1-fold), Vimentin (-1.7-fold), Peroxiredoxin 4 (-1.6-fold), Fascin (-1.8-fold), Heme oxygenase-2 (-0.67-fold**p < 0.0055), Hsp27 (-0.57-fold**p < 0.004), and Hsp70 (-0.39-fold **p < 0.001), indicating reduced cell growth, cell migration, and metastasis. The upregulation of 40S ribosomal protein S9 (3-fold), 40S ribosomal protein S15 (4.2-fold), 40S ribosomal protein S18 (2.5-fold), and 60S ribosomal protein L22 (4.4-fold) implied the induction of translation machinery. These results reiterate the decisive role of 5-Aza-CdR in lung cancer treatment since it induces the epigenetic regulation of NY-ESO-1 antigen, inhibits cell proliferation, increases apoptosis, and decreases invasiveness.
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Affiliation(s)
- Varghese P Inchakalody
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Shereena P Hydrose
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Roopesh Krishnankutty
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Maysaloun Merhi
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Lubna Therachiyil
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; College of Pharmacy, Qatar University, Doha, Qatar
| | - Varun Sasidharan Nair
- Department of Experimental Immunology, Helmholtz Centre for Infection Research, Germany
| | - Asma A Elashi
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Sara Taleb
- Genomics and Precision Medicine, Hamad Bin Khalifa University, Doha, Qatar
| | - Afsheen Raza
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Zeenath Safira K M Yoosuf
- Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Queenie Fernandes
- Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; College of Medicine, Qatar University, Doha, Qatar
| | - Lobna Al-Zaidan
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Sarra Mestiri
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Nassiba Taib
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Takwa Bedhiafi
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Dina Moustafa
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Laila Assami
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Karama Makni Maalej
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Eyad Elkord
- Natural and Medical Sciences Research Center, University of Nizwa, Oman; Biomedical Research Center, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Translational Research Institute and Dermatology Institute, Academic Health System, Doha, Qatar
| | - Ussama Al Homsi
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Said Dermime
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.
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13
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Jiang Y, Liu L, Yang ZQ. KDM4 Demethylases: Structure, Function, and Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:87-111. [PMID: 37751137 DOI: 10.1007/978-3-031-38176-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
KDM4 histone demethylases mainly catalyze the removal of methyl marks from H3K9 and H3K36 to epigenetically regulate chromatin structure and gene expression. KDM4 expression is strictly regulated to ensure proper function in a myriad of biological processes, including transcription, cellular proliferation and differentiation, DNA damage repair, immune response, and stem cell self-renewal. Aberrant expression of KDM4 demethylase has been documented in many types of blood and solid tumors, and thus, KDM4s represent promising therapeutic targets. In this chapter, we summarize the current knowledge of the structures and regulatory mechanisms of KDM4 proteins and our understanding of their alterations in human pathological processes with a focus on development and cancer. We also review the reported KDM4 inhibitors and discuss their potential as therapeutic agents.
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Affiliation(s)
- Yuanyuan Jiang
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, 4100 John R Street, HWCRC 815, Detroit, MI, 48201, USA
| | - Lanxin Liu
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, 4100 John R Street, HWCRC 815, Detroit, MI, 48201, USA
| | - Zeng-Quan Yang
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, 4100 John R Street, HWCRC 815, Detroit, MI, 48201, USA.
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14
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Molenaar TM, Malik M, Silva J, Liu NQ, Haarhuis JHI, Ambrosi C, Kwesi-Maliepaard EM, van Welsem T, Baubec T, Faller WJ, van Leeuwen F. The histone methyltransferase SETD2 negatively regulates cell size. J Cell Sci 2022; 135:jcs259856. [PMID: 36052643 PMCID: PMC9659392 DOI: 10.1242/jcs.259856] [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: 01/29/2022] [Accepted: 08/23/2022] [Indexed: 11/20/2022] Open
Abstract
Cell size varies between cell types but is tightly regulated by cell intrinsic and extrinsic mechanisms. Cell size control is important for cell function, and changes in cell size are frequently observed in cancer. Here, we uncover a role for SETD2 in regulating cell size. SETD2 is a lysine methyltransferase and a tumor suppressor protein involved in transcription, RNA processing and DNA repair. At the molecular level, SETD2 is best known for associating with RNA polymerase II through its Set2-Rbp1 interacting (SRI) domain and methylating histone H3 on lysine 36 (H3K36) during transcription. Using multiple independent perturbation strategies, we identify SETD2 as a negative regulator of global protein synthesis rates and cell size. We provide evidence that overexpression of the H3K36 demethylase KDM4A or the oncohistone H3.3K36M also increase cell size. In addition, ectopic overexpression of a decoy SRI domain increased cell size, suggesting that the relevant substrate is engaged by SETD2 via its SRI domain. These data add a central role of SETD2 in regulating cellular physiology and warrant further studies on separating the different functions of SETD2 in cancer development.
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Affiliation(s)
- Thom M. Molenaar
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Muddassir Malik
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Joana Silva
- Division of Oncogenomics, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Ning Qing Liu
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Judith H. I. Haarhuis
- Division of Cell Biology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Christina Ambrosi
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zurich and ETH Zurich, CH-8057 Zurich, Switzerland
| | | | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - William J. Faller
- Division of Oncogenomics, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
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15
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Ulicna L, Kimmey SC, Weber CM, Allard GM, Wang A, Bui NQ, Bendall SC, Crabtree GR, Bean GR, Van Rechem C. The Interaction of SWI/SNF with the Ribosome Regulates Translation and Confers Sensitivity to Translation Pathway Inhibitors in Cancers with Complex Perturbations. Cancer Res 2022; 82:2829-2837. [PMID: 35749589 PMCID: PMC9379364 DOI: 10.1158/0008-5472.can-21-1360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 01/10/2022] [Accepted: 06/15/2022] [Indexed: 01/09/2023]
Abstract
Subunits from the chromatin remodelers mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) are mutated, deleted, or amplified in more than 40% of cancers. Understanding their functions in normal cells and the consequences of cancerous alterations will provide insight into developing new targeted therapies. Here we examined whether mSWI/SNF mutations increase cellular sensitivity to specific drugs. Taking advantage of the DepMap studies, we demonstrate that cancer cells harboring mutations of specific mSWI/SNF subunits exhibit a genetic dependency on translation factors and are sensitive to translation pathway inhibitors. Furthermore, mSWI/SNF subunits were present in the cytoplasm and interacted with the translation initiation machinery, and short-term inhibition and depletion of specific subunits decreased global translation, implicating a direct role for these factors in translation. Depletion of specific mSWI/SNF subunits also increased sensitivity to mTOR-PI3K inhibitors. In patient-derived breast cancer samples, mSWI/SNF subunits expression in both the nucleus and the cytoplasm was substantially altered. In conclusion, an unexpected cytoplasmic role for mSWI/SNF complexes in translation suggests potential new therapeutic opportunities for patients afflicted by cancers demonstrating alterations in their subunits. SIGNIFICANCE This work establishes direct functions for mSWI/SNF in translation and demonstrates that alterations in mSWI/SNF confer a therapeutic vulnerability to translation pathway inhibitors in cancer cells.
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Affiliation(s)
- Livia Ulicna
- Department of Pathology, Stanford University, Stanford, California
| | - Samuel C. Kimmey
- Department of Pathology, Stanford University, Stanford, California.,Department of Medicine/Oncology, Stanford University, Stanford, California
| | | | - Grace M. Allard
- Department of Pathology, Stanford University, Stanford, California
| | - Aihui Wang
- Department of Pathology, Stanford University, Stanford, California
| | - Nam Q. Bui
- Department of Medicine/Oncology, Stanford University, Stanford, California
| | - Sean C. Bendall
- Department of Pathology, Stanford University, Stanford, California
| | - Gerald R. Crabtree
- Department of Pathology, Stanford University, Stanford, California.,Department of Developmental Biology, Stanford University, Stanford, California
| | - Gregory R. Bean
- Department of Pathology, Stanford University, Stanford, California
| | - Capucine Van Rechem
- Department of Pathology, Stanford University, Stanford, California.,Corresponding Author: Capucine Van Rechem, Ph.D. Stanford Medicine Department of Pathology, 269 Campus Drive, CCSR-3245C, Stanford, CA 94305-5176. Phone: 650-723-7698; E-mail:
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16
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Wu Q, Young B, Wang Y, Davidoff AM, Rankovic Z, Yang J. Recent Advances with KDM4 Inhibitors and Potential Applications. J Med Chem 2022; 65:9564-9579. [PMID: 35838529 PMCID: PMC9531573 DOI: 10.1021/acs.jmedchem.2c00680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The histone lysine demethylase 4 (KDM4) family plays an important role in regulating gene transcription, DNA repair, and metabolism. The dysregulation of KDM4 functions is associated with many human disorders, including cancer, obesity, and cardiovascular diseases. Selective and potent KDM4 inhibitors may help not only to understand the role of KDM4 in these disorders but also to provide potential therapeutic opportunities. Here, we provide an overview of the field and discuss current status, challenges, and opportunities lying ahead in the development of KDM4-based anticancer therapeutics.
