1
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Zaman SU, Pagare PP, Ma H, Hoyle RG, Zhang Y, Li J. Novel PROTAC probes targeting KDM3 degradation to eliminate colorectal cancer stem cells through inhibition of Wnt/β-catenin signaling. RSC Med Chem 2024:d4md00122b. [PMID: 39281802 PMCID: PMC11393732 DOI: 10.1039/d4md00122b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 08/20/2024] [Indexed: 09/18/2024] Open
Abstract
It has been demonstrated that the KDM3 family of histone demethylases (KDM3A and KDM3B) epigenetically control the functional properties of colorectal cancer stem cells (CSCs) through Wnt/β-catenin signaling. Meanwhile, a broad-spectrum histone demethylase inhibitor, IOX1, suppresses Wnt-induced colorectal tumorigenesis predominantly through inhibiting the enzymatic activity of KDM3. In this work, several cereblon (CRBN)-recruiting PROTACs with various linker lengths were designed and synthesized using IOX1 as a warhead to target KDM3 proteins for degradation. Two of the synthesized PROTACs demonstrated favorable degradation profile and selectivity towards KDM3A and KDM3B. Compound 4 demonstrated favorable in vitro metabolic profile in liver enzymes as well as no hERG-associated cardiotoxicity. Compound 4 also showed dramatic ability in suppressing oncogenic Wnt signaling to eliminate colorectal CSCs and inhibit tumor growth, with around 10- to 35-fold increased potency over IOX1. In summary, this study suggests that PROTACs provide a unique molecular tool for the development of novel small molecules from the IOX1 skeleton for selective degradation of KDM3 to eliminate colorectal CSCs via suppressing oncogenic Wnt signaling.
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Affiliation(s)
- Shadid U Zaman
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
| | - Piyusha P Pagare
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
| | - Hongguang Ma
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
| | - Rosalie G Hoyle
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
| | - Yan Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
| | - Jiong Li
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
- Department of Oral and Craniofacial Molecular Biology, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
- Massey Cancer Center, Virginia Commonwealth University Richmond Virginia 23298-0540 USA
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2
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Sasaki M, Kato D, Murakami K, Yoshida H, Takase S, Otsubo T, Ogiwara H. Targeting dependency on a paralog pair of CBP/p300 against de-repression of KREMEN2 in SMARCB1-deficient cancers. Nat Commun 2024; 15:4770. [PMID: 38839769 PMCID: PMC11153594 DOI: 10.1038/s41467-024-49063-w] [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: 06/19/2023] [Accepted: 05/22/2024] [Indexed: 06/07/2024] Open
Abstract
SMARCB1, a subunit of the SWI/SNF chromatin remodeling complex, is the causative gene of rhabdoid tumors and epithelioid sarcomas. Here, we identify a paralog pair of CBP and p300 as a synthetic lethal target in SMARCB1-deficient cancers by using a dual siRNA screening method based on the "simultaneous inhibition of a paralog pair" concept. Treatment with CBP/p300 dual inhibitors suppresses growth of cell lines and tumor xenografts derived from SMARCB1-deficient cells but not from SMARCB1-proficient cells. SMARCB1-containing SWI/SNF complexes localize with H3K27me3 and its methyltransferase EZH2 at the promotor region of the KREMEN2 locus, resulting in transcriptional downregulation of KREMEN2. By contrast, SMARCB1 deficiency leads to localization of H3K27ac, and recruitment of its acetyltransferases CBP and p300, at the KREMEN2 locus, resulting in transcriptional upregulation of KREMEN2, which cooperates with the SMARCA1 chromatin remodeling complex. Simultaneous inhibition of CBP/p300 leads to transcriptional downregulation of KREMEN2, followed by apoptosis induction via monomerization of KREMEN1 due to a failure to interact with KREMEN2, which suppresses anti-apoptotic signaling pathways. Taken together, our findings indicate that simultaneous inhibitors of CBP/p300 could be promising therapeutic agents for SMARCB1-deficient cancers.
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Affiliation(s)
- Mariko Sasaki
- Division of Cancer Therapeutics, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Daiki Kato
- Cancer Research Unit, Sumitomo Pharma Co., Ltd, 3-1-98 Kasugade-naka, Konohana-ku, Osaka, 554-0022, Japan
| | - Karin Murakami
- Cancer Research Unit, Sumitomo Pharma Co., Ltd, 3-1-98 Kasugade-naka, Konohana-ku, Osaka, 554-0022, Japan
| | - Hiroshi Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shohei Takase
- Division of Cancer Therapeutics, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tsuguteru Otsubo
- Cancer Research Unit, Sumitomo Pharma Co., Ltd, 3-1-98 Kasugade-naka, Konohana-ku, Osaka, 554-0022, Japan
| | - Hideaki Ogiwara
- Division of Cancer Therapeutics, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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3
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Belle R, Saraç H, Salah E, Bhushan B, Szykowska A, Roper G, Tumber A, Kriaucionis S, Burgess-Brown N, Schofield CJ, Brown T, Kawamura A. Focused Screening Identifies Different Sensitivities of Human TET Oxygenases to the Oncometabolite 2-Hydroxyglutarate. J Med Chem 2024; 67:4525-4540. [PMID: 38294854 PMCID: PMC10983004 DOI: 10.1021/acs.jmedchem.3c01820] [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: 09/28/2023] [Revised: 12/10/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
Ten-eleven translocation enzymes (TETs) are Fe(II)/2-oxoglutarate (2OG) oxygenases that catalyze the sequential oxidation of 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine in eukaryotic DNA. Despite their roles in epigenetic regulation, there is a lack of reported TET inhibitors. The extent to which 2OG oxygenase inhibitors, including clinically used inhibitors and oncometabolites, modulate DNA modifications via TETs has been unclear. Here, we report studies on human TET1-3 inhibition by a set of 2OG oxygenase-focused inhibitors, employing both enzyme-based and cellular assays. Most inhibitors manifested similar potencies for TET1-3 and caused increases in cellular 5hmC levels. (R)-2-Hydroxyglutarate, an oncometabolite elevated in isocitrate dehydrogenase mutant cancer cells, showed different degrees of inhibition, with TET1 being less potently inhibited than TET3 and TET2, potentially reflecting the proposed role of TET2 mutations in tumorigenesis. The results highlight the tractability of TETs as drug targets and provide starting points for selective inhibitor design.
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Affiliation(s)
- Roman Belle
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Hilal Saraç
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Bhaskar Bhushan
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
| | - Aleksandra Szykowska
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Grace Roper
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Skirmantas Kriaucionis
- Ludwig
Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Nicola Burgess-Brown
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Tom Brown
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Akane Kawamura
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
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4
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Vergnes L, Wiese CB, Zore T, Riestenberg C, Avetisyan R, Reue K. Gene Regulation and Mitochondrial Activity During White and Brown Adipogenesis Are Modulated by KDM5 Histone Demethylase. J Endocr Soc 2024; 8:bvae029. [PMID: 38425435 PMCID: PMC10904225 DOI: 10.1210/jendso/bvae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Indexed: 03/02/2024] Open
Abstract
Body fat accumulation differs between males and females and is influenced by both gonadal sex (ovaries vs testes) and chromosomal sex (XX vs XY). We previously showed that an X chromosome gene, Kdm5c, is expressed at higher levels in females compared to males and correlates with adiposity in mice and humans. Kdm5c encodes a KDM5 histone demethylase that regulates gene expression by modulating histone methylation at gene promoters and enhancers. Here, we use chemical inhibition and genetic knockdown to identify a role for KDM5 activity during early stages of white and brown preadipocyte differentiation, with specific effects on white adipocyte clonal expansion, and white and brown adipocyte gene expression and mitochondrial activity. In white adipogenesis, KDM5 activity modulates H3K4 histone methylation at the Dlk1 gene promoter to repress gene expression and promote progression from preadipocytes to mature adipocytes. In brown adipogenesis, KDM5 activity modulates H3K4 methylation and gene expression of Ucp1, which is required for thermogenesis. Unbiased transcriptome analysis revealed that KDM5 activity regulates genes associated with cell cycle regulation and mitochondrial function, and this was confirmed by functional analyses of cell proliferation and cellular bioenergetics. Using genetic knockdown, we demonstrate that KDM5C is the likely KDM5 family member that is responsible for regulation of white and brown preadipocyte programming. Given that KDM5C levels are higher in females compared to males, our findings suggest that sex differences in white and brown preadipocyte gene regulation may contribute to sex differences in adipose tissue function.
