1
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Tong D, Tang Y, Zhong P. The emerging roles of histone demethylases in cancers. Cancer Metastasis Rev 2024; 43:795-821. [PMID: 38227150 DOI: 10.1007/s10555-023-10160-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
Modulation of histone methylation status is regarded as an important mechanism of epigenetic regulation and has substantial clinical potential for the therapy of diseases, including cancer and other disorders. The present study aimed to provide a comprehensive introduction to the enzymology of histone demethylases, as well as their cancerous roles, molecular mechanisms, therapeutic possibilities, and challenges for targeting them, in order to advance drug design for clinical therapy and highlight new insight into the mechanisms of these enzymes in cancer. A series of clinical trials have been performed to explore potential roles of histone demethylases in several cancer types. Numerous targeted inhibitors associated with immunotherapy, chemotherapy, radiotherapy, and targeted therapy have been used to exert anticancer functions. Future studies should evaluate the dynamic transformation of histone demethylases leading to carcinogenesis and explore individual therapy.
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Affiliation(s)
- Dali Tong
- Department of Urological Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, People's Republic of China.
| | - Ying Tang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China.
| | - Peng Zhong
- Department of Pathology, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, People's Republic of China.
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2
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Li CY, Wang W, Leung CH, Yang GJ, Chen J. KDM5 family as therapeutic targets in breast cancer: Pathogenesis and therapeutic opportunities and challenges. Mol Cancer 2024; 23:109. [PMID: 38769556 PMCID: PMC11103982 DOI: 10.1186/s12943-024-02011-0] [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: 02/23/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024] Open
Abstract
Breast cancer (BC) is the most frequent malignant cancer diagnosis and is a primary factor for cancer deaths in women. The clinical subtypes of BC include estrogen receptor (ER) positive, progesterone receptor (PR) positive, human epidermal growth factor receptor 2 (HER2) positive, and triple-negative BC (TNBC). Based on the stages and subtypes of BC, various treatment methods are available with variations in the rates of progression-free disease and overall survival of patients. However, the treatment of BC still faces challenges, particularly in terms of drug resistance and recurrence. The study of epigenetics has provided new ideas for treating BC. Targeting aberrant epigenetic factors with inhibitors represents a promising anticancer strategy. The KDM5 family includes four members, KDM5A, KDM5B, KDM5C, and KDMD, all of which are Jumonji C domain-containing histone H3K4me2/3 demethylases. KDM5 proteins have been extensively studied in BC, where they are involved in suppressing or promoting BC depending on their specific upstream and downstream pathways. Several KDM5 inhibitors have shown potent BC inhibitory activity in vitro and in vivo, but challenges still exist in developing KDM5 inhibitors. In this review, we introduce the subtypes of BC and their current therapeutic options, summarize KDM5 family context-specific functions in the pathobiology of BC, and discuss the outlook and pitfalls of KDM5 inhibitors in this disease.
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Affiliation(s)
- Chang-Yun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau, China.
- Macao Centre for Research and Development in Chinese Medicine, University of Macau, Macau, China.
- MoE Frontiers Science Centre for Precision Oncology, University of Macau, Macau, China.
| | - Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China.
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China.
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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3
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Guo CC, Xu HE, Ma X. ARID3a from the ARID family: structure, role in autoimmune diseases and drug discovery. Acta Pharmacol Sin 2023; 44:2139-2150. [PMID: 37488425 PMCID: PMC10618457 DOI: 10.1038/s41401-023-01134-2] [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: 03/13/2023] [Accepted: 07/09/2023] [Indexed: 07/26/2023] Open
Abstract
The AT-rich interaction domain (ARID) family of DNA-binding proteins is a group of transcription factors and chromatin regulators with a highly conserved ARID domain that recognizes specific AT-rich DNA sequences. Dysfunction of ARID family members has been implicated in various human diseases including cancers and intellectual disability. Among them, ARID3a has gained increasing attention due to its potential involvement in autoimmunity. In this article we provide an overview of the ARID family, focusing on the structure and biological functions of ARID3a. It explores the role of ARID3a in autoreactive B cells and its contribution to autoimmune diseases such as systemic lupus erythematosus and primary biliary cholangitis. Furthermore, we also discuss the potential for drug discovery targeting ARID3a and present a plan for future research in this field.
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Affiliation(s)
- Cheng-Cen Guo
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, 200001, China.
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xiong Ma
- Department of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, 200001, China.