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Affiliation(s)
- Qiong Wu
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Brandon Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yan Wang
- Department of Geriatrics and Occupational Disease, Qingdao Central Hospital, Qingdao 266044, China
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Avenue, Suite 500, Memphis, Tennessee 38163, United States
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17
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Hara N, Sawada Y. Epigenetics of Cutaneous T-Cell Lymphomas. Int J Mol Sci 2022; 23:ijms23073538. [PMID: 35408897 PMCID: PMC8998216 DOI: 10.3390/ijms23073538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/16/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
Epigenetic modifications rarely occur in isolation (as single “epigenetic modifications”). They usually appear together and form a network to control the epigenetic system. Cutaneous malignancies are usually affected by epigenetic changes. However, there is limited knowledge regarding the epigenetic changes associated with cutaneous lymphomas. In this review, we focused on cutaneous T-cell lymphomas such as mycosis fungoides, Sézary syndrome, and anaplastic large cell lymphoma. With regard to epigenetic changes, we summarize the detailed chemical modifications categorized into DNA methylation and histone acetylation and methylation. We also summarize the epigenetic modifications and characteristics of the drug for cutaneous T-cell lymphoma (CTCL). Furthermore, we discuss current research on epigenetic-targeted therapy against cutaneous T-cell lymphomas. Although the current method of treatment with histone deacetylase inhibitors does not exhibit sufficient therapeutic benefits in all cases of CTCL, epigenetic-targeted combination therapy might overcome this limitation for patients with CTCL.
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18
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Hypoxia Enhances HIF1α Transcription Activity by Upregulating KDM4A and Mediating H3K9me3, Thus Inducing Ferroptosis Resistance in Cervical Cancer Cells. Stem Cells Int 2022; 2022:1608806. [PMID: 35287356 PMCID: PMC8917951 DOI: 10.1155/2022/1608806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/06/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023] Open
Abstract
Objective Cervical cancer (CC) is a prevalent cancer in women. Hypoxia plays a critical role in CC cell ferroptosis resistance. This study explored the mechanism of hypoxia in CC cell ferroptosis resistance by regulating HIF1α/KDM4A/H3K9me3. Methods Cultured SiHa and Hela cells were exposed to CoCl2 and treated with Erastin. Cell viability was detected by MTT assay, and concentrations of iron ion, MDA and GSH were determined using corresponding kits. Expressions of KDM4A, HIF1α, TfR1, DMT1, and H3k9me3 were detected by RT-qPCR, Western blot, and ChIP assay. The correlation of KDM4A and HIF1α was analyzed on Oncomine, UALCAN, and Starbase. CC cells were co-transfected with shKDM4A or/and pcDNA3.1-HIF1α. Iron uptake and release were assessed using the isotopic tracer method. The binding relationship between HIF1α and HRE sequence was verified by dual-luciferase assay. Results Cell viability and GSH were decreased while iron concentration, MDA, KDM4A, and HIF1α levels were increased in hypoxia conditions. The 2-h hypoxia induced ferroptosis resistance. KDM4A and HIF1α were highly-expressed in CC tissues and positively correlated with each other. KDM4A knockdown attenuated cell resistance to Erastin, increased H3K9me3 level in the HIF1α promoter region, and downregulated HIF1α transcription and translation. H3K9me3 level was increased in the HIF1α promoter after hypoxia. HIF1α overexpression abrogated the function of KDM4A knockdown on ferroptosis in hypoxia conditions. Iron uptake/release and TfR1/DMT1 levels were increased after hypoxia. Hypoxia activated HRE sequence in TfR1 and DMT1 promoters. Conclusion Hypoxia upregulated KDM4A, enhanced HIF1α transcription, and activated HRE sequence in TfR1 and DMT1 promoters via H3K9me3, thus inducing ferroptosis resistance in CC cells.
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19
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Mills RH, Dulai PS, Vázquez-Baeza Y, Sauceda C, Daniel N, Gerner RR, Batachari LE, Malfavon M, Zhu Q, Weldon K, Humphrey G, Carrillo-Terrazas M, Goldasich LD, Bryant M, Raffatellu M, Quinn RA, Gewirtz AT, Chassaing B, Chu H, Sandborn WJ, Dorrestein PC, Knight R, Gonzalez DJ. Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity. Nat Microbiol 2022; 7:262-276. [PMID: 35087228 PMCID: PMC8852248 DOI: 10.1038/s41564-021-01050-3] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/15/2021] [Indexed: 12/19/2022]
Abstract
Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. To understand how host-microbiota interactions become disrupted in UC, we collected and analysed six faecal- or serum-based omic datasets (metaproteomic, metabolomic, metagenomic, metapeptidomic and amplicon sequencing profiles of faecal samples and proteomic profiles of serum samples) from 40 UC patients at a single inflammatory bowel disease centre, as well as various clinical, endoscopic and histologic measures of disease activity. A validation cohort of 210 samples (73 UC, 117 Crohn's disease, 20 healthy controls) was collected and analysed separately and independently. Data integration across both cohorts showed that a subset of the clinically active UC patients had an overabundance of proteases that originated from the bacterium Bacteroides vulgatus. To test whether B. vulgatus proteases contribute to UC disease activity, we first profiled B. vulgatus proteases found in patients and bacterial cultures. Use of a broad-spectrum protease inhibitor improved B. vulgatus-induced barrier dysfunction in vitro, and prevented colitis in B. vulgatus monocolonized, IL10-deficient mice. Furthermore, transplantation of faeces from UC patients with a high abundance of B. vulgatus proteases into germfree mice induced colitis dependent on protease activity. These results, stemming from a multi-omics approach, improve understanding of functional microbiota alterations that drive UC and provide a resource for identifying other pathways that could be inhibited as a strategy to treat this disease.
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Affiliation(s)
- Robert H Mills
- Department of Pharmacology, University of California, San Diego, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA.,Department of Pediatrics, University of California, San Diego, CA, USA
| | - Parambir S Dulai
- Division of Gastroenterology, University of California, San Diego, CA, USA
| | - Yoshiki Vázquez-Baeza
- Department of Pediatrics, University of California, San Diego, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, CA, USA
| | - Consuelo Sauceda
- Department of Pharmacology, University of California, San Diego, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Noëmie Daniel
- INSERM U1016, team Mucosal microbiota in chronic inflammatory diseases, CNRS UMR 8104, Université de Paris, Paris, France
| | - Romana R Gerner
- Department of Pediatrics, University of California, San Diego, CA, USA.,Division of Host-Microbe Systems and Therapeutics, University of California, San Diego, CA, USA
| | | | - Mario Malfavon
- Department of Pharmacology, University of California, San Diego, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California, San Diego, CA, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Kelly Weldon
- Center for Microbiome Innovation, University of California, San Diego, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California, San Diego, CA, USA
| | - Marvic Carrillo-Terrazas
- Department of Pharmacology, University of California, San Diego, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, CA, USA
| | | | - MacKenzie Bryant
- Department of Pediatrics, University of California, San Diego, CA, USA
| | - Manuela Raffatellu
- Center for Microbiome Innovation, University of California, San Diego, CA, USA.,Division of Host-Microbe Systems and Therapeutics, University of California, San Diego, CA, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Andrew T Gewirtz
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Benoit Chassaing
- INSERM U1016, team Mucosal microbiota in chronic inflammatory diseases, CNRS UMR 8104, Université de Paris, Paris, France
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, CA, USA
| | - William J Sandborn
- Division of Gastroenterology, University of California, San Diego, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA.,Department of Pediatrics, University of California, San Diego, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, CA, USA. .,Department of Computer Science and Engineering, University of California, San Diego, CA, USA. .,Center for Microbiome Innovation, University of California, San Diego, CA, USA.
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, CA, USA. .,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA. .,Center for Microbiome Innovation, University of California, San Diego, CA, USA.
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20
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Mortazavi A, Fayed I, Bachani M, Dowdy T, Jahanipour J, Khan A, Owotade J, Walbridge S, Inati SK, Steiner J, Wu J, Gilbert M, Yang CZ, Larion M, Maric D, Ksendzovsky A, Zaghloul KA. IDH-mutated gliomas promote epileptogenesis through d-2-hydroxyglutarate-dependent mTOR hyperactivation. Neuro Oncol 2022; 24:1423-1435. [PMID: 34994387 PMCID: PMC9435503 DOI: 10.1093/neuonc/noac003] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Uncontrolled seizures in patients with gliomas have a significant impact on quality of life and morbidity, yet the mechanisms through which these tumors cause seizures remain unknown. Here, we hypothesize that the active metabolite d-2-hydroxyglutarate (d-2-HG) produced by the IDH-mutant enzyme leads to metabolic disruptions in surrounding cortical neurons that consequently promote seizures. METHODS We use a complementary study of in vitro neuron-glial cultures and electrographically sorted human cortical tissue from patients with IDH-mutant gliomas to test this hypothesis. We utilize micro-electrode arrays for in vitro electrophysiological studies in combination with pharmacological manipulations and biochemical studies to better elucidate the impact of d-2-HG on cortical metabolism and neuronal spiking activity. RESULTS We demonstrate that d-2-HG leads to increased neuronal spiking activity and promotes a distinct metabolic profile in surrounding neurons, evidenced by distinct metabolomic shifts and increased LDHA expression, as well as upregulation of mTOR signaling. The increases in neuronal activity are induced by mTOR activation and reversed with mTOR inhibition. CONCLUSION Together, our data suggest that metabolic disruptions in the surrounding cortex due to d-2-HG may be a driving event for epileptogenesis in patients with IDH-mutant gliomas.