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Affiliation(s)
- Laurent Vergnes
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Carrie B Wiese
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Temeka Zore
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Carrie Riestenberg
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Rozeta Avetisyan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Karen Reue
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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5
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Chen HL, Jin WL. Diapause-like Drug-Tolerant Persister State: The Key to Nirvana Rebirth. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:228. [PMID: 38399515 PMCID: PMC10890489 DOI: 10.3390/medicina60020228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024]
Abstract
Cancer is one of the leading causes of death in the world. Various drugs have been developed to eliminate it but to no avail because a tumor can go into dormancy to avoid therapy. In the past few decades, tumor dormancy has become a popular topic in cancer therapy. Recently, there has been an important breakthrough in the study of tumor dormancy. That is, cancer cells can enter a reversible drug-tolerant persister (DTP) state to avoid therapy, but no exact mechanism has been found. The study of the link between the DTP state and diapause seems to provide an opportunity for a correct understanding of the mechanism of the DTP state. Completely treating cancer and avoiding dormancy by targeting the expression of key genes in diapause are possible. This review delves into the characteristics of the DTP state and its connection with embryonic diapause, and possible treatment strategies are summarized. The authors believe that this review will promote the development of cancer therapy.
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Affiliation(s)
- Han-Lin Chen
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China;
- Institute of Cancer Neuroscience, Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Wei-Lin Jin
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China;
- Institute of Cancer Neuroscience, Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou 730000, China
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6
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Corner TP, Teo RZR, Wu Y, Salah E, Nakashima Y, Fiorini G, Tumber A, Brasnett A, Holt-Martyn JP, Figg WD, Zhang X, Brewitz L, Schofield CJ. Structure-guided optimisation of N-hydroxythiazole-derived inhibitors of factor inhibiting hypoxia-inducible factor-α. Chem Sci 2023; 14:12098-12120. [PMID: 37969593 PMCID: PMC10631261 DOI: 10.1039/d3sc04253g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023] Open
Abstract
The human 2-oxoglutarate (2OG)- and Fe(ii)-dependent oxygenases factor inhibiting hypoxia-inducible factor-α (FIH) and HIF-α prolyl residue hydroxylases 1-3 (PHD1-3) regulate the response to hypoxia in humans via catalysing hydroxylation of the α-subunits of the hypoxia-inducible factors (HIFs). Small-molecule PHD inhibitors are used for anaemia treatment; by contrast, few selective inhibitors of FIH have been reported, despite their potential to regulate the hypoxic response, either alone or in combination with PHD inhibition. We report molecular, biophysical, and cellular evidence that the N-hydroxythiazole scaffold, reported to inhibit PHD2, is a useful broad spectrum 2OG oxygenase inhibitor scaffold, the inhibition potential of which can be tuned to achieve selective FIH inhibition. Structure-guided optimisation resulted in the discovery of N-hydroxythiazole derivatives that manifest substantially improved selectivity for FIH inhibition over PHD2 and other 2OG oxygenases, including Jumonji-C domain-containing protein 5 (∼25-fold), aspartate/asparagine-β-hydroxylase (>100-fold) and histone Nε-lysine demethylase 4A (>300-fold). The optimised N-hydroxythiazole-based FIH inhibitors modulate the expression of FIH-dependent HIF target genes and, consistent with reports that FIH regulates cellular metabolism, suppressed lipid accumulation in adipocytes. Crystallographic studies reveal that the N-hydroxythiazole derivatives compete with both 2OG and the substrate for binding to the FIH active site. Derivatisation of the N-hydroxythiazole scaffold has the potential to afford selective inhibitors for 2OG oxygenases other than FIH.
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Affiliation(s)
- Thomas P Corner
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Ryan Z R Teo
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Yue Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization and Department of Chemistry, China Pharmaceutical University Nanjing 211198 China
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Yu Nakashima
- Institute of Natural Medicine, University of Toyama 2630-Sugitani 930-0194 Toyama Japan
| | - Giorgia Fiorini
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Amelia Brasnett
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - James P Holt-Martyn
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - William D Figg
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Xiaojin Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization and Department of Chemistry, China Pharmaceutical University Nanjing 211198 China
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
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7
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Srivastava R, Singh R, Jauhari S, Lodhi N, Srivastava R. Histone Demethylase Modulation: Epigenetic Strategy to Combat Cancer Progression. EPIGENOMES 2023; 7:epigenomes7020010. [PMID: 37218871 DOI: 10.3390/epigenomes7020010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Epigenetic modifications are heritable, reversible changes in histones or the DNA that control gene functions, being exogenous to the genomic sequence itself. Human diseases, particularly cancer, are frequently connected to epigenetic dysregulations. One of them is histone methylation, which is a dynamically reversible and synchronously regulated process that orchestrates the three-dimensional epigenome, nuclear processes of transcription, DNA repair, cell cycle, and epigenetic functions, by adding or removing methylation groups to histones. Over the past few years, reversible histone methylation has become recognized as a crucial regulatory mechanism for the epigenome. With the development of numerous medications that target epigenetic regulators, epigenome-targeted therapy has been used in the treatment of malignancies and has shown meaningful therapeutic potential in preclinical and clinical trials. The present review focuses on the recent advances in our knowledge on the role of histone demethylases in tumor development and modulation, in emphasizing molecular mechanisms that control cancer cell progression. Finally, we emphasize current developments in the advent of new molecular inhibitors that target histone demethylases to regulate cancer progression.
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Affiliation(s)
- Rashmi Srivastava
- Department of Zoology, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, Uttar Pradesh, India
| | - Rubi Singh
- Department of Hematology, Bioreference Laboratories, Elmwood Park, NJ 07407, USA
| | - Shaurya Jauhari
- Division of Education, Training, and Assessment, Global Education Center, Infosys Limited, Mysuru 570027, Karnataka, India
| | - Niraj Lodhi
- Clinical Research (Research and Development Division) Mirna Analytics LLC, Harlem Bio-Space, New York, NY 10027, USA
| | - Rakesh Srivastava
- Molecular Biology and Microbiology, GenTox Research and Development, Lucknow 226001, Uttar Pradesh, India
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8
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Skouras P, Markouli M, Strepkos D, Piperi C. Advances on Epigenetic Drugs for Pediatric Brain Tumors. Curr Neuropharmacol 2023; 21:1519-1535. [PMID: 36154607 PMCID: PMC10472812 DOI: 10.2174/1570159x20666220922150456] [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: 05/17/2022] [Revised: 08/14/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
Pediatric malignant brain tumors represent the most frequent cause of cancer-related deaths in childhood. The therapeutic scheme of surgery, radiotherapy and chemotherapy has improved patient management, but with minimal progress in patients' prognosis. Emerging molecular targets and mechanisms have revealed novel approaches for pediatric brain tumor therapy, enabling personalized medical treatment. Advances in the field of epigenetic research and their interplay with genetic changes have enriched our knowledge of the molecular heterogeneity of these neoplasms and have revealed important genes that affect crucial signaling pathways involved in tumor progression. The great potential of epigenetic therapy lies mainly in the widespread location and the reversibility of epigenetic alterations, proposing a wide range of targeting options, including the possible combination of chemoand immunotherapy, significantly increasing their efficacy. Epigenetic drugs, including inhibitors of DNA methyltransferases, histone deacetylases and demethylases, are currently being tested in clinical trials on pediatric brain tumors. Additional novel epigenetic drugs include protein and enzyme inhibitors that modulate epigenetic modification pathways, such as Bromodomain and Extraterminal (BET) proteins, Cyclin-Dependent Kinase 9 (CDK9), AXL, Facilitates Chromatin Transcription (FACT), BMI1, and CREB Binding Protein (CBP) inhibitors, which can be used either as standalone or in combination with current treatment approaches. In this review, we discuss recent progress on epigenetic drugs that could possibly be used against the most common malignant tumors of childhood, such as medulloblastomas, high-grade gliomas and ependymomas.