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4
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Yheskel M, Sidoli S, Secombe J. Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5. Epigenetics Chromatin 2023; 16:8. [PMID: 36803422 PMCID: PMC9938590 DOI: 10.1186/s13072-023-00481-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/03/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND KDM5 family proteins are multi-domain regulators of transcription that when dysregulated contribute to cancer and intellectual disability. KDM5 proteins can regulate transcription through their histone demethylase activity in addition to demethylase-independent gene regulatory functions that remain less characterized. To expand our understanding of the mechanisms that contribute to KDM5-mediated transcription regulation, we used TurboID proximity labeling to identify KDM5-interacting proteins. RESULTS Using Drosophila melanogaster, we enriched for biotinylated proteins from KDM5-TurboID-expressing adult heads using a newly generated control for DNA-adjacent background in the form of dCas9:TurboID. Mass spectrometry analyses of biotinylated proteins identified both known and novel candidate KDM5 interactors, including members of the SWI/SNF and NURF chromatin remodeling complexes, the NSL complex, Mediator, and several insulator proteins. CONCLUSIONS Combined, our data shed new light on potential demethylase-independent activities of KDM5. In the context of KDM5 dysregulation, these interactions may play key roles in the alteration of evolutionarily conserved transcriptional programs implicated in human disorders.
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Affiliation(s)
- Matanel Yheskel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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5
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Ugur FS, Kelly MJS, Fujimori DG. Chromatin Sensing by the Auxiliary Domains of KDM5C Regulates Its Demethylase Activity and Is Disrupted by X-linked Intellectual Disability Mutations. J Mol Biol 2023; 435:167913. [PMID: 36495919 PMCID: PMC10247153 DOI: 10.1016/j.jmb.2022.167913] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/10/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
The H3K4me3 chromatin modification, a hallmark of promoters of actively transcribed genes, is dynamically removed by the KDM5 family of histone demethylases. The KDM5 demethylases have a number of accessory domains, two of which, ARID and PHD1, lie between the segments of the catalytic domain. KDM5C, which has a unique role in neural development, harbors a number of mutations adjacent to its accessory domains that cause X-linked intellectual disability (XLID). The roles of these accessory domains remain unknown, limiting an understanding of how XLID mutations affect KDM5C activity. Through in vitro binding and kinetic studies using nucleosomes, we find that while the ARID domain is required for efficient nucleosome demethylation, the PHD1 domain alone has an inhibitory role in KDM5C catalysis. In addition, the unstructured linker region between the ARID and PHD1 domains interacts with PHD1 and is necessary for nucleosome binding. Our data suggests a model in which the PHD1 domain inhibits DNA recognition by KDM5C. This inhibitory effect is relieved by the H3 tail, enabling recognition of flanking DNA on the nucleosome. Importantly, we find that XLID mutations adjacent to the ARID and PHD1 domains break this regulation by enhancing DNA binding, resulting in the loss of specificity of substrate chromatin recognition and rendering demethylase activity lower in the presence of flanking DNA. Our findings suggest a model by which specific XLID mutations could alter chromatin recognition and enable euchromatin-specific dysregulation of demethylation by KDM5C.
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Affiliation(s)
- Fatima S Ugur
- Chemistry and Chemical Biology Graduate Program, 600 16th St., San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, 600 16th St., San Francisco, CA 94158, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, 600 16th St., San Francisco, CA 94158, USA
| | - Danica Galonić Fujimori
- Department of Pharmaceutical Chemistry, 600 16th St., San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, 600 16th St., San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, 600 16th St., San Francisco, CA 94158, USA.
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6
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Di Nisio E, Licursi V, Mannironi C, Buglioni V, Paiardini A, Robusti G, Noberini R, Bonaldi T, Negri R. A truncated and catalytically inactive isoform of KDM5B histone demethylase accumulates in breast cancer cells and regulates H3K4 tri-methylation and gene expression. Cancer Gene Ther 2023:10.1038/s41417-022-00584-w. [PMID: 36697763 DOI: 10.1038/s41417-022-00584-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/27/2023]
Abstract
KDM5B histone demethylase is overexpressed in many cancers and plays an ambivalent role in oncogenesis, depending on the specific context. This ambivalence could be explained by the expression of KDM5B protein isoforms with diverse functional roles, which could be present at different levels in various cancer cell lines. We show here that one of these isoforms, namely KDM5B-NTT, accumulates in breast cancer cell lines due to remarkable protein stability relative to the canonical PLU-1 isoform, which shows a much faster turnover. This isoform is the truncated and catalytically inactive product of an mRNA with a transcription start site downstream of the PLU-1 isoform, and the consequent usage of an alternative ATG for translation initiation. It also differs from the PLU-1 transcript in the inclusion of an additional exon (exon-6), previously attributed to other putative isoforms. Overexpression of this isoform in MCF7 cells leads to an increase in bulk H3K4 methylation and induces derepression of a gene cluster, including the tumor suppressor Cav1 and several genes involved in the interferon-alpha and -gamma response. We discuss the relevance of this finding considering the hypothesis that KDM5B may possess regulatory roles independent of its catalytic activity.