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Affiliation(s)
- Armin Mortazavi
- Surgical Neurology Branch, NINDS, National Institutes of Health, Bethesda, Maryland, USA
| | - Islam Fayed
- Department of Neurosurgery, Georgetown University, Washington, District of Columbia, USA
| | - Muzna Bachani
- NeuroTherapeutics Development Unit, NINDS, National Institutes of Health, Bethesda, Maryland, USA
| | - Tyrone Dowdy
- NeuroOncology Branch, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Jahandar Jahanipour
- Flow and Cytometry Core, NINDS, National Institutes of Health, Bethesda, Maryland, USA
| | - Anas Khan
- Surgical Neurology Branch, NINDS, National Institutes of Health, Bethesda, Maryland, USA
| | - Jemima Owotade
- Surgical Neurology Branch, NINDS, National Institutes of Health, Bethesda, Maryland, USA
| | - Stuart Walbridge
- Surgical Neurology Branch, NINDS, National Institutes of Health, Bethesda, Maryland, USA
| | - Sara K Inati
- Surgical Neurology Branch, NINDS, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph Steiner
- NeuroTherapeutics Development Unit, NINDS, National Institutes of Health, Bethesda, Maryland, USA
| | - Jing Wu
- NeuroOncology Branch, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark Gilbert
- NeuroOncology Branch, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Chun Zhang Yang
- NeuroOncology Branch, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Mioara Larion
- NeuroOncology Branch, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Dragan Maric
- Flow and Cytometry Core, NINDS, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Kareem A Zaghloul
- Corresponding Author: Kareem A. Zaghloul, MD, PhD, Surgical Neurology Branch, NINDS, National Institutes of Health, Building 10, Room 3D20, 10 Center Drive Bethesda, MD 20892-1414, USA ()
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21
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Yang T, Yang Y, Wang Y. Predictive biomarkers and potential drug combinations of epi-drugs in cancer therapy. Clin Epigenetics 2021; 13:113. [PMID: 34001246 PMCID: PMC8130364 DOI: 10.1186/s13148-021-01098-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 05/03/2021] [Indexed: 02/07/2023] Open
Abstract
Epigenetics studies heritable genomic modifications that occur with the participation of epigenetic modifying enzymes but without alterations of the nucleotide structure. Small-molecule inhibitors of these epigenetic modifying enzymes are known as epigenetic drugs (epi-drugs), which can cause programmed death of tumor cells by affecting the cell cycle, angiogenesis, proliferation, and migration. Epi-drugs include histone methylation inhibitors, histone demethylation inhibitors, histone deacetylation inhibitors, and DNA methylation inhibitors. Currently, epi-drugs undergo extensive development, research, and application. Although epi-drugs have convincing anti-tumor effects, the patient's sensitivity to epi-drug application is also a fundamental clinical issue. The development and research of biomarkers for epi-drugs provide a promising direction for screening drug-sensitive patients. Here, we review the predictive biomarkers of 12 epi-drugs as well as the progress of combination therapy with chemotherapeutic drugs or immunotherapy. Further, we discuss the improvement in the development of natural ingredients with low toxicity and low side effects as epi-drugs.
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Affiliation(s)
- Tianshu Yang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yunkai Yang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yan Wang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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22
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Mechanistic insights into KDM4A driven genomic instability. Biochem Soc Trans 2021; 49:93-105. [PMID: 33492339 PMCID: PMC7925003 DOI: 10.1042/bst20191219] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022]
Abstract
Alterations in global epigenetic signatures on chromatin are well established to contribute to tumor initiation and progression. Chromatin methylation status modulates several key cellular processes that maintain the integrity of the genome. KDM4A, a demethylase that belongs to the Fe-II dependent dioxygenase family that uses α-ketoglutarate and molecular oxygen as cofactors, is overexpressed in several cancers and is associated with an overall poor prognosis. KDM4A demethylates lysine 9 (H3K9me2/3) and lysine 36 (H3K36me3) methyl marks on histone H3. Given the complexity that exists with these marks on chromatin and their effects on transcription and proliferation, it naturally follows that demethylation serves an equally important role in these cellular processes. In this review, we highlight the role of KDM4A in transcriptional modulation, either dependent or independent of its enzymatic activity, arising from the amplification of this demethylase in cancer. KDM4A modulates re-replication of distinct genomic loci, activates cell cycle inducers, and represses proteins involved in checkpoint control giving rise to proliferative damage, mitotic disturbances and chromosomal breaks, ultimately resulting in genomic instability. In parallel, emerging evidence of non-nuclear substrates of epigenetic modulators emphasize the need to investigate the role of KDM4A in regulating non-nuclear substrates and evaluate their contribution to genomic instability in this context. The existence of promising KDM-specific inhibitors makes these demethylases an attractive target for therapeutic intervention in cancers.
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23
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Arifuzzaman S, Khatun MR, Khatun R. Emerging of lysine demethylases (KDMs): From pathophysiological insights to novel therapeutic opportunities. Biomed Pharmacother 2020; 129:110392. [PMID: 32574968 DOI: 10.1016/j.biopha.2020.110392] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years, there have been remarkable scientific advancements in the understanding of lysine demethylases (KDMs) because of their demethylation of diverse substrates, including nucleic acids and proteins. Novel structural architectures, physiological roles in the gene expression regulation, and ability to modify protein functions made KDMs the topic of interest in biomedical research. These structural diversities allow them to exert their function either alone or in complex with numerous other bio-macromolecules. Impressive number of studies have demonstrated that KDMs are localized dynamically across the cellular and tissue microenvironment. Their dysregulation is often associated with human diseases, such as cancer, immune disorders, neurological disorders, and developmental abnormalities. Advancements in the knowledge of the underlying biochemistry and disease associations have led to the development of a series of modulators and technical compounds. Given the distinct biophysical and biochemical properties of KDMs, in this review we have focused on advances related to the structure, function, disease association, and therapeutic targeting of KDMs highlighting improvements in both the specificity and efficacy of KDM modulation.
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Affiliation(s)
- Sarder Arifuzzaman
- Department of Pharmacy, Jahangirnagar University, Dhaka-1342, Bangladesh; Everest Pharmaceuticals Ltd., Dhaka-1208, Bangladesh.
| | - Mst Reshma Khatun
- Department of Pharmacy, Jahangirnagar University, Dhaka-1342, Bangladesh
| | - Rabeya Khatun
- Department of Pediatrics, TMSS Medical College and Rafatullah Community Hospital, Gokul, Bogura, 5800, Bangladesh
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24
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Li M, Cheng J, Ma Y, Guo H, Shu H, Huang H, Kuang Y, Yang T. The histone demethylase JMJD2A promotes glioma cell growth via targeting Akt-mTOR signaling. Cancer Cell Int 2020; 20:101. [PMID: 32256210 PMCID: PMC7106579 DOI: 10.1186/s12935-020-01177-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 03/17/2020] [Indexed: 02/02/2023] Open
Abstract
Background A number of JmjC domain-containing histone demethylases have been identified and biochemically characterized in mammalian models and humans. JMJD2A is a transcriptional co-factor and enzyme that catalyzes the demethylation of histone H3 lysine 9 and 36 (H3K9 and H3K36). Here in this study, we reported the role of JMJD2A in human glioma. Methods Quantitative real-time PCR and western blot were performed to analyzed JMJD2A expression in glioma. Log-rank was performed to plot the survival curve. JMJD2A was knocked or overexpressed with lentivirus. Cell proliferation and colony formation were performed to assess the effects of JMJD2A on glioma cell growth. Xenograft experiment was performed the evaluate the growth rate of glioma cells in vivo. The signaling pathway was analyzed with western blot and mTOR was inhibited with rapamycin. Results Quantitative real-time PCR and western blot experiments revealed higher expression of JMJD2A and lower levels of H3K9me3/H3K36me3 in glioma tissues than that in normal brain tissues. We showed that knockdown of JMJD2A expression attenuated the growth and colony formation in three lines of glioma cells (U251, T98G, and U87MG), whereas JMJD2A overexpression resulted in opposing effects. Furthermore, we performed in vivo xenograft experiments and our data demonstrated that JMJD2A knockdown reduced the growth of glioma T98G cells in vivo. Further mechanism study implicated that JMJD2A activated the Akt-mTOR pathway and promoted protein synthesis in glioma cells via promoting phosphoinositide-dependent kinase-1 (PDK1) expression. The activation of the Akt-mTOR pathway was also validated in human glioma tissues. Finally, we showed that inhibition of mTOR with rapamycin blocked the effects of JMJD2A on protein synthesis, cell proliferation and colony formation of glioma cells. Conclusions These findings demonstrated that JMJD2A regulated glioma growth and implicated that JMJD2A might be a promising target for intervention.