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Affiliation(s)
- Panagiotis Skouras
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Mariam Markouli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Strepkos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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9
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Němec V, Schwalm MP, Müller S, Knapp S. PROTAC degraders as chemical probes for studying target biology and target validation. Chem Soc Rev 2022; 51:7971-7993. [PMID: 36004812 DOI: 10.1039/d2cs00478j] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecule degraders such as PROTACs (PROteolysis TArgeting Chimeras) have emerged as new promising pharmacological modalities and the first PROTAC drug candidates are now studied clinically. The catalytic properties of PROTACs, acting as chemical degraders of a protein of interest (POI), represent an attractive new strategy for drug development. The development and characterization of PROTACs requires an array of additional assay systems that track the degradation pathway leading ultimately to degradation of the POI, identifying critical steps for PROTAC optimization. In addition to their exciting translational potential, PROTACs represent versatile chemical tools that considerably expanded our chemical biology toolbox and significantly enlarged the proteome that can be modulated by small molecules. Similar to conventional chemical probes, PROTACs used as chemical probes in target validation require comprehensive characterization. As a consequence, PROTAC-specific quality criteria should be defined by the chemical biology community. These criteria need to comprise additional or alternative parameters compared to those for conventional occupancy-driven chemical probes, such as the maximum level of target degradation (Dmax), confirmation of a proteasome dependent degradation mechanism and, importantly, also kinetic parameters of POI degradation. The kinetic aspects are particularly relevant for PROTACs that harbor covalent binding moieties. Here, we review recent progress in the development of assay systems for PROTAC characterization and suggest a set of criteria for PROTACs as high quality chemical probes.
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Affiliation(s)
- Václav Němec
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK site Frankfurt-Mainz, 69120 Heidelberg, Germany
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10
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Varghese B, Del Gaudio N, Cobellis G, Altucci L, Nebbioso A. KDM4 Involvement in Breast Cancer and Possible Therapeutic Approaches. Front Oncol 2021; 11:750315. [PMID: 34778065 PMCID: PMC8581295 DOI: 10.3389/fonc.2021.750315] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) is the second leading cause of cancer death in women, although recent scientific and technological achievements have led to significant improvements in progression-free disease and overall survival of patients. Genetic mutations and epigenetic modifications play a critical role in deregulating gene expression, leading to uncontrolled cell proliferation and cancer progression. Aberrant histone modifications are one of the most frequent epigenetic mechanisms occurring in cancer. In particular, methylation and demethylation of specific lysine residues alter gene accessibility via histone lysine methyltransferases (KMTs) and histone lysine demethylases (KDMs). The KDM family includes more than 30 members, grouped into six subfamilies and two classes based on their sequency homology and catalytic mechanisms, respectively. Specifically, the KDM4 gene family comprises six members, KDM4A-F, which are associated with oncogene activation, tumor suppressor silencing, alteration of hormone receptor downstream signaling, and chromosomal instability. Blocking the activity of KDM4 enzymes renders them "druggable" targets with therapeutic effects. Several KDM4 inhibitors have already been identified as anticancer drugs in vitro in BC cells. However, no KDM4 inhibitors have as yet entered clinical trials due to a number of issues, including structural similarities between KDM4 members and conservation of the active domain, which makes the discovery of selective inhibitors challenging. Here, we summarize our current knowledge of the molecular functions of KDM4 members in BC, describe currently available KDM4 inhibitors, and discuss their potential use in BC therapy.
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Affiliation(s)
- Benluvankar Varghese
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Nunzio Del Gaudio
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Gilda Cobellis
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy.,Biogem Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
| | - Angela Nebbioso
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy.,Saint Camillus International University of Health and Medical Sciences, Rome, Italy
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11
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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12
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Siklos M, Kubicek S. Therapeutic targeting of chromatin: status and opportunities. FEBS J 2021; 289:1276-1301. [PMID: 33982887 DOI: 10.1111/febs.15966] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/25/2021] [Accepted: 05/10/2021] [Indexed: 12/13/2022]
Abstract
The molecular characterization of mechanisms underlying transcriptional control and epigenetic inheritance since the 1990s has paved the way for the development of targeted therapies that modulate these pathways. In the past two decades, cancer genome sequencing approaches have uncovered a plethora of mutations in chromatin modifying enzymes across tumor types, and systematic genetic screens have identified many of these proteins as specific vulnerabilities in certain cancers. Now is the time when many of these basic and translational efforts start to bear fruit and more and more chromatin-targeting drugs are entering the clinic. At the same time, novel pharmacological approaches harbor the potential to modulate chromatin in unprecedented fashion, thus generating entirely novel opportunities. Here, we review the current status of chromatin targets in oncology and describe a vision for the epigenome-modulating drugs of the future.
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Affiliation(s)
- Marton Siklos
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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13
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Neganova ME, Klochkov SG, Aleksandrova YR, Aliev G. Histone modifications in epigenetic regulation of cancer: Perspectives and achieved progress. Semin Cancer Biol 2020; 83:452-471. [PMID: 32814115 DOI: 10.1016/j.semcancer.2020.07.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
Epigenetic changes associated with histone modifications play an important role in the emergence and maintenance of the phenotype of various cancer types. In contrast to direct mutations in the main DNA sequence, these changes are reversible, which makes the development of inhibitors of enzymes of post-translational histone modifications one of the most promising strategies for the creation of anticancer drugs. To date, a wide variety of histone modifications have been found that play an important role in the regulation of chromatin state, gene expression, and other nuclear events. This review examines the main features of the most common and studied epigenetic histone modifications with a proven role in the pathogenesis of a wide range of malignant neoplasms: acetylation / deacetylation and methylation / demethylation of histone proteins, as well as the role of enzymes of the HAT / HDAC and HMT / HDMT families in the development of oncological pathologies. The data on the relationship between histone modifications and certain types of cancer are presented and discussed. Special attention is devoted to the consideration of various strategies for the development of epigenetic inhibitors. The main directions of the development of inhibitors of histone modifications are analyzed and effective strategies for their creation are identified and discussed. The most promising strategy is the use of multitarget drugs, which will affect multiple molecular targets of cancer. A critical analysis of the current status of approved epigenetic anticancer drugs has also been performed.
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Affiliation(s)
- Margarita E Neganova
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Sergey G Klochkov
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Yulia R Aleksandrova
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Gjumrakch Aliev
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation.,I. M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Str., Moscow, 119991, Russian Federation.,Laboratory of Cellular Pathology, Federal State Budgetary Institution «Research Institute of Human Morphology», 3, Tsyurupy Str., Moscow, 117418, Russian Federation.,GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX, 78229, USA.
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14
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Tricarico R, Nicolas E, Hall MJ, Golemis EA. X- and Y-Linked Chromatin-Modifying Genes as Regulators of Sex-Specific Cancer Incidence and Prognosis. Clin Cancer Res 2020; 26:5567-5578. [PMID: 32732223 DOI: 10.1158/1078-0432.ccr-20-1741] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/24/2020] [Accepted: 07/27/2020] [Indexed: 12/15/2022]
Abstract
Biological sex profoundly conditions organismal development and physiology, imposing wide-ranging effects on cell signaling, metabolism, and immune response. These effects arise from sex-specified differences in hormonal exposure, and from intrinsic genetic and epigenetic differences associated with the presence of an XX versus XY chromosomal complement. In addition, biological sex is now recognized to be a determinant of the incidence, presentation, and therapeutic response of multiple forms of cancer, including cancers not specifically associated with male or female anatomy. Although multiple factors contribute to sex-based differences in cancer, a growing body of research emphasizes a role for differential activity of X- and Y-linked tumor-suppressor genes in males and females. Among these, the X-linked KDM6A/UTX and KDM5C/JARID1C/SMCX, and their Y-linked paralogs UTY/KDM6C and KDM5D/JARID1D/SMCY encode lysine demethylases. These epigenetic modulators profoundly influence gene expression, based on enzymatic activity in demethylating H3K27me3 and H3K4me3, and nonenzymatic scaffolding roles for large complexes that open and close chromatin for transcription. In a growing number of cases, mutations affecting these proteins have been recognized to strongly influence cancer risk, prognosis, and response to specific therapies. However, sex-specific patterns of mutation, expression, and activity of these genes, coupled with tissue-specific requirement for their function as tumor suppressors, together exemplify the complex relationship between sex and cancer vulnerabilities. In this review, we summarize and discuss the current state of the literature on the roles of these proteins in contributing to sex bias in cancer, and the status of clinical agents relevant to their function.