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Affiliation(s)
- Elena Di Nisio
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi 70, 00185, Rome, Italy.,MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Sir James Black Centre, Dow Street, DD1 5EH, Dundee, Scotland, UK
| | - Valerio Licursi
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy, Via degli Apuli 4, 00185, Rome, Italy
| | - Cecilia Mannironi
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy, Via degli Apuli 4, 00185, Rome, Italy
| | - Valentina Buglioni
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi 70, 00185, Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences, Sapienza University of Rome, p.le Aldo Moro 5, 00185, Rome, Italy
| | - Giulia Robusti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy.,Department of Oncology and Hematology-Oncology, University of Milan, Milan, 20122, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi 70, 00185, Rome, Italy. .,Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy, Via degli Apuli 4, 00185, Rome, Italy.
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7
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Zhang SM, Cao J, Yan Q. KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:113-137. [PMID: 37751138 DOI: 10.1007/978-3-031-38176-8_6] [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] [Indexed: 09/27/2023]
Abstract
The histone lysine demethylase 5 (KDM5) family proteins are Fe2+ and α-ketoglutarate-dependent dioxygenases, with jumonji C (JmjC) domain as their catalytic core and several plant homeodomains (PHDs) to bind different histone methylation marks. These enzymes are capable of demethylating tri-, di- and mono-methylated lysine 4 in histone H3 (H3K4me3/2/1), the key epigenetic marks for active chromatin. Thus, this H3K4 demethylase family plays critical roles in cell fate determination during development as well as malignant transformation. KDM5 demethylases have both oncogenic and tumor suppressive functions in a cancer type-dependent manner. In solid tumors, KDM5A/B are generally oncogenic, whereas KDM5C/D have tumor suppressive roles. Their involvement in de-differentiation, cancer metastasis, drug resistance, and tumor immunoevasion indicated that KDM5 family proteins are promising drug targets for cancer therapy. Significant efforts from both academia and industry have led to the development of potent and selective KDM5 inhibitors for preclinical experiments and phase I clinical trials. However, a better understanding of the roles of KDM5 demethylases in different physiological and pathological conditions is critical for further developing KDM5 modulators for clinical applications.
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Affiliation(s)
- Shang-Min Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jian Cao
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA.
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
| | - Qin Yan
- Department of Pathology, Yale Cancer Center, Yale Stem Cell Center, Yale Center for Immuno-Oncology, Yale Center for Research on Aging, Yale School of Medicine, P.O. Box 208023, New Haven, CT, 06520-8023, USA.
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8
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Pavlenko E, Ruengeler T, Engel P, Poepsel S. Functions and Interactions of Mammalian KDM5 Demethylases. Front Genet 2022; 13:906662. [PMID: 35899196 PMCID: PMC9309374 DOI: 10.3389/fgene.2022.906662] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/06/2022] [Indexed: 12/26/2022] Open
Abstract
Mammalian histone demethylases of the KDM5 family are mediators of gene expression dynamics during developmental, cellular differentiation, and other nuclear processes. They belong to the large group of JmjC domain containing, 2-oxoglutarate (2-OG) dependent oxygenases and target methylated lysine 4 of histone H3 (H3K4me1/2/3), an epigenetic mark associated with active transcription. In recent years, KDM5 demethylases have gained increasing attention due to their misregulation in many cancer entities and are intensively explored as therapeutic targets. Despite these implications, the molecular basis of KDM5 function has so far remained only poorly understood. Little is known about mechanisms of nucleosome recognition, the recruitment to genomic targets, as well as the local regulation of demethylase activity. Experimental evidence suggests close physical and functional interactions with epigenetic regulators such as histone deacetylase (HDAC) containing complexes, as well as the retinoblastoma protein (RB). To understand the regulation of KDM5 proteins in the context of chromatin, these interactions have to be taken into account. Here, we review the current state of knowledge on KDM5 function, with a particular emphasis on molecular interactions and their potential implications. We will discuss and outline open questions that need to be addressed to better understand histone demethylation and potential demethylation-independent functions of KDM5s. Addressing these questions will increase our understanding of histone demethylation and allow us to develop strategies to target individual KDM5 enzymes in specific biological and disease contexts.