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Affiliation(s)
- Min Li
- Department of Neurosurgery, General Hospital of Western Theater Command, Chengdu, No. 270, Rongdu Avenue, Jinniu District, Chengdu, China
| | - Jingmin Cheng
- Department of Neurosurgery, General Hospital of Western Theater Command, Chengdu, No. 270, Rongdu Avenue, Jinniu District, Chengdu, China
| | - Yuan Ma
- Department of Neurosurgery, General Hospital of Western Theater Command, Chengdu, No. 270, Rongdu Avenue, Jinniu District, Chengdu, China
| | - Heng Guo
- Department of Neurosurgery, General Hospital of Western Theater Command, Chengdu, No. 270, Rongdu Avenue, Jinniu District, Chengdu, China
| | - Haifeng Shu
- Department of Neurosurgery, General Hospital of Western Theater Command, Chengdu, No. 270, Rongdu Avenue, Jinniu District, Chengdu, China
| | - Haidong Huang
- Department of Neurosurgery, General Hospital of Western Theater Command, Chengdu, No. 270, Rongdu Avenue, Jinniu District, Chengdu, China
| | - Yongqin Kuang
- Department of Neurosurgery, General Hospital of Western Theater Command, Chengdu, No. 270, Rongdu Avenue, Jinniu District, Chengdu, China
| | - Tao Yang
- Department of Neurosurgery, General Hospital of Western Theater Command, Chengdu, No. 270, Rongdu Avenue, Jinniu District, Chengdu, China
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25
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Cornett EM, Ferry L, Defossez PA, Rothbart SB. Lysine Methylation Regulators Moonlighting outside the Epigenome. Mol Cell 2020; 75:1092-1101. [PMID: 31539507 DOI: 10.1016/j.molcel.2019.08.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/14/2019] [Accepted: 08/27/2019] [Indexed: 01/21/2023]
Abstract
Landmark discoveries made nearly two decades ago identified known transcriptional regulators as histone lysine methyltransferases. Since then, the field of lysine methylation signaling has been dominated by studies of how this small chemical posttranslational modification regulates gene expression and other chromatin-based processes. However, recent advances in mass-spectrometry-based proteomics have revealed that histones are just a subset of the thousands of eukaryotic proteins marked by lysine methylation. As the writers, erasers, and readers of histone lysine methylation are emerging as a promising therapeutic target class for cancer and other diseases, a key challenge for the field is to define the full spectrum of activities for these proteins. Here we summarize recent discoveries implicating non-histone lysine methylation as a major regulator of diverse cellular processes. We further discuss recent technological innovations that are enabling the expanded study of lysine methylation signaling. Collectively, these findings are shaping our understanding of the fundamental mechanisms of non-histone protein regulation through this dynamic and multi-functional posttranslational modification.
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Affiliation(s)
- Evan M Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Laure Ferry
- Université de Paris, Epigenetics and Cell Fate, CNRS, 75013 Paris, France
| | | | - Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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26
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Lee DH, Kim GW, Jeon YH, Yoo J, Lee SW, Kwon SH. Advances in histone demethylase KDM4 as cancer therapeutic targets. FASEB J 2020; 34:3461-3484. [PMID: 31961018 DOI: 10.1096/fj.201902584r] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/20/2019] [Accepted: 01/08/2020] [Indexed: 12/26/2022]
Abstract
The KDM4 subfamily H3K9 histone demethylases are epigenetic regulators that control chromatin structure and gene expression by demethylating histone H3K9, H3K36, and H1.4K26. The KDM4 subfamily mainly consists of four proteins (KDM4A-D), all harboring the Jumonji C domain (JmjC) but with differential substrate specificities. KDM4A-C proteins also possess the double PHD and Tudor domains, whereas KDM4D lacks these domains. KDM4 proteins are overexpressed or deregulated in multiple cancers, cardiovascular diseases, and mental retardation and are thus potential therapeutic targets. Despite extensive efforts, however, there are very few KDM4-selective inhibitors. Defining the exact physiological and oncogenic functions of KDM4 demethylase will provide the foundation for the discovery of novel potent inhibitors. In this review, we focus on recent studies highlighting the oncogenic functions of KDM4s and the interplay between KDM4-mediated epigenetic and metabolic pathways in cancer. We also review currently available KDM4 inhibitors and discuss their potential as therapeutic agents for cancer treatment.
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Affiliation(s)
- Dong Hoon Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Yu Hyun Jeon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Jung Yoo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Sang Wu Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea.,Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul, Republic of Korea
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27
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Huang H, Kong W, Jean M, Fiches G, Zhou D, Hayashi T, Que J, Santoso N, Zhu J. A CRISPR/Cas9 screen identifies the histone demethylase MINA53 as a novel HIV-1 latency-promoting gene (LPG). Nucleic Acids Res 2019; 47:7333-7347. [PMID: 31165872 PMCID: PMC6698651 DOI: 10.1093/nar/gkz493] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 05/17/2019] [Accepted: 05/24/2019] [Indexed: 12/17/2022] Open
Abstract
Although combination antiretroviral therapy is potent to block active replication of HIV-1 in AIDS patients, HIV-1 persists as transcriptionally inactive proviruses in infected cells. These HIV-1 latent reservoirs remain a major obstacle for clearance of HIV-1. Investigation of host factors regulating HIV-1 latency is critical for developing novel antiretroviral reagents to eliminate HIV-1 latent reservoirs. From our recently accomplished CRISPR/Cas9 sgRNA screens, we identified that the histone demethylase, MINA53, is potentially a novel HIV-1 latency-promoting gene (LPG). We next validated MINA53’s function in maintenance of HIV-1 latency by depleting MINA53 using the alternative RNAi approach. We further identified that in vitro MINA53 preferentially demethylates the histone substrate, H3K36me3 and that in cells MINA53 depletion by RNAi also increases the local level of H3K36me3 at LTR. The effort to map the downstream effectors unraveled that H3K36me3 has the cross-talk with another epigenetic mark H4K16ac, mediated by KAT8 that recognizes the methylated H3K36 and acetylated H4K16. Removing the MINA53-mediated latency mechanisms could benefit the reversal of post-integrated latent HIV-1 proviruses for purging of reservoir cells. We further demonstrated that a pan jumonji histone demethylase inhibitor, JIB-04, inhibits MINA53-mediated demethylation of H3K36me3, and JIB-04 synergizes with other latency-reversing agents (LRAs) to reactivate latent HIV-1.
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Affiliation(s)
- Huachao Huang
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Weili Kong
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Maxime Jean
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Guillaume Fiches
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Dawei Zhou
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Tsuyoshi Hayashi
- National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Jianwen Que
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Netty Santoso
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jian Zhu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
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28
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Tran HQ, Mills RH, Peters NV, Holder MK, de Vries GJ, Knight R, Chassaing B, Gonzalez DJ, Gewirtz AT. Associations of the Fecal Microbial Proteome Composition and Proneness to Diet-induced Obesity. Mol Cell Proteomics 2019; 18:1864-1879. [PMID: 31262998 PMCID: PMC6731084 DOI: 10.1074/mcp.ra119.001623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Indexed: 12/16/2022] Open
Abstract
Consumption of refined high-fat, low-fiber diets promotes development of obesity and its associated consequences. Although genetics play an important role in dictating susceptibility to such obesogenic diets, mice with nearly uniform genetics exhibit marked heterogeneity in their extent of obesity in response to such diets. This suggests non-genetic determinants play a role in diet-induced obesity. Hence, we sought to identify parameters that predict, and/or correlate with, development of obesity in response to an obesogenic diet. We assayed behavior, metabolic parameters, inflammatory markers/cytokines, microbiota composition, and the fecal metaproteome, in a cohort of mice (n = 50) prior to, and the 8 weeks following, administration of an obesogenic high-fat low-fiber diet. Neither behavioral testing nor quantitation of inflammatory markers broadly predicted severity of diet-induced obesity. Although, the small subset of mice that exhibited basal elevations in serum IL-6 (n = 5) were among the more obese mice in the cohort. While fecal microbiota composition changed markedly in response to the obesogenic diet, it lacked the ability to predict which mice were relative prone or resistant to obesity. In contrast, fecal metaproteome analysis revealed functional and taxonomic differences among the proteins associated with proneness to obesity. Targeted interrogation of microbiota composition data successfully validated the taxonomic differences seen in the metaproteome. Although future work will be needed to determine the breadth of applicability of these associations to other cohorts of animals and humans, this study nonetheless highlights the potential power of gut microbial proteins to predict and perhaps impact development of obesity.
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Affiliation(s)
- Hao Q Tran
- ‡Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA
| | - Robert H Mills
- §Department of Pharmacology, University of California, San Diego, CA; ¶Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA; ‖Department of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, CA; **Center for Microbiome Innovation, University of California, San Diego, CA
| | - Nicole V Peters
- ‡‡Neuroscience Institute, Georgia State University, Atlanta, GA
| | - Mary K Holder
- ‡‡Neuroscience Institute, Georgia State University, Atlanta, GA; §§School of Psychology, Georgia Institute of Technology, Atlanta, GA 30332
| | | | - Rob Knight
- ‖Department of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, CA; **Center for Microbiome Innovation, University of California, San Diego, CA
| | - Benoit Chassaing
- ‡Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA; ‡‡Neuroscience Institute, Georgia State University, Atlanta, GA
| | - David J Gonzalez
- §Department of Pharmacology, University of California, San Diego, CA; ¶Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA; **Center for Microbiome Innovation, University of California, San Diego, CA.
| | - Andrew T Gewirtz
- ‡Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA.