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Affiliation(s)
- Rossella Tricarico
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania. .,Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Emmanuelle Nicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michael J Hall
- Cancer Prevention and Control Program, Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Erica A Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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15
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Dzobo K. Epigenomics-Guided Drug Development: Recent Advances in Solving the Cancer Treatment "jigsaw puzzle". OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 23:70-85. [PMID: 30767728 DOI: 10.1089/omi.2018.0206] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The human epigenome plays a key role in determining cellular identity and eventually function. Drug discovery undertakings have focused mainly on the role of genomics in carcinogenesis, with the focus turning to the epigenome recently. Drugs targeting DNA and histone modifications are under development with some such as 5-azacytidine, decitabine, vorinostat, and panobinostat already approved by the Food and Drug Administration (FDA) and the European Medicines Agency (EMA). This expert review offers a critical analysis of the epigenomics-guided drug discovery and development and the opportunities and challenges for the next decade. Importantly, the coupling of epigenetic editing techniques, such as clustered regularly interspersed short palindromic repeat (CRISPR)-CRISPR-associated protein-9 (Cas9) and APOBEC-coupled epigenetic sequencing (ACE-seq) with epigenetic drug screens, will allow the identification of small-molecule inhibitors or drugs able to reverse epigenetic changes responsible for many diseases. In addition, concrete and sustainable innovation in cancer treatment ought to integrate epigenome targeting drugs with classic therapies such as chemotherapy and immunotherapy.
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Affiliation(s)
- Kevin Dzobo
- 1 International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, South Africa.,2 Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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16
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Saraç H, Morova T, Pires E, McCullagh J, Kaplan A, Cingöz A, Bagci-Onder T, Önder T, Kawamura A, Lack NA. Systematic characterization of chromatin modifying enzymes identifies KDM3B as a critical regulator in castration resistant prostate cancer. Oncogene 2020; 39:2187-2201. [PMID: 31822799 PMCID: PMC7056651 DOI: 10.1038/s41388-019-1116-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 11/05/2019] [Accepted: 11/11/2019] [Indexed: 12/28/2022]
Abstract
Androgen deprivation therapy (ADT) is the standard care for prostate cancer (PCa) patients who fail surgery or radiotherapy. While initially effective, the cancer almost always recurs as a more aggressive castration resistant prostate cancer (CRPC). Previous studies have demonstrated that chromatin modifying enzymes can play a critical role in the conversion to CRPC. However, only a handful of these potential pharmacological targets have been tested. Therefore, in this study, we conducted a focused shRNA screen of chromatin modifying enzymes previously shown to be involved in cellular differentiation. We found that altering the balance between histone methylation and demethylation impacted growth and proliferation. Of all genes tested, KDM3B, a histone H3K9 demethylase, was found to have the most antiproliferative effect. These results were phenocopied with a KDM3B CRISPR/Cas9 knockout. When tested in several PCa cell lines, the decrease in proliferation was remarkably specific to androgen-independent cells. Genetic rescue experiments showed that only the enzymatically active KDM3B could recover the phenotype. Surprisingly, despite the decreased proliferation of androgen-independent cell no alterations in the cell cycle distribution were observed following KDM3B knockdown. Whole transcriptome analyses revealed changes in the gene expression profile following loss of KDM3B, including downregulation of metabolic enzymes such as ARG2 and RDH11. Metabolomic analysis of KDM3B knockout showed a decrease in several critical amino acids. Overall, our work reveals, for the first time, the specificity and the dependence of KDM3B in CRPC proliferation.
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Affiliation(s)
- Hilal Saraç
- School of Medicine, Koç University, Istanbul, 34450, Turkey
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Tunç Morova
- School of Medicine, Koç University, Istanbul, 34450, Turkey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, V6H 3Z6, Canada
| | - Elisabete Pires
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - James McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Anıl Kaplan
- School of Medicine, Koç University, Istanbul, 34450, Turkey
| | - Ahmet Cingöz
- School of Medicine, Koç University, Istanbul, 34450, Turkey
| | | | - Tamer Önder
- School of Medicine, Koç University, Istanbul, 34450, Turkey
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Nathan A Lack
- School of Medicine, Koç University, Istanbul, 34450, Turkey.
- Vancouver Prostate Centre, University of British Columbia, Vancouver, V6H 3Z6, Canada.
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17
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Abstract
Here we show that the histone demethylase JMJD2B is induced in endothelial cells by EndMT provoking stimuli and thereby contributes to the acquirement of a mesenchymal/smooth muscle phenotype. Silencing of JMJD2B inhibited EndMT in vitro and reduced the induction of EndMT after myocardial infarction in vivo. Inhibition of JMJD2B prevents the demethylation of repressive trimethylated histone H3 at lysine 9 (H3K9me3) at promoters of mesenchymal and EndMT-controlling genes, thereby reducing EndMT. Together, our study reports a crucial role for JMJD2B in controlling histone modifications during the transition of endothelial cells toward a mesenchymal phenotype. Endothelial cells play an important role in maintenance of the vascular system and the repair after injury. Under proinflammatory conditions, endothelial cells can acquire a mesenchymal phenotype by a process named endothelial-to-mesenchymal transition (EndMT), which affects the functional properties of endothelial cells. Here, we investigated the epigenetic control of EndMT. We show that the histone demethylase JMJD2B is induced by EndMT-promoting, proinflammatory, and hypoxic conditions. Silencing of JMJD2B reduced TGF-β2-induced expression of mesenchymal genes, prevented the alterations in endothelial morphology and impaired endothelial barrier function. Endothelial-specific deletion of JMJD2B in vivo confirmed a reduction of EndMT after myocardial infarction. EndMT did not affect global H3K9me3 levels but induced a site-specific reduction of repressive H3K9me3 marks at promoters of mesenchymal genes, such as Calponin (CNN1), and genes involved in TGF-β signaling, such as AKT Serine/Threonine Kinase 3 (AKT3) and Sulfatase 1 (SULF1). Silencing of JMJD2B prevented the EndMT-induced reduction of H3K9me3 marks at these promotors and further repressed these EndMT-related genes. Our study reveals that endothelial identity and function is critically controlled by the histone demethylase JMJD2B, which is induced by EndMT-promoting, proinflammatory, and hypoxic conditions, and supports the acquirement of a mesenchymal phenotype.
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18
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Montano MM, Yeh IJ, Chen Y, Hernandez C, Kiselar JG, de la Fuente M, Lawes AM, Nieman MT, Kiser PD, Jacobberger J, Exner AA, Lawes MC. Inhibition of the histone demethylase, KDM5B, directly induces re-expression of tumor suppressor protein HEXIM1 in cancer cells. Breast Cancer Res 2019; 21:138. [PMID: 31805991 PMCID: PMC6896798 DOI: 10.1186/s13058-019-1228-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/14/2019] [Indexed: 01/07/2023] Open
Abstract
Background The tumor suppressor actions of hexamethylene bis-acetamide (HMBA)-inducible protein 1 (HEXIM1) in the breast, prostate, melanomas, and AML have been reported by our group and others. Increased HEXIM1 expression caused differentiation and inhibited proliferation and metastasis of cancer cells. Historically, HEXIM1 has been experimentally induced with the hybrid polar compound HMBA, but HMBA is a poor clinical candidate due to lack of a known target, poor pharmacological properties, and unfavorable ADMETox characteristics. Thus, HEXIM1 induction is an intriguing therapeutic approach to cancer treatment, but requires better chemical tools than HMBA. Methods We identified and verified KDM5B as a target of HEXIM1 inducers using a chemical proteomics approach, biotin–NeutrAvidin pull-down assays, surface plasmon resonance, and molecular docking. The regulation of HEXIM1 by KDM5B and KDM5B inhibitors was assessed using chromatin immunoprecipitation assays, RT-PCR, western blotting, and depletion of KDM5B with shRNAs. The regulation of breast cancer cell phenotype by KDM5B inhibitors was assessed using western blots, differentiation assays, proliferation assays, and a mouse model of breast cancer metastasis. The relative role of HEXIM1 in the action of KDM5B inhibitors was determined by depleting HEXIM1 using shRNAs followed by western blots, differentiation assays, and proliferation assays. Results We have identified a highly druggable target, KDM5B, which is inhibited by small molecule inducers of HEXIM1. RNAi knockdown of KDM5B induced HEXIM1 expression, thus validating the specific negative regulation of tumor suppressor HEXIM1 by the H3K4me3/2 demethylase KDM5B. Known inhibitors of KDM5B were also able to induce HEXIM1 expression, inhibit cell proliferation, induce differentiation, potentiate sensitivity to cancer chemotherapy, and inhibit breast tumor metastasis. Conclusion HMBA and 4a1 induce HEXIM1 expression by inhibiting KDM5B. Upregulation of HEXIM1 expression levels plays a critical role in the inhibition of proliferation of breast cancer cells using KDM5B inhibitors. Based on the novel molecular scaffolds that we identified which more potently induced HEXIM1 expression and data in support that KDM5B is a target of these compounds, we have opened up new lead discovery and optimization directions.
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Affiliation(s)
- Monica M Montano
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA. .,Oncostatyx, 11000 Cedar Avenue Suite 26, Cleveland, OH, 44106, USA.
| | - I-Ju Yeh
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Yinghua Chen
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Chris Hernandez
- General Medical Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Janna G Kiselar
- Department of Radiology, and Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Maria de la Fuente
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Adriane M Lawes
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Marvin T Nieman
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Philip D Kiser
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - James Jacobberger
- General Medical Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Agata A Exner
- Department of Radiology, and Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Matthew C Lawes
- Oncostatyx, 11000 Cedar Avenue Suite 26, Cleveland, OH, 44106, USA
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19
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Le Bihan YV, Lanigan RM, Atrash B, McLaughlin MG, Velupillai S, Malcolm AG, England KS, Ruda GF, Mok NY, Tumber A, Tomlin K, Saville H, Shehu E, McAndrew C, Carmichael L, Bennett JM, Jeganathan F, Eve P, Donovan A, Hayes A, Wood F, Raynaud FI, Fedorov O, Brennan PE, Burke R, van Montfort RLM, Rossanese OW, Blagg J, Bavetsias V. C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur J Med Chem 2019; 177:316-337. [PMID: 31158747 PMCID: PMC6580095 DOI: 10.1016/j.ejmech.2019.05.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 12/25/2022]
Abstract
Residues in the histone substrate binding sites that differ between the KDM4 and KDM5 subfamilies were identified. Subsequently, a C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one series was designed to rationally exploit these residue differences between the histone substrate binding sites in order to improve affinity for the KDM4-subfamily over KDM5-subfamily enzymes. In particular, residues E169 and V313 (KDM4A numbering) were targeted. Additionally, conformational restriction of the flexible pyridopyrimidinone C8-substituent was investigated. These approaches yielded potent and cell-penetrant dual KDM4/5-subfamily inhibitors including 19a (KDM4A and KDM5B Ki = 0.004 and 0.007 μM, respectively). Compound cellular profiling in two orthogonal target engagement assays revealed a significant reduction from biochemical to cell-based activity across multiple analogues; this decrease was shown to be consistent with 2OG competition, and suggests that sub-nanomolar biochemical potency will be required with C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one compounds to achieve sub-micromolar target inhibition in cells.
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Affiliation(s)
- Yann-Vaï Le Bihan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Rachel M Lanigan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Butrus Atrash
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Mark G McLaughlin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Srikannathasan Velupillai
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Andrew G Malcolm
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Katherine S England
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Gian Filippo Ruda
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - N Yi Mok
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Anthony Tumber
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Kathy Tomlin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Harry Saville
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Erald Shehu
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Craig McAndrew
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - LeAnne Carmichael
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - James M Bennett
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Fiona Jeganathan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Paul Eve
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Adam Donovan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Angela Hayes
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Francesca Wood
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Florence I Raynaud
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Oleg Fedorov
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Paul E Brennan
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Rosemary Burke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Rob L M van Montfort
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Olivia W Rossanese
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
| | - Vassilios Bavetsias
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
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20
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Kumar R, Paul AM, Rameshwar P, Pillai MR. Epigenetic Dysregulation at the Crossroad of Women's Cancer. Cancers (Basel) 2019; 11:cancers11081193. [PMID: 31426393 PMCID: PMC6721458 DOI: 10.3390/cancers11081193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
An increasingly number of women of all age groups are affected by cancer, despite substantial progress in our understanding of cancer pathobiology, the underlying genomic alterations and signaling cascades, and cellular-environmental interactions. Though our understanding of women’s cancer is far more complete than ever before, there is no comprehensive model to explain the reasons behind the increased incidents of certain reproductive cancer among older as well as younger women. It is generally suspected that environmental and life-style factors affecting hormonal and growth control pathways might help account for the rise of women’s cancers in younger age, as well, via epigenetic mechanisms. Epigenetic regulators play an important role in orchestrating an orderly coordination of cellular signals in gene activity in response to upstream signaling and/or epigenetic modifiers present in a dynamic extracellular milieu. Here we will discuss the broad principles of epigenetic regulation of DNA methylation and demethylation, histone acetylation and deacetylation, and RNA methylation in women’s cancers in the context of gene expression, hormonal action, and the EGFR family of cell surface receptor tyrosine kinases. We anticipate that a better understanding of the epigenetics of women’s cancers may provide new regulatory leads and further fuel the development of new epigenetic biomarkers and therapeutic approaches.
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Affiliation(s)
- Rakesh Kumar
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India.
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA.
| | - Aswathy Mary Paul
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
- Graduate Degree Program, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Pranela Rameshwar
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - M Radhakrishna Pillai
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
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21
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Bayo J, Fiore EJ, Dominguez LM, Real A, Malvicini M, Rizzo M, Atorrasagasti C, García MG, Argemi J, Martinez ED, Mazzolini GD. A comprehensive study of epigenetic alterations in hepatocellular carcinoma identifies potential therapeutic targets. J Hepatol 2019; 71:78-90. [PMID: 30880225 DOI: 10.1016/j.jhep.2019.03.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 02/26/2019] [Accepted: 03/06/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND & AIMS A causal link has recently been established between epigenetic alterations and hepatocarcinogenesis, indicating that epigenetic inhibition may have therapeutic potential. We aimed to identify and target epigenetic modifiers that show molecular alterations in hepatocellular carcinoma (HCC). METHODS We studied the molecular-clinical correlations of epigenetic modifiers including bromodomains, histone acetyltransferases, lysine methyltransferases and lysine demethylases in HCC using The Cancer Genome Atlas (TCGA) data of 365 patients with HCC. The therapeutic potential of epigenetic inhibitors was evaluated in vitro and in vivo. RNA sequencing analysis and its correlation with expression and clinical data in the TCGA dataset were used to identify expression programs normalized by Jumonji lysine demethylase (JmjC) inhibitors. RESULTS Genetic alterations, aberrant expression, and correlation between tumor expression and poor patient prognosis of epigenetic enzymes are common events in HCC. Epigenetic inhibitors that target bromodomain (JQ-1), lysine methyltransferases (BIX-1294 and LLY-507) and JmjC lysine demethylases (JIB-04, GSK-J4 and SD-70) reduce HCC aggressiveness. The pan-JmjC inhibitor JIB-04 had a potent antitumor effect in tumor bearing mice. HCC cells treated with JmjC inhibitors showed overlapping changes in expression programs related with inhibition of cell proliferation and induction of cell death. JmjC inhibition reverses an aggressive HCC gene expression program that is also altered in patients with HCC. Several genes downregulated by JmjC inhibitors are highly expressed in tumor vs. non-tumor parenchyma, and their high expression correlates with a poor prognosis. We identified and validated a 4-gene expression prognostic signature consisting of CENPA, KIF20A, PLK1, and NCAPG. CONCLUSIONS The epigenetic alterations identified in HCC can be used to predict prognosis and to define a subgroup of high-risk patients that would potentially benefit from JmjC inhibitor therapy. LAY SUMMARY In this study, we found that mutations and changes in expression of epigenetic modifiers are common events in human hepatocellular carcinoma, leading to an aggressive gene expression program and poor clinical prognosis. The transcriptional program can be reversed by pharmacological inhibition of Jumonji enzymes. This inhibition blocks hepatocellular carcinoma progression, providing a novel potential therapeutic strategy.
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Affiliation(s)
- Juan Bayo
- Gene Therapy Laboratory, Instituto de Investigaciones en Medicina Traslacional, Facultad de Ciencias Biomédicas, CONICET, Universidad Austral, Derqui-Pilar, Argentina
| | - Esteban J Fiore
- Gene Therapy Laboratory, Instituto de Investigaciones en Medicina Traslacional, Facultad de Ciencias Biomédicas, CONICET, Universidad Austral, Derqui-Pilar, Argentina
| | - Luciana M Dominguez
- Gene Therapy Laboratory, Instituto de Investigaciones en Medicina Traslacional, Facultad de Ciencias Biomédicas, CONICET, Universidad Austral, Derqui-Pilar, Argentina
| | - Alejandrina Real
- Gene Therapy Laboratory, Instituto de Investigaciones en Medicina Traslacional, Facultad de Ciencias Biomédicas, CONICET, Universidad Austral, Derqui-Pilar, Argentina
| | - Mariana Malvicini
- Gene Therapy Laboratory, Instituto de Investigaciones en Medicina Traslacional, Facultad de Ciencias Biomédicas, CONICET, Universidad Austral, Derqui-Pilar, Argentina
| | - Manglio Rizzo
- Gene Therapy Laboratory, Instituto de Investigaciones en Medicina Traslacional, Facultad de Ciencias Biomédicas, CONICET, Universidad Austral, Derqui-Pilar, Argentina
| | - Catalina Atorrasagasti
- Gene Therapy Laboratory, Instituto de Investigaciones en Medicina Traslacional, Facultad de Ciencias Biomédicas, CONICET, Universidad Austral, Derqui-Pilar, Argentina
| | - Mariana G García
- Gene Therapy Laboratory, Instituto de Investigaciones en Medicina Traslacional, Facultad de Ciencias Biomédicas, CONICET, Universidad Austral, Derqui-Pilar, Argentina
| | - Josepmaria Argemi
- Center for Liver Diseases, Pittsburgh Research Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Elisabeth D Martinez
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Guillermo D Mazzolini
- Gene Therapy Laboratory, Instituto de Investigaciones en Medicina Traslacional, Facultad de Ciencias Biomédicas, CONICET, Universidad Austral, Derqui-Pilar, Argentina; Liver Unit, Hospital Universitario Austral, Derqui-Pilar, Argentina.