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29
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Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease. mSystems 2019; 4:mSystems00337-18. [PMID: 30801026 PMCID: PMC6372841 DOI: 10.1128/msystems.00337-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/17/2019] [Indexed: 02/07/2023] Open
Abstract
Although genetic approaches are the standard in microbiome analysis, proteome-level information is largely absent. This discrepancy warrants a better understanding of the relationship between gene copy number and protein abundance, as this is crucial information for inferring protein-level changes from metagenomic data. As it remains unknown how metaproteomic systems evolve during dynamic disease states, we leveraged a 4.5-year fecal time series using samples from a single patient with colonic Crohn's disease. Utilizing multiplexed quantitative proteomics and shotgun metagenomic sequencing of eight time points in technical triplicate, we quantified over 29,000 protein groups and 110,000 genes and compared them to five protein biomarkers of disease activity. Broad-scale observations were consistent between data types, including overall clustering by principal-coordinate analysis and fluctuations in Gene Ontology terms related to Crohn's disease. Through linear regression, we determined genes and proteins fluctuating in conjunction with inflammatory metrics. We discovered conserved taxonomic differences relevant to Crohn's disease, including a negative association of Faecalibacterium and a positive association of Escherichia with calprotectin. Despite concordant associations of genera, the specific genes correlated with these metrics were drastically different between metagenomic and metaproteomic data sets. This resulted in the generation of unique functional interpretations dependent on the data type, with metaproteome evidence for previously investigated mechanisms of dysbiosis. An example of one such mechanism was a connection between urease enzymes, amino acid metabolism, and the local inflammation state within the patient. This proof-of-concept approach prompts further investigation of the metaproteome and its relationship with the metagenome in biologically complex systems such as the microbiome. IMPORTANCE A majority of current microbiome research relies heavily on DNA analysis. However, as the field moves toward understanding the microbial functions related to healthy and disease states, it is critical to evaluate how changes in DNA relate to changes in proteins, which are functional units of the genome. This study tracked the abundance of genes and proteins as they fluctuated during various inflammatory states in a 4.5-year study of a patient with colonic Crohn's disease. Our results indicate that despite a low level of correlation, taxonomic associations were consistent in the two data types. While there was overlap of the data types, several associations were uniquely discovered by analyzing the metaproteome component. This case study provides unique and important insights into the fundamental relationship between the genes and proteins of a single individual's fecal microbiome associated with clinical consequences.
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30
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Wang W, Oguz G, Lee PL, Bao Y, Wang P, Terp MG, Ditzel HJ, Yu Q. KDM4B-regulated unfolded protein response as a therapeutic vulnerability in PTEN-deficient breast cancer. J Exp Med 2018; 215:2833-2849. [PMID: 30266800 PMCID: PMC6219741 DOI: 10.1084/jem.20180439] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/23/2018] [Accepted: 08/29/2018] [Indexed: 12/21/2022] Open
Abstract
Wang et al. report an unexpected role of demethylase KDM4B in regulating unfolded protein response (UPR). A stepwise hyperactivation of UPR by co-targeting the KDM4B and PI3K pathway uncovers a therapeutic vulnerability of PTEN-deficient TNBC that otherwise would be resistant to PI3K inhibition. PTEN deficiency in breast cancer leads to resistance to PI3K–AKT inhibitor treatment despite aberrant activation of this signaling pathway. Here, we report that genetic depletion or small molecule inhibition of KDM4B histone demethylase activates the unfolded protein response (UPR) pathway and results in preferential apoptosis in PTEN-deficient triple-negative breast cancers (TNBCs). Intriguingly, this function of KDM4B on UPR requires its demethylase activity but is independent of its canonical role in histone modification, and acts through its cytoplasmic interaction with eIF2α, a crucial component of UPR signaling, resulting in reduced phosphorylation of this component. Targeting KDM4B in combination with PI3K inhibition induces further activation of UPR, leading to robust synergy in apoptosis. These findings identify KDM4B as a therapeutic vulnerability in PTEN-deficient TNBC that otherwise would be resistant to PI3K inhibition.
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Affiliation(s)
- Wenyu Wang
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Gokce Oguz
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Puay Leng Lee
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Yi Bao
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Panpan Wang
- Cancer Research Institute and School of Pharmacy, Jinan University, Guangzhou, China
| | - Mikkel Green Terp
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Qiang Yu
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore .,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School of Singapore, Singapore
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31
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Mishra S, Van Rechem C, Pal S, Clarke TL, Chakraborty D, Mahan SD, Black JC, Murphy SE, Lawrence MS, Daniels DL, Whetstine JR. Cross-talk between Lysine-Modifying Enzymes Controls Site-Specific DNA Amplifications. Cell 2018; 174:803-817.e16. [PMID: 30057114 PMCID: PMC6212369 DOI: 10.1016/j.cell.2018.06.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/02/2018] [Accepted: 06/08/2018] [Indexed: 12/28/2022]
Abstract
Acquired chromosomal DNA amplifications are features of many tumors. Although overexpression and stabilization of the histone H3 lysine 9/36 (H3K9/36) tri-demethylase KDM4A generates transient site-specific copy number gains (TSSGs), additional mechanisms directly controlling site-specific DNA copy gains are not well defined. In this study, we uncover a collection of H3K4-modifying chromatin regulators that function with H3K9 and H3K36 regulators to orchestrate TSSGs. Specifically, the H3K4 tri-demethylase KDM5A and specific COMPASS/KMT2 H3K4 methyltransferases modulate different TSSG loci through H3K4 methylation states and KDM4A recruitment. Furthermore, a distinct chromatin modifier network, MLL1-KDM4B-KDM5B, controls copy number regulation at a specific genomic locus in a KDM4A-independent manner. These pathways comprise an epigenetic addressing system for defining site-specific DNA rereplication and amplifications.
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Affiliation(s)
- Sweta Mishra
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Capucine Van Rechem
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Sangita Pal
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Thomas L Clarke
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Damayanti Chakraborty
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Sarah D Mahan
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA
| | - Joshua C Black
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Sedona E Murphy
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center and Department of Pathology, Harvard Medical School, 13th Street, Charlestown, MA 02129, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | | | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA.
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32
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Chen C, Aihemaiti M, Zhang X, Qu H, Sun QL, He QS, Yu WB. Downregulation of histone demethylase JMJD1C inhibits colorectal cancer metastasis through targeting ATF2. Am J Cancer Res 2018; 8:852-865. [PMID: 29888107 PMCID: PMC5992515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/29/2018] [Indexed: 06/08/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant gastrointestinal cancers. Metastasis is a major leading of death in patients with CRC and many patients have metastatic disease at diagnosis. However, the underlying molecular mechanisms are still elusive. Here, we showed that JMJD1C was overexpressed in colon cancer tissues compared to normal samples and was positively associated with metastasis and poor prognosis. Silencing JMJD1C strongly inhibits CRC migration and invasion both in vitro and in vivo. Further, we found that knockdown of JMJD1C decreased the protein and mRNA levels of ATF2, mechanistically, and JMJD1C regulated the expression of ATF2 by modulating the H3K9me2 but not H3K9me1 activity. In addition, we further performed some "rescues experiments". We found that overexpression of ATF2 could reverse the abrogated migration and invasion ability by knockdown of JMJD1C in CRC. Our results demonstrated that an increase of JMJD1C was observed in colon cancer and knockdown of JMJD1C regulated CRC metastasis by inactivation of the ATF2 pathway. This novel JMJD1C/ATF2 signaling pathway may be a promising therapeutic target for CRC metastasis.
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Affiliation(s)
- Cheng Chen
- Department of General Surgery, Qilu Hospital of Shandong University 107 West Wenhua Road, Jinan 250012, China
| | - Maimaiti Aihemaiti
- Department of General Surgery, Qilu Hospital of Shandong University 107 West Wenhua Road, Jinan 250012, China
| | - Xin Zhang
- Department of General Surgery, Qilu Hospital of Shandong University 107 West Wenhua Road, Jinan 250012, China
| | - Hui Qu
- Department of General Surgery, Qilu Hospital of Shandong University 107 West Wenhua Road, Jinan 250012, China
| | - Qi-Long Sun
- Department of General Surgery, Qilu Hospital of Shandong University 107 West Wenhua Road, Jinan 250012, China
| | - Qing-Si He
- Department of General Surgery, Qilu Hospital of Shandong University 107 West Wenhua Road, Jinan 250012, China
| | - Wen-Bin Yu
- Department of General Surgery, Qilu Hospital of Shandong University 107 West Wenhua Road, Jinan 250012, China
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33
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Wei Y, Liang J, Zhang R, Guo Y, Shen S, Su L, Lin X, Moran S, Helland Å, Bjaanæs MM, Karlsson A, Planck M, Esteller M, Fleischer T, Staaf J, Zhao Y, Chen F, Christiani DC. Epigenetic modifications in KDM lysine demethylases associate with survival of early-stage NSCLC. Clin Epigenetics 2018; 10:41. [PMID: 29619118 PMCID: PMC5879927 DOI: 10.1186/s13148-018-0474-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/16/2018] [Indexed: 12/20/2022] Open
Abstract
Background KDM lysine demethylase family members are related to lung cancer clinical outcomes and are potential biomarkers for chemotherapeutics. However, little is known about epigenetic alterations in KDM genes and their roles in lung cancer survival. Methods Tumor tissue samples of 1230 early-stage non-small cell lung cancer (NSCLC) patients were collected from the five independent cohorts. The 393 methylation sites in KDM genes were extracted from epigenome-wide datasets and analyzed by weighted random forest (Ranger) in discovery phase and validation dataset, respectively. The variable importance scores (VIS) for the sites in top 5% of both discovery and validation sets were carried forward for Cox regression to further evaluate the association with patient’s overall survival. TCGA transcriptomic data were used to evaluate the correlation with the corresponding DNA methylation. Results DNA methylation at sites cg11637544 in KDM2A and cg26662347 in KDM1A were in the top 5% of VIS in both discovery phase and validation for squamous cell carcinomas (SCC), which were also significantly associated with SCC survival (HRcg11637544 = 1.32, 95%CI, 1.16–1.50, P = 1.1 × 10−4; HRcg26662347 = 1.88, 95%CI, 1.37–2.60, P = 3.7 × 10−3), and correlated with corresponding gene expression (cg11637544 for KDM2A, P = 1.3 × 10−10; cg26662347 for KDM1A P = 1.5 × 10−5). In addition, by using flexible criteria for Ranger analysis followed by survival classification tree analysis, we identified four clusters for adenocarcinomas and five clusters for squamous cell carcinomas which showed a considerable difference of clinical outcomes with statistical significance. Conclusions These findings highlight the association between somatic DNA methylation in KDM genes and early-stage NSCLC patient survival, which may reveal potential epigenetic therapeutic targets. Electronic supplementary material The online version of this article (10.1186/s13148-018-0474-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yongyue Wei
- 1Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166 China.,2China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, 211166 China.,3Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115 USA
| | - Junya Liang
- 1Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166 China.,2China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, 211166 China
| | - Ruyang Zhang
- 1Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166 China.,2China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, 211166 China.,3Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115 USA
| | - Yichen Guo
- 3Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115 USA
| | - Sipeng Shen
- 1Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166 China.,2China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, 211166 China.,3Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115 USA
| | - Li Su
- 2China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, 211166 China
| | - Xihong Lin
- 4Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115 USA
| | - Sebastian Moran
- 5Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet, Barcelona, Catalonia Spain
| | - Åslaug Helland
- 6Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Maria M Bjaanæs
- 6Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anna Karlsson
- 7Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381 Lund, Sweden
| | - Maria Planck
- 7Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381 Lund, Sweden
| | - Manel Esteller
- 5Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet, Barcelona, Catalonia Spain
| | - Thomas Fleischer
- 6Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Johan Staaf
- 7Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381 Lund, Sweden
| | - Yang Zhao
- 1Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166 China.,2China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, 211166 China.,3Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115 USA
| | - Feng Chen
- 1Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166 China.,2China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, 211166 China.,3Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115 USA
| | - David C Christiani
- 2China International Cooperation Center (CICC) for Environment and Human Health, Nanjing Medical University, Nanjing, 211166 China.,3Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115 USA.,8Pulmonary and Critical Care Unit, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Boston, MA 02114 USA
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34
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Lyons J, Brubaker DK, Ghazi PC, Baldwin KR, Edwards A, Boukhali M, Strasser SD, Suarez-Lopez L, Lin YJ, Yajnik V, Kissil JL, Haas W, Lauffenburger DA, Haigis KM. Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis. Sci Signal 2018; 11:eaan3580. [PMID: 29487189 PMCID: PMC6719711 DOI: 10.1126/scisignal.aan3580] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic disorder of the gastrointestinal tract that has limited treatment options. To gain insight into the pathogenesis of chronic colonic inflammation (colitis), we performed a multiomics analysis that integrated RNA microarray, total protein mass spectrometry (MS), and phosphoprotein MS measurements from a mouse model of the disease. Because we collected all three types of data from individual samples, we tracked information flow from RNA to protein to phosphoprotein and identified signaling molecules that were coordinately or discordantly regulated and pathways that had complex regulation in vivo. For example, the genes encoding acute-phase proteins were expressed in the liver, but the proteins were detected by MS in the colon during inflammation. We also ascertained the types of data that best described particular facets of chronic inflammation. Using gene set enrichment analysis and trans-omics coexpression network analysis, we found that each data set provided a distinct viewpoint on the molecular pathogenesis of colitis. Combining human transcriptomic data with the mouse multiomics data implicated increased p21-activated kinase (Pak) signaling as a driver of colitis. Chemical inhibition of Pak1 and Pak2 with FRAX597 suppressed active colitis in mice. These studies provide translational insights into the mechanisms contributing to colitis and identify Pak as a potential therapeutic target in IBD.
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Affiliation(s)
- Jesse Lyons
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas K Brubaker
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Phaedra C Ghazi
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Katherine R Baldwin
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Pediatric Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Amanda Edwards
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Myriam Boukhali
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha Dale Strasser
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lucia Suarez-Lopez
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yi-Jang Lin
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Vijay Yajnik
- Department of Medicine, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Joseph L Kissil
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Wilhelm Haas
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kevin M Haigis
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA.
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Harvard Digestive Disease Center, Harvard Medical School, Boston, MA 02115, USA
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35
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Peña-Llopis S, Wan Y, Martinez ED. Unique epigenetic gene profiles define human breast cancers with poor prognosis. Oncotarget 2018; 7:85819-85831. [PMID: 27863398 PMCID: PMC5349877 DOI: 10.18632/oncotarget.13334] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 10/29/2016] [Indexed: 01/09/2023] Open
Abstract
Epigenetic enzymes are at the nexus of cellular regulatory cascades and can drive cancer-specific deregulation at all stages of the oncogenic process, yet little is known about their prognostic value in human patients. Here, we used qRT-PCR to profile at high resolution the expression of fifty-five epigenetic genes in over one hundred human breast cancer samples and patient-matched benign tissues. We correlated expression patterns with clinical and histological parameters and validated our findings in two independent large patient cohorts (TCGA and METABRIC). We found that human breast malignancies have unique epigenetic profiles and cluster into epigenetic subgroups. A subset of epigenetic genes defined an Epigenetic Signature as an independent predictor of patient survival that outperforms triple negative status and other clinical variables. Our results also suggest that breast cancer grade, but not stage, is driven by transcriptional alterations of epigenetic modifiers. Overall, this study uncovers the presence of epigenetic subtypes within human mammary malignancies and identifies tumor subgroups with specific pharmacologically targetable epigenetic susceptibilities not yet therapeutically exploited.
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Affiliation(s)
- Samuel Peña-Llopis
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany
| | - Yihong Wan
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
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36
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Wang LY, Hung CL, Chen YR, Yang JC, Wang J, Campbell M, Izumiya Y, Chen HW, Wang WC, Ann DK, Kung HJ. KDM4A Coactivates E2F1 to Regulate the PDK-Dependent Metabolic Switch between Mitochondrial Oxidation and Glycolysis. Cell Rep 2017; 16:3016-3027. [PMID: 27626669 DOI: 10.1016/j.celrep.2016.08.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/23/2016] [Accepted: 08/04/2016] [Indexed: 12/21/2022] Open
Abstract
The histone lysine demethylase KDM4A/JMJD2A has been implicated in prostate carcinogenesis through its role in transcriptional regulation. Here, we describe KDM4A as a E2F1 coactivator and demonstrate a functional role for the E2F1-KDM4A complex in the control of tumor metabolism. KDM4A associates with E2F1 on target gene promoters and enhances E2F1 chromatin binding and transcriptional activity, thereby modulating the transcriptional profile essential for cancer cell proliferation and survival. The pyruvate dehydrogenase kinases (PDKs) PDK1 and PDK3 are direct targets of KDM4A and E2F1 and modulate the switch between glycolytic metabolism and mitochondrial oxidation. Downregulation of KDM4A leads to elevated activity of pyruvate dehydrogenase and mitochondrial oxidation, resulting in excessive accumulation of reactive oxygen species. The altered metabolic phenotypes can be partially rescued by ectopic expression of PDK1 and PDK3, indicating a KDM4A-dependent tumor metabolic regulation via PDK. Our results suggest that KDM4A is a key regulator of tumor metabolism and a potential therapeutic target for prostate cancer.
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Affiliation(s)
- Ling-Yu Wang
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Chiu-Lien Hung
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA 95817, USA; Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Yun-Ru Chen
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA 91010, USA
| | - Joy C Yang
- Department of Urology, University of California, Davis, Sacramento, CA 95817, USA
| | - Junjian Wang
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Mel Campbell
- Department of Dermatology, University of California, Davis, Sacramento, CA 95817, USA
| | - Yoshihiro Izumiya
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA 95817, USA; Department of Dermatology, University of California, Davis, Sacramento, CA 95817, USA
| | - Hong-Wu Chen
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Wen-Ching Wang
- Department of Life Sciences, National Tsinghua University, Hsinchu 30013, Taiwan
| | - David K Ann
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA 91010, USA
| | - Hsing-Jien Kung
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA 95817, USA; Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 35053, Taiwan.
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37
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Jambhekar A, Anastas JN, Shi Y. Histone Lysine Demethylase Inhibitors. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026484. [PMID: 28049654 DOI: 10.1101/cshperspect.a026484] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The dynamic regulation of covalent modifications to histones is essential for maintaining genomic integrity and cell identity and is often compromised in cancer. Aberrant expression of histone lysine demethylases has been documented in many types of blood and solid tumors, and thus demethylases represent promising therapeutic targets. Recent advances in high-throughput chemical screening, structure-based drug design, and structure-activity relationship studies have improved both the specificity and the in vivo efficacy of demethylase inhibitors. This review will briefly outline the connection between demethylases and cancer and will provide a comprehensive overview of the structure, specificity, and utility of currently available demethylase inhibitors. To date, a select group of demethylase inhibitors is being evaluated in clinical trials, and additional compounds may soon follow from the bench to the bedside.