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22
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Pippa S, Mannironi C, Licursi V, Bombardi L, Colotti G, Cundari E, Mollica A, Coluccia A, Naccarato V, La Regina G, Silvestri R, Negri R. Small Molecule Inhibitors of KDM5 Histone Demethylases Increase the Radiosensitivity of Breast Cancer Cells Overexpressing JARID1B. Molecules 2019; 24:molecules24091739. [PMID: 31060229 PMCID: PMC6540222 DOI: 10.3390/molecules24091739] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/24/2019] [Accepted: 05/01/2019] [Indexed: 12/18/2022] Open
Abstract
Background: KDM5 enzymes are H3K4 specific histone demethylases involved in transcriptional regulation and DNA repair. These proteins are overexpressed in different kinds of cancer, including breast, prostate and bladder carcinomas, with positive effects on cancer proliferation and chemoresistance. For these reasons, these enzymes are potential therapeutic targets. Methods: In the present study, we analyzed the effects of three different inhibitors of KDM5 enzymes in MCF-7 breast cancer cells over-expressing one of them, namely KDM5B/JARID1B. In particular we tested H3K4 demethylation (western blot); radio-sensitivity (cytoxicity and clonogenic assays) and damage accumulation (COMET assay and kinetics of H2AX phosphorylation). Results: we show that all three compounds with completely different chemical structures can selectively inhibit KDM5 enzymes and are capable of increasing sensitivity of breast cancer cells to ionizing radiation and radiation-induced damage. Conclusions: These findings confirm the involvement of H3K4 specific demethylases in the response to DNA damage, show a requirement of the catalytic function and suggest new strategies for the therapeutic use of their inhibitors.
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Affiliation(s)
- Simone Pippa
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Cecilia Mannironi
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Valerio Licursi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
- Institute for Systems Analysis and Computer Science "A. Ruberti", Italian National Research Council, 00185 Rome, Italy.
| | - Luca Bombardi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Enrico Cundari
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Adriano Mollica
- Department of Pharmacy, University "G. d' Annunzio" of Chieti, Via dei Vestini 31, 66100 Chieti, Italy.
| | - Antonio Coluccia
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Valentina Naccarato
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Giuseppe La Regina
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Romano Silvestri
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
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23
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Targeting epigenetic modifications in cancer therapy: erasing the roadmap to cancer. Nat Med 2019; 25:403-418. [PMID: 30842676 DOI: 10.1038/s41591-019-0376-8] [Citation(s) in RCA: 255] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 01/25/2019] [Indexed: 12/31/2022]
Abstract
Epigenetic dysregulation is a common feature of most cancers, often occurring directly through alteration of epigenetic machinery. Over the last several years, a new generation of drugs directed at epigenetic modulators have entered clinical development, and results from these trials are now being disclosed. Unlike first-generation epigenetic therapies, these new agents are selective, and many are targeted to proteins which are mutated or translocated in cancer. This review will provide a summary of the epigenetic modulatory agents currently in clinical development and discuss the opportunities and challenges in their development. As these drugs advance in the clinic, drug discovery has continued with a focus on both novel and existing epigenetic targets. We will provide an overview of these efforts and the strategies being employed.
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24
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Miyake Y, Itoh Y, Hatanaka A, Suzuma Y, Suzuki M, Kodama H, Arai Y, Suzuki T. Identification of novel lysine demethylase 5-selective inhibitors by inhibitor-based fragment merging strategy. Bioorg Med Chem 2019; 27:1119-1129. [DOI: 10.1016/j.bmc.2019.02.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 01/23/2019] [Accepted: 02/01/2019] [Indexed: 12/13/2022]
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25
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Wilson C, Krieg AJ. KDM4B: A Nail for Every Hammer? Genes (Basel) 2019; 10:E134. [PMID: 30759871 PMCID: PMC6410163 DOI: 10.3390/genes10020134] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/05/2019] [Accepted: 02/07/2019] [Indexed: 01/01/2023] Open
Abstract
Epigenetic changes are well-established contributors to cancer progression and normal developmental processes. The reversible modification of histones plays a central role in regulating the nuclear processes of gene transcription, DNA replication, and DNA repair. The KDM4 family of Jumonj domain histone demethylases specifically target di- and tri-methylated lysine 9 on histone H3 (H3K9me3), removing a modification central to defining heterochromatin and gene repression. KDM4 enzymes are generally over-expressed in cancers, making them compelling targets for study and therapeutic inhibition. One of these family members, KDM4B, is especially interesting due to its regulation by multiple cellular stimuli, including DNA damage, steroid hormones, and hypoxia. In this review, we discuss what is known about the regulation of KDM4B in response to the cellular environment, and how this context-dependent expression may be translated into specific biological consequences in cancer and reproductive biology.
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Affiliation(s)
- Cailin Wilson
- Department of Pathology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Adam J Krieg
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR 97239, USA.
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, OR 97006, USA.
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26
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Vazquez‐Rodriguez S, Wright M, Rogers CM, Cribbs AP, Velupillai S, Philpott M, Lee H, Dunford JE, Huber KVM, Robers MB, Vasta JD, Thezenas M, Bonham S, Kessler B, Bennett J, Fedorov O, Raynaud F, Donovan A, Blagg J, Bavetsias V, Oppermann U, Bountra C, Kawamura A, Brennan PE. Design, Synthesis and Characterization of Covalent KDM5 Inhibitors. Angew Chem Int Ed Engl 2019; 58:515-519. [PMID: 30431220 PMCID: PMC6391970 DOI: 10.1002/anie.201810179] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/30/2018] [Indexed: 01/05/2023]
Abstract
Histone lysine demethylases (KDMs) are involved in the dynamic regulation of gene expression and they play a critical role in several biological processes. Achieving selectivity over the different KDMs has been a major challenge for KDM inhibitor development. Here we report potent and selective KDM5 covalent inhibitors designed to target cysteine residues only present in the KDM5 sub-family. The covalent binding to the targeted proteins was confirmed by MS and time-dependent inhibition. Additional competition assays show that compounds were non 2-OG competitive. Target engagement and ChIP-seq analysis showed that the compounds inhibited the KDM5 members in cells at nano- to micromolar levels and induce a global increase of the H3K4me3 mark at transcriptional start sites.
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Affiliation(s)
- Saleta Vazquez‐Rodriguez
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | - Miranda Wright
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Catherine M. Rogers
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | - Adam P. Cribbs
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of OxfordOxfordOX3 7DQUK
| | - Srikannathasan Velupillai
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | - Martin Philpott
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of OxfordOxfordOX3 7DQUK
| | - Henry Lee
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of OxfordOxfordOX3 7DQUK
| | - James E. Dunford
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of OxfordOxfordOX3 7DQUK
| | - Kilian V. M. Huber
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | | | - James D. Vasta
- Promega Corporation2800 Woods Hollow RoadFitchburgWI53711USA
| | - Marie‐Laetitia Thezenas
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOX3 7FZOxfordUK
| | - Sarah Bonham
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOX3 7FZOxfordUK
| | - Benedikt Kessler
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOX3 7FZOxfordUK
| | - James Bennett
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | - Oleg Fedorov
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | - Florence Raynaud
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research15 Cotswold RoadLondonSM2 5NGUK
| | - Adam Donovan
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research15 Cotswold RoadLondonSM2 5NGUK
| | - Julian Blagg
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research15 Cotswold RoadLondonSM2 5NGUK
| | - Vassilios Bavetsias
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research15 Cotswold RoadLondonSM2 5NGUK
| | - Udo Oppermann
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of OxfordOxfordOX3 7DQUK
- FRIAS—Freiburg Institute of Advanced Studies79104FreiburgGermany
| | - Chas Bountra
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
| | - Akane Kawamura
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Paul E. Brennan
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7DQ and OX3 7FZUK
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27
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Ryan DG, Murphy MP, Frezza C, Prag HA, Chouchani ET, O'Neill LA, Mills EL. Coupling Krebs cycle metabolites to signalling in immunity and cancer. Nat Metab 2019; 1:16-33. [PMID: 31032474 PMCID: PMC6485344 DOI: 10.1038/s42255-018-0014-7] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Metabolic reprogramming has become a key focus for both immunologists and cancer biologists, with exciting advances providing new insights into underlying mechanisms of disease. Metabolites traditionally associated with bioenergetics or biosynthesis have been implicated in immunity and malignancy in transformed cells, with a particular focus on intermediates of the mitochondrial pathway known as the Krebs cycle. Among these, the intermediates succinate, fumarate, itaconate, 2-hydroxyglutarate isomers (D-2-hydroxyglutarate and L-2-hydroxyglutarate) and acetyl-CoA now have extensive evidence for "non-metabolic" signalling functions in both physiological immune contexts and in disease contexts, such as the initiation of carcinogenesis. This review will describe how metabolic reprogramming, with emphasis placed on these metabolites, leads to altered immune cell and transformed cell function. The latest findings are informative for new therapeutic approaches which could be transformative for a range of diseases.
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Affiliation(s)
- Dylan G Ryan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Hiran A Prag
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Edward T Chouchani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Luke A O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Evanna L Mills
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
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28
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Lysine demethylase 5B (KDM5B): A potential anti-cancer drug target. Eur J Med Chem 2019; 161:131-140. [DOI: 10.1016/j.ejmech.2018.10.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 12/12/2022]
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29
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Vazquez‐Rodriguez S, Wright M, Rogers CM, Cribbs AP, Velupillai S, Philpott M, Lee H, Dunford JE, Huber KVM, Robers MB, Vasta JD, Thezenas M, Bonham S, Kessler B, Bennett J, Fedorov O, Raynaud F, Donovan A, Blagg J, Bavetsias V, Oppermann U, Bountra C, Kawamura A, Brennan PE. Design, Synthesis and Characterization of Covalent KDM5 Inhibitors. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Saleta Vazquez‐Rodriguez
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Miranda Wright
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
- Chemistry Research LaboratoryUniversity of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Catherine M. Rogers
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Adam P. Cribbs
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of Oxford Oxford OX3 7DQ UK
| | - Srikannathasan Velupillai
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Martin Philpott
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of Oxford Oxford OX3 7DQ UK
| | - Henry Lee
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of Oxford Oxford OX3 7DQ UK
| | - James E. Dunford
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of Oxford Oxford OX3 7DQ UK
| | - Kilian V. M. Huber
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | | | - James D. Vasta
- Promega Corporation 2800 Woods Hollow Road Fitchburg WI 53711 USA
| | - Marie‐Laetitia Thezenas
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Roosevelt Drive OX3 7FZ Oxford UK
| | - Sarah Bonham
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Roosevelt Drive OX3 7FZ Oxford UK
| | - Benedikt Kessler
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Roosevelt Drive OX3 7FZ Oxford UK
| | - James Bennett
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Oleg Fedorov
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Florence Raynaud
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research 15 Cotswold Road London SM2 5NG UK
| | - Adam Donovan
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research 15 Cotswold Road London SM2 5NG UK
| | - Julian Blagg
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research 15 Cotswold Road London SM2 5NG UK
| | - Vassilios Bavetsias
- Cancer Research (UK) Cancer Therapeutics UnitThe Institute of Cancer Research 15 Cotswold Road London SM2 5NG UK
| | - Udo Oppermann
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
- Botnar Research CenterNuffield Department of OrthopedicsRheumatology and Musculoskeletal SciencesNIHR Oxford BRCUniversity of Oxford Oxford OX3 7DQ UK
- FRIAS—Freiburg Institute of Advanced Studies 79104 Freiburg Germany
| | - Chas Bountra
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Akane Kawamura
- Chemistry Research LaboratoryUniversity of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Paul E. Brennan
- Structural Genomics Consortium & Target Discovery InstituteUniversity of OxfordNDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
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30
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Guillade L, Sarno F, Tarhonskaya H, Nebbioso A, Alvarez S, Kawamura A, Schofield CJ, Altucci L, de Lera ÁR. Synthesis and Biological Evaluation of Tripartin, a Putative KDM4 Natural Product Inhibitor, and 1-Dichloromethylinden-1-ol Analogues. ChemMedChem 2018; 13:1949-1956. [PMID: 30047603 DOI: 10.1002/cmdc.201800377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/19/2018] [Indexed: 12/17/2022]
Abstract
The natural product tripartin has been reported to inhibit the N-methyl-lysine histone demethylase KDM4A. A synthesis of tripartin starting from 3,5-dimethoxyphenylacrylic acid was developed, and the enantiomers were separated by chiral HPLC. We observed that both tripartin enantiomers manifested an apparent increase in H3K9me3 levels when dosed in cells, as measured by western blot analysis. Thus, there is no enantiomeric discrimination toward this natural product in terms of its effects on cellular histone methylation status. Interestingly, tripartin did not inhibit isolated KDM4A-E under our assay conditions (IC50 >100 μm). Tripartin analogues with a dichloromethylcarbinol group derived from the indanone scaffold were synthesized and found to be inactive against isolated recombinant KDM4 enzymes and in cell-based assays. Although the precise cellular mode of action of tripartin is unclear, our evidence suggests that it may affect histone methylation status via a mechanism other than direct inhibition of the KDM4 histone demethylases.
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Affiliation(s)
- Lucía Guillade
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IBIV, Universidade de Vigo, Campus As Lagoas-Marcosende, 36310, Vigo, Spain
| | - Federica Sarno
- Università degli Studi della Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Hanna Tarhonskaya
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Angela Nebbioso
- Università degli Studi della Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Susana Alvarez
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IBIV, Universidade de Vigo, Campus As Lagoas-Marcosende, 36310, Vigo, Spain
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Lucia Altucci
- Università degli Studi della Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Ángel R de Lera
- Departamento de Química Orgánica, Facultade de Química, CINBIO and IBIV, Universidade de Vigo, Campus As Lagoas-Marcosende, 36310, Vigo, Spain
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Lin H, Li Q, Li Q, Zhu J, Gu K, Jiang X, Hu Q, Feng F, Qu W, Chen Y, Sun H. Small molecule KDM4s inhibitors as anti-cancer agents. J Enzyme Inhib Med Chem 2018; 33:777-793. [PMID: 29651880 PMCID: PMC6010108 DOI: 10.1080/14756366.2018.1455676] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Histone demethylation is a vital process in epigenetic regulation of gene expression. A number of histone demethylases are present to control the methylated states of histone. Among these enzymes, KDM4s are one subfamily of JmjC KDMs and play important roles in both normal and cancer cells. The discovery of KDM4s inhibitors is a potential therapeutic strategy against different diseases including cancer. Here, we summarize the development of KDM4s inhibitors and some related pharmaceutical information to provide an update of recent progress in KDM4s inhibitors.
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Affiliation(s)
- Hongzhi Lin
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qihang Li
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qi Li
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Jie Zhu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Kai Gu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Xueyang Jiang
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qianqian Hu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Feng Feng
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Wei Qu
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Yao Chen
- c School of Pharmacy , Nanjing University of Chinese Medicine , Nanjing , China
| | - Haopeng Sun
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
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Levin M, Stark M, Assaraf YG. The JmjN domain as a dimerization interface and a targeted inhibitor of KDM4 demethylase activity. Oncotarget 2018; 9:16861-16882. [PMID: 29682190 PMCID: PMC5908291 DOI: 10.18632/oncotarget.24717] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/25/2018] [Indexed: 12/14/2022] Open
Abstract
Histone methylation is regulated to shape the epigenome by modulating DNA compaction, thus playing central roles in fundamental chromatin-based processes including transcriptional regulation, DNA repair and cell proliferation. Histone methylation is erased by demethylases including the well-established KDM4 subfamily members, however, little is known about their dimerization capacity and its impact on their demethylase activity. Using the powerful bimolecular fluorescence complementation technique, we herein show the in situ formation of human KDM4A and KDM4C homodimers and heterodimers in nuclei of live transfectant cells and evaluate their H3K9me3 demethylation activity. Using size exclusion HPLC as well as Western blot analysis, we show that endogenous KDM4C undergoes dimerization under physiological conditions. Importantly, we identify the JmjN domain as the KDM4C dimerization interface and pin-point specific charged residues therein to be essential for this dimerization. We further demonstrate that KDM4A/C dimerization is absolutely required for their demethylase activity which was abolished by the expression of free JmjN peptides. In contrast, KDM4B does not dimerize and functions as a monomer, and hence was not affected by free JmjN expression. KDM4 proteins are overexpressed in numerous malignancies and their pharmacological inhibition or depletion in cancer cells was shown to impair tumor cell proliferation, invasion and metastasis. Thus, the KDM4 dimer-interactome emerging from the present study bears potential implications for cancer therapeutics via selective inhibition of KDM4A/C demethylase activity using JmjN-based peptidomimetics.