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Affiliation(s)
- Ashwini Jambhekar
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Jamie N Anastas
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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38
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Bavetsias V, Lanigan RM, Ruda GF, Atrash B, McLaughlin MG, Tumber A, Mok NY, Le Bihan YV, Dempster S, Boxall K, Jeganathan F, Hatch SB, Savitsky P, Velupillai S, Krojer T, England K, Sejberg J, Thai C, Donovan A, Pal A, Scozzafava G, Bennett J, Kawamura A, Johansson C, Szykowska A, Gileadi C, Burgess-Brown N, von Delft F, Oppermann U, Walters Z, Shipley J, Raynaud FI, Westaway SM, Prinjha RK, Fedorov O, Burke R, Schofield C, Westwood IM, Bountra C, Müller S, van Montfort RL, Brennan PE, Blagg J. 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J Med Chem 2016; 59:1388-409. [PMID: 26741168 PMCID: PMC4770324 DOI: 10.1021/acs.jmedchem.5b01635] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Indexed: 11/29/2022]
Abstract
We report the discovery of N-substituted 4-(pyridin-2-yl)thiazole-2-amine derivatives and their subsequent optimization, guided by structure-based design, to give 8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-ones, a series of potent JmjC histone N-methyl lysine demethylase (KDM) inhibitors which bind to Fe(II) in the active site. Substitution from C4 of the pyrazole moiety allows access to the histone peptide substrate binding site; incorporation of a conformationally constrained 4-phenylpiperidine linker gives derivatives such as 54j and 54k which demonstrate equipotent activity versus the KDM4 (JMJD2) and KDM5 (JARID1) subfamily demethylases, selectivity over representative exemplars of the KDM2, KDM3, and KDM6 subfamilies, cellular permeability in the Caco-2 assay, and, for 54k, inhibition of H3K9Me3 and H3K4Me3 demethylation in a cell-based assay.
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Affiliation(s)
- Vassilios Bavetsias
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Rachel M. Lanigan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Gian Filippo Ruda
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Butrus Atrash
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Mark G. McLaughlin
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Anthony Tumber
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - N. Yi Mok
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Yann-Vaï Le Bihan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Sally Dempster
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Katherine
J. Boxall
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Fiona Jeganathan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Stephanie B. Hatch
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Pavel Savitsky
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Srikannathasan Velupillai
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Tobias Krojer
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Katherine
S. England
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Jimmy Sejberg
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Ching Thai
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Adam Donovan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Akos Pal
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Giuseppe Scozzafava
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - James
M. Bennett
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Catrine Johansson
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Botnar Research
Centre, NIHR Oxford Biomedical Research
Unit, Oxford OX3 7LD, U.K.
| | - Aleksandra Szykowska
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Carina Gileadi
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Nicola
A. Burgess-Brown
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Frank von Delft
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Udo Oppermann
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Botnar Research
Centre, NIHR Oxford Biomedical Research
Unit, Oxford OX3 7LD, U.K.
| | - Zoe Walters
- Divisions of Molecular Pathology and Cancer
Therapeutics, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Janet Shipley
- Divisions of Molecular Pathology and Cancer
Therapeutics, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Florence I. Raynaud
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Susan M. Westaway
- Epinova Discovery Performance Unit, Medicines
Research Centre, GlaxoSmithKline R&D, Stevenage SG1 2NY, U.K.
| | - Rab K. Prinjha
- Epinova Discovery Performance Unit, Medicines
Research Centre, GlaxoSmithKline R&D, Stevenage SG1 2NY, U.K.
| | - Oleg Fedorov
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Rosemary Burke
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | | | - Isaac M. Westwood
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Chas Bountra
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Susanne Müller
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Rob L.
M. van Montfort
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Paul E. Brennan
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Julian Blagg
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
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39
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Horton JR, Engstrom A, Zoeller EL, Liu X, Shanks JR, Zhang X, Johns MA, Vertino PM, Fu H, Cheng X. Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases. J Biol Chem 2016; 291:2631-46. [PMID: 26645689 PMCID: PMC4742734 DOI: 10.1074/jbc.m115.698449] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 11/17/2015] [Indexed: 12/18/2022] Open
Abstract
The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases remove methyl groups from tri- and dimethylated lysine 4 of histone H3. Accumulating evidence from primary tumors and model systems supports a role for KDM5A (JARID1A/RBP2) and KDM5B (JARID1B/PLU1) as oncogenic drivers. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC). Here we demonstrate that internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes. We present a crystal structure of the linked JmjN-JmjC domain from KDM5A, which reveals that the linked domain fully reconstitutes the cofactor (metal ion and α-ketoglutarate) binding characteristics of other structurally characterized Jumonji domain demethylases. Docking studies with GSK-J1, a selective inhibitor of the KDM6/KDM5 subfamilies, identify critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain. Further, we found that GSK-J1 inhibited the demethylase activity of KDM5C with 8.5-fold increased potency compared with that of KDM5B at 1 mm α-ketoglutarate. In contrast, JIB-04 (a pan-inhibitor of the Jumonji demethylase superfamily) had the opposite effect and was ~8-fold more potent against KDM5B than against KDM5C. Interestingly, the relative selectivity of JIB-04 toward KDM5B over KDM5C in vitro translates to a ~10-50-fold greater growth-inhibitory activity against breast cancer cell lines. These data define the minimal requirements for enzymatic activity of the KDM5 family to be the linked JmjN-JmjC domain coupled with the immediate C-terminal helical zinc-binding domain and provide structural characterization of the linked JmjN-JmjC domain for the KDM5 family, which should prove useful in the design of KDM5 demethylase inhibitors with improved potency and selectivity.
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Affiliation(s)
| | - Amanda Engstrom
- the Graduate Program in Biochemistry, Cell and Developmental Biology
| | | | - Xu Liu
- From the Departments of Biochemistry
| | | | | | | | - Paula M Vertino
- Radiation Oncology, the Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Haian Fu
- the Winship Cancer Institute, Emory University, Atlanta, Georgia 30322 Radiation Oncology, the Emory Chemical Biology Discovery Center, and Hematology and Medical Oncology, and
| | - Xiaodong Cheng
- From the Departments of Biochemistry, the Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
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40
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Salifou K, Ray S, Verrier L, Aguirrebengoa M, Trouche D, Panov KI, Vandromme M. The histone demethylase JMJD2A/KDM4A links ribosomal RNA transcription to nutrients and growth factors availability. Nat Commun 2016; 7:10174. [PMID: 26729372 PMCID: PMC5157185 DOI: 10.1038/ncomms10174] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 11/11/2015] [Indexed: 12/15/2022] Open
Abstract
The interplay between methylation and demethylation of histone lysine residues is an essential component of gene expression regulation and there is considerable interest in elucidating the roles of proteins involved. Here we report that histone demethylase KDM4A/JMJD2A, which is involved in the regulation of cell proliferation and is overexpressed in some cancers, interacts with RNA Polymerase I, associates with active ribosomal RNA genes and is required for serum-induced activation of rDNA transcription. We propose that KDM4A controls the initial stages of transition from 'poised', non-transcribed rDNA chromatin into its active form. We show that PI3K, a major signalling transducer central for cell proliferation and survival, controls cellular localization of KDM4A and consequently its association with ribosomal DNA through the SGK1 downstream kinase. We propose that the interplay between PI3K/SGK1 signalling cascade and KDM4A constitutes a mechanism by which cells adapt ribosome biogenesis level to the availability of growth factors and nutrients.
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Affiliation(s)
- Kader Salifou
- Centre for Integrative Biology, Université de Toulouse, UT3 Toulouse, France
- Centre for Integrative Biology, CNRS, UT3 Toulouse, France
| | - Swagat Ray
- School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Laure Verrier
- Centre for Integrative Biology, Université de Toulouse, UT3 Toulouse, France
- Centre for Integrative Biology, CNRS, UT3 Toulouse, France
| | - Marion Aguirrebengoa
- Centre for Integrative Biology, Université de Toulouse, UT3 Toulouse, France
- Centre for Integrative Biology, CNRS, UT3 Toulouse, France
| | - Didier Trouche
- Centre for Integrative Biology, Université de Toulouse, UT3 Toulouse, France
- Centre for Integrative Biology, CNRS, UT3 Toulouse, France
| | - Konstantin I. Panov
- School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Marie Vandromme
- Centre for Integrative Biology, Université de Toulouse, UT3 Toulouse, France
- Centre for Integrative Biology, CNRS, UT3 Toulouse, France
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41
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Kim TD, Jin F, Shin S, Oh S, Lightfoot SA, Grande JP, Johnson AJ, van Deursen JM, Wren JD, Janknecht R. Histone demethylase JMJD2A drives prostate tumorigenesis through transcription factor ETV1. J Clin Invest 2016; 126:706-20. [PMID: 26731476 DOI: 10.1172/jci78132] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/13/2015] [Indexed: 02/06/2023] Open
Abstract
Histone demethylase upregulation has been observed in human cancers, yet it is unknown whether this is a bystander event or a driver of tumorigenesis. We found that overexpression of lysine-specific demethylase 4A (KDM4A, also known as JMJD2A) was positively correlated with Gleason score and metastasis in human prostate tumors. Overexpression of JMJD2A resulted in the development of prostatic intraepithelial neoplasia in mice, demonstrating that JMJD2A can initiate prostate cancer development. Moreover, combined overexpression of JMJD2A and the ETS transcription factor ETV1, a JMJD2A-binding protein, resulted in prostate carcinoma formation in mice haplodeficient for the phosphatase and tensin homolog (Pten) tumor-suppressor gene. Additionally, JMJD2A cooperated with ETV1 to increase expression of yes associated protein 1 (YAP1), a Hippo pathway component that itself was associated with prostate tumor aggressiveness. ETV1 facilitated the recruitment of JMJD2A to the YAP1 promoter, leading to changes in histone lysine methylation in a human prostate cancer cell line. Further, YAP1 expression largely rescued the growth inhibitory effects of JMJD2A depletion in prostate cancer cells, indicating that YAP1 is a downstream effector of JMJD2A. Taken together, these data reveal a JMJD2A/ETV1/YAP1 axis that promotes prostate cancer initiation and that may be a suitable target for therapeutic inhibition.
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42
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Rothbart SB, Dickson BM, Strahl BD. From histones to ribosomes: a chromatin regulator tangoes with translation. Cancer Discov 2016; 5:228-30. [PMID: 25749972 DOI: 10.1158/2159-8290.cd-15-0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Histone lysine methylation is a critical regulator of chromatin-templated processes such as gene transcription and DNA repair, and is dynamically controlled by enzymes that write and erase this posttranslational modification. Although histone methylation has been well studied, the functions of nonhistone lysine methylation and its regulatory enzymes, particularly outside the nucleus, are poorly defined. In this issue of Cancer Discovery, Van Rechem and colleagues shed light on a new role for the lysine demethylase KDM4A as a regulator of protein translation and identify a single-nucleotide polymorphism in the KDM4A gene as a candidate biomarker for mTOR inhibitor therapy.
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Affiliation(s)
- Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan.
| | - Bradley M Dickson
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina. Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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43
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D'Oto A, Tian QW, Davidoff AM, Yang J. Histone demethylases and their roles in cancer epigenetics. JOURNAL OF MEDICAL ONCOLOGY AND THERAPEUTICS 2016; 1:34-40. [PMID: 28149961 PMCID: PMC5279889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The genetic abnormalities that drive tumorigenesis are usually coupled with epigenetic alterations, such as DNA methylation and aberrant histone modifications, which may help oncogenic drivers accelerate cancer progression, metastasis, and therapy resistance. The discovery of histone demethylases has provided us new insight for understanding the epigenetic landscape of the chromatin environment of cancer cells. This review aims to summarize the current knowledge on the human histone lysine demethylases and their functions in cancers, and recent advances in development of small molecule inhibitors to target histone demethylases in cancer treatment.
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Affiliation(s)
- Alexandra D'Oto
- Department of Surgery, St Jude Children's Research Hospital, Memphis, USA
| | - Qing-wu Tian
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, China
| | - Andrew M Davidoff
- Department of Surgery, St Jude Children's Research Hospital, Memphis, USA
| | - Jun Yang
- Department of Surgery, St Jude Children's Research Hospital, Memphis, USA
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44
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Salony, Solé X, Alves CP, Dey-Guha I, Ritsma L, Boukhali M, Lee JH, Chowdhury J, Ross KN, Haas W, Vasudevan S, Ramaswamy S. AKT Inhibition Promotes Nonautonomous Cancer Cell Survival. Mol Cancer Ther 2015; 15:142-53. [PMID: 26637368 DOI: 10.1158/1535-7163.mct-15-0414] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 10/21/2015] [Indexed: 12/20/2022]
Abstract
Small molecule inhibitors of AKT (v-akt murine thymoma viral oncogene homolog) signaling are being evaluated in patients with various cancer types, but have so far proven therapeutically disappointing for reasons that remain unclear. Here, we treat cancer cells with subtherapeutic doses of Akti-1/2, an allosteric small molecule AKT inhibitor, in order to experimentally model pharmacologic inhibition of AKT signaling in vitro. We then apply a combined RNA, protein, and metabolite profiling approach to develop an integrated, multiscale, molecular snapshot of this "AKT(low)" cancer cell state. We find that AKT-inhibited cancer cells suppress thousands of mRNA transcripts, and proteins related to the cell cycle, ribosome, and protein translation. Surprisingly, however, these AKT-inhibited cells simultaneously upregulate a host of other proteins and metabolites posttranscriptionally, reflecting activation of their endo-vesiculo-membrane system, secretion of inflammatory proteins, and elaboration of extracellular microvesicles. Importantly, these microvesicles enable rapidly proliferating cancer cells of various types to better withstand different stress conditions, including serum deprivation, hypoxia, or cytotoxic chemotherapy in vitro and xenografting in vivo. These findings suggest a model whereby cancer cells experiencing a partial inhibition of AKT signaling may actually promote the survival of neighbors through non-cell autonomous communication.
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Affiliation(s)
- Salony
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Xavier Solé
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Cleidson P Alves
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Ipsita Dey-Guha
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Laila Ritsma
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Myriam Boukhali
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Ju H Lee
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Joeeta Chowdhury
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Kenneth N Ross
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Shobha Vasudevan
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts
| | - Sridhar Ramaswamy
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard & MIT, Cambridge, Massachusetts. Harvard Stem Cell Institute, Cambridge, Massachusetts. Harvard-Ludwig Center for Cancer Research, Boston, Massachusetts.
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45
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Dimitrova E, Turberfield AH, Klose RJ. Histone demethylases in chromatin biology and beyond. EMBO Rep 2015; 16:1620-39. [PMID: 26564907 PMCID: PMC4687429 DOI: 10.15252/embr.201541113] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/06/2015] [Indexed: 01/05/2023] Open
Abstract
Histone methylation plays fundamental roles in regulating chromatin‐based processes. With the discovery of histone demethylases over a decade ago, it is now clear that histone methylation is dynamically regulated to shape the epigenome and regulate important nuclear processes including transcription, cell cycle control and DNA repair. In addition, recent observations suggest that these enzymes could also have functions beyond their originally proposed role as histone demethylases. In this review, we focus on recent advances in our understanding of the molecular mechanisms that underpin the role of histone demethylases in a wide variety of normal cellular processes.
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Affiliation(s)
| | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
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46
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Successful strategies in the discovery of small-molecule epigenetic modulators with anticancer potential. Future Med Chem 2015; 7:2243-61. [DOI: 10.4155/fmc.15.140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
As a class, epigenetic enzymes have been identified as clear targets for cancer therapeutics based on their broad hyperactivity in solid and hematological malignancies. The search for effective inhibitors of histone writers and of histone erasers has been a focus of drug discovery efforts both in academic and pharmaceutical laboratories and has led to the identification of some promising leads. This review focuses on the discovery strategies and preclinical evaluation studies of a subset of the more advanced compounds that target histone writers or histone erasers. The specificity and anticancer potential of these small molecules is discussed within the context of their development pipeline.
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47
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Abstract
Black et al. demonstrate that hypoxia induces transient, site-specific copy gains in primary, nontransformed, and transformed human cells. Hypoxia-driven copy gains are dependent on the KDM4A histone demethylase and are blocked by inhibition of KDM4A with a small molecule or the natural metabolite succinate. Copy number heterogeneity is a prominent feature within tumors. The molecular basis for this heterogeneity remains poorly characterized. Here, we demonstrate that hypoxia induces transient site-specific copy gains (TSSGs) in primary, nontransformed, and transformed human cells. Hypoxia-driven copy gains are not dependent on HIF1α or HIF2α; however, they are dependent on the KDM4A histone demethylase and are blocked by inhibition of KDM4A with a small molecule or the natural metabolite succinate. Furthermore, this response is conserved at a syntenic region in zebrafish cells. Regions with site-specific copy gain are also enriched for amplifications in hypoxic primary tumors. These tumors exhibited amplification and overexpression of the drug resistance gene CKS1B, which we recapitulated in hypoxic breast cancer cells. Our results demonstrate that hypoxia provides a biological stimulus to create transient site-specific copy alterations that could result in heterogeneity within tumors and cell populations. These findings have major implications in our understanding of copy number heterogeneity and the emergence of drug resistance genes in cancer.
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48
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Van Rechem C, Black JC, Greninger P, Zhao Y, Donado C, Burrowes PD, Ladd B, Christiani DC, Benes CH, Whetstine JR. A coding single-nucleotide polymorphism in lysine demethylase KDM4A associates with increased sensitivity to mTOR inhibitors. Cancer Discov 2015; 5:245-54. [PMID: 25564517 DOI: 10.1158/2159-8290.cd-14-1159] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED SNPs occur within chromatin-modulating factors; however, little is known about how these variants within the coding sequence affect cancer progression or treatment. Therefore, there is a need to establish their biochemical and/or molecular contribution, their use in subclassifying patients, and their impact on therapeutic response. In this report, we demonstrate that coding SNP-A482 within the lysine tridemethylase gene KDM4A/JMJD2A has different allelic frequencies across ethnic populations, associates with differential outcome in patients with non-small cell lung cancer (NSCLC), and promotes KDM4A protein turnover. Using an unbiased drug screen against 87 preclinical and clinical compounds, we demonstrate that homozygous SNP-A482 cells have increased mTOR inhibitor sensitivity. mTOR inhibitors significantly reduce SNP-A482 protein levels, which parallels the increased drug sensitivity observed with KDM4A depletion. Our data emphasize the importance of using variant status as candidate biomarkers and highlight the importance of studying SNPs in chromatin modifiers to achieve better targeted therapy. SIGNIFICANCE This report documents the first coding SNP within a lysine demethylase that associates with worse outcome in patients with NSCLC. We demonstrate that this coding SNP alters the protein turnover and associates with increased mTOR inhibitor sensitivity, which identifies a candidate biomarker for mTOR inhibitor therapy and a therapeutic target for combination therapy.
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Affiliation(s)
- Capucine Van Rechem
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Joshua C Black
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Patricia Greninger
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Yang Zhao
- Department of Environmental Health, Harvard School of Public Health, Harvard University, Boston, Massachusetts. Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Carlos Donado
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Paul D Burrowes
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Brendon Ladd
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - David C Christiani
- Department of Environmental Health, Harvard School of Public Health, Harvard University, Boston, Massachusetts. Pulmonary and Critical Care Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts.
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