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Affiliation(s)
- May Levin
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Michal Stark
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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Passioura T, Bhushan B, Tumber A, Kawamura A, Suga H. Structure-activity studies of a macrocyclic peptide inhibitor of histone lysine demethylase 4A. Bioorg Med Chem 2018; 26:1225-1231. [PMID: 29402611 DOI: 10.1016/j.bmc.2018.01.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 01/13/2018] [Accepted: 01/18/2018] [Indexed: 11/18/2022]
Abstract
The combination of genetic code reprogramming and mRNA display is a powerful approach for the identification of macrocyclic peptides with high affinities to a target of interest. We have previously used such an approach to identify a potent inhibitor (CP2) of the human KDM4A and KDM4C lysine demethylases; important regulators of gene expression. In the present study, we have used genetic code reprogramming to synthesise very high diversity focused libraries (>1012 compounds) based on CP2 and, through affinity screening, used these to delineate the structure activity relationship of CP2 binding to KDM4A. In the course of these experiments we identified a CP2 analogue (CP2f-7) with ∼4-fold greater activity than CP2 in in vitro inhibition assays. This work will facilitate the development of more potent, selective inhibitors of lysine demethylases.
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Affiliation(s)
- Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
| | - Bhaskar Bhushan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Anthony Tumber
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom; Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford,Roosevelt Drive, Oxford, OX3 7DQ United Kingdom
| | - Akane Kawamura
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan; Japan Science and Technology Agency (JST), Core Research for Evolutionary Science and Technology (CREST), Saitama 332-0012, Japan.
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Gerken PA, Wolstenhulme JR, Tumber A, Hatch SB, Zhang Y, Müller S, Chandler SA, Mair B, Li F, Nijman SMB, Konietzny R, Szommer T, Yapp C, Fedorov O, Benesch JLP, Vedadi M, Kessler BM, Kawamura A, Brennan PE, Smith MD. Discovery of a Highly Selective Cell-Active Inhibitor of the Histone Lysine Demethylases KDM2/7. Angew Chem Int Ed Engl 2017; 56:15555-15559. [PMID: 28976073 PMCID: PMC5725665 DOI: 10.1002/anie.201706788] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/07/2017] [Indexed: 12/13/2022]
Abstract
Histone lysine demethylases (KDMs) are of critical importance in the epigenetic regulation of gene expression, yet there are few selective, cell-permeable inhibitors or suitable tool compounds for these enzymes. We describe the discovery of a new class of inhibitor that is highly potent towards the histone lysine demethylases KDM2A/7A. A modular synthetic approach was used to explore the chemical space and accelerate the investigation of key structure-activity relationships, leading to the development of a small molecule with around 75-fold selectivity towards KDM2A/7A versus other KDMs, as well as cellular activity at low micromolar concentrations.
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Affiliation(s)
- Philip A. Gerken
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | | | - Anthony Tumber
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Stephanie B. Hatch
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Yijia Zhang
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Susanne Müller
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Shane A. Chandler
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Barbara Mair
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Fengling Li
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioM5G 1L7Canada
| | - Sebastian M. B. Nijman
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Rebecca Konietzny
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Tamas Szommer
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Clarence Yapp
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Oleg Fedorov
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Justin L. P. Benesch
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Masoud Vedadi
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioM5G 1L7Canada
| | - Benedikt M. Kessler
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Akane Kawamura
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Paul E. Brennan
- Structural Genomics Consortium and Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordRoosevelt DriveOxfordOX3 7DQUK
| | - Martin D. Smith
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
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35
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Gerken PA, Wolstenhulme JR, Tumber A, Hatch SB, Zhang Y, Müller S, Chandler SA, Mair B, Li F, Nijman SMB, Konietzny R, Szommer T, Yapp C, Fedorov O, Benesch JLP, Vedadi M, Kessler BM, Kawamura A, Brennan PE, Smith MD. Discovery of a Highly Selective Cell-Active Inhibitor of the Histone Lysine Demethylases KDM2/7. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Philip A. Gerken
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Jamie R. Wolstenhulme
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Anthony Tumber
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Stephanie B. Hatch
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Yijia Zhang
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Susanne Müller
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Shane A. Chandler
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Barbara Mair
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Fengling Li
- Structural Genomics Consortium; University of Toronto; Toronto Ontario M5G 1L7 Canada
| | - Sebastian M. B. Nijman
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Rebecca Konietzny
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Tamas Szommer
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Clarence Yapp
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Oleg Fedorov
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Justin L. P. Benesch
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Masoud Vedadi
- Structural Genomics Consortium; University of Toronto; Toronto Ontario M5G 1L7 Canada
| | - Benedikt M. Kessler
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Akane Kawamura
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Paul E. Brennan
- Structural Genomics Consortium and Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Roosevelt Drive Oxford OX3 7DQ UK
| | - Martin D. Smith
- Chemistry Research Laboratory; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
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Tarhonskaya H, Nowak RP, Johansson C, Szykowska A, Tumber A, Hancock RL, Lang P, Flashman E, Oppermann U, Schofield CJ, Kawamura A. Studies on the Interaction of the Histone Demethylase KDM5B with Tricarboxylic Acid Cycle Intermediates. J Mol Biol 2017; 429:2895-2906. [PMID: 28827149 PMCID: PMC5636616 DOI: 10.1016/j.jmb.2017.08.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 12/21/2022]
Abstract
Methylation of lysine-4 of histone H3 (H3K4men) is an important regulatory factor in eukaryotic transcription. Removal of the transcriptionally activating H3K4 methylation is catalyzed by histone demethylases, including the Jumonji C (JmjC) KDM5 subfamily. The JmjC KDMs are Fe(II) and 2-oxoglutarate (2OG)-dependent oxygenases, some of which are associated with cancer. Altered levels of tricarboxylic acid (TCA) cycle intermediates and the associated metabolites D- and L-2-hydroxyglutarate (2HG) can cause changes in chromatin methylation status. We report comprehensive biochemical, structural and cellular studies on the interaction of TCA cycle intermediates with KDM5B, which is a current medicinal chemistry target for cancer. The tested TCA intermediates were poor or moderate KDM5B inhibitors, except for oxaloacetate and succinate, which were shown to compete for binding with 2OG. D- and L-2HG were moderate inhibitors at levels that might be relevant in cancer cells bearing isocitrate dehydrogenase mutations. Crystallographic analyses with succinate, fumarate, L-malate, oxaloacetate, pyruvate and D- and L-2HG support the kinetic studies showing competition with 2OG. An unexpected binding mode for oxaloacetate was observed in which it coordinates the active site metal via its C-4 carboxylate rather than the C-1 carboxylate/C-2 keto groups. Studies employing immunofluorescence antibody-based assays reveal no changes in H3K4me3 levels in cells ectopically overexpressing KDM5B in response to dosing with TCA cycle metabolite pro-drug esters, suggesting that the high levels of cellular 2OG may preclude inhibition. The combined results reveal the potential for KDM5B inhibition by TCA cycle intermediates, but suggest that in cells, such inhibition will normally be effectively competed by 2OG.
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Affiliation(s)
- Hanna Tarhonskaya
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Radosław P Nowak
- Structural Genomic Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Catrine Johansson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom; Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Windmill Road, Oxford, OX3 7LD, United Kingdom
| | - Aleksandra Szykowska
- Structural Genomic Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Anthony Tumber
- Structural Genomic Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Rebecca L Hancock
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Pauline Lang
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Emily Flashman
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Udo Oppermann
- Structural Genomic Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom; Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Windmill Road, Oxford, OX3 7LD, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.
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