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Affiliation(s)
- Egor Pavlenko
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Till Ruengeler
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Paulina Engel
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Simon Poepsel
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- *Correspondence: Simon Poepsel,
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9
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Diverse Functions of KDM5 in Cancer: Transcriptional Repressor or Activator? Cancers (Basel) 2022; 14:cancers14133270. [PMID: 35805040 PMCID: PMC9265395 DOI: 10.3390/cancers14133270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 11/16/2022] Open
Abstract
Epigenetic modifications are crucial for chromatin remodeling and transcriptional regulation. Post-translational modifications of histones are epigenetic processes that are fine-tuned by writer and eraser enzymes, and the disorganization of these enzymes alters the cellular state, resulting in human diseases. The KDM5 family is an enzymatic family that removes di- and tri-methyl groups (me2 and me3) from lysine 4 of histone H3 (H3K4), and its dysregulation has been implicated in cancer. Although H3K4me3 is an active chromatin marker, KDM5 proteins serve as not only transcriptional repressors but also transcriptional activators in a demethylase-dependent or -independent manner in different contexts. Notably, KDM5 proteins regulate the H3K4 methylation cycle required for active transcription. Here, we review the recent findings regarding the mechanisms of transcriptional regulation mediated by KDM5 in various contexts, with a focus on cancer, and further shed light on the potential of targeting KDM5 for cancer therapy.
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10
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Chauvistré H, Shannan B, Daignault-Mill SM, Ju RJ, Picard D, Egetemaier S, Váraljai R, Gibhardt CS, Sechi A, Kaschani F, Keminer O, Stehbens SJ, Liu Q, Yin X, Jeyakumar K, Vogel FCE, Krepler C, Rebecca VW, Kubat L, Lueong SS, Forster J, Horn S, Remke M, Ehrmann M, Paschen A, Becker JC, Helfrich I, Rauh D, Kaiser M, Gul S, Herlyn M, Bogeski I, Rodríguez-López JN, Haass NK, Schadendorf D, Roesch A. Persister state-directed transitioning and vulnerability in melanoma. Nat Commun 2022; 13:3055. [PMID: 35650266 PMCID: PMC9160289 DOI: 10.1038/s41467-022-30641-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/10/2022] [Indexed: 12/30/2022] Open
Abstract
Melanoma is a highly plastic tumor characterized by dynamic interconversion of different cell identities depending on the biological context. Melanoma cells with high expression of the H3K4 demethylase KDM5B (JARID1B) rest in a slow-cycling, yet reversible persister state. Over time, KDM5Bhigh cells can promote rapid tumor repopulation with equilibrated KDM5B expression heterogeneity. The cellular identity of KDM5Bhigh persister cells has not been studied so far, missing an important cell state-directed treatment opportunity in melanoma. Here, we have established a doxycycline-titratable system for genetic induction of permanent intratumor expression of KDM5B and screened for chemical agents that phenocopy this effect. Transcriptional profiling and cell functional assays confirmed that the dihydropyridine 2-phenoxyethyl 4-(2-fluorophenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxylate (termed Cpd1) supports high KDM5B expression and directs melanoma cells towards differentiation along the melanocytic lineage and to cell cycle-arrest. The high KDM5B state additionally prevents cell proliferation through negative regulation of cytokinetic abscission. Moreover, treatment with Cpd1 promoted the expression of the melanocyte-specific tyrosinase gene specifically sensitizing melanoma cells for the tyrosinase-processed antifolate prodrug 3-O-(3,4,5-trimethoxybenzoyl)-(-)-epicatechin (TMECG). In summary, our study provides proof-of-concept for a dual hit strategy in melanoma, in which persister state-directed transitioning limits tumor plasticity and primes melanoma cells towards lineage-specific elimination.
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Affiliation(s)
- Heike Chauvistré
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Batool Shannan
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Sheena M Daignault-Mill
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Robert J Ju
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Daniel Picard
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Stefanie Egetemaier
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Renáta Váraljai
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Christine S Gibhardt
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Antonio Sechi
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Farnusch Kaschani
- Department of Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Oliver Keminer
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Samantha J Stehbens
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Qin Liu
- The Wistar Institute, Philadelphia, PA, USA
| | | | - Kirujan Jeyakumar
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Felix C E Vogel
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Division of Tumor Metabolism and Microenvironment, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | | | | | - Linda Kubat
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Translational Skin Cancer Research (TSCR), German Cancer Consortium (DKTK), University Hospital of Essen, Universitätsstrasse 1, 45141, Essen, Germany
| | - Smiths S Lueong
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, 45122, Essen, Germany
| | - Jan Forster
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Department of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122, Essen, Germany
| | - Susanne Horn
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Marc Remke
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Michael Ehrmann
- Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
- Department of Microbiology, University of Duisburg-Essen, Universitätsstraße 2, 45117, Essen, Germany
| | - Annette Paschen
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Jürgen C Becker
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Translational Skin Cancer Research (TSCR), German Cancer Consortium (DKTK), University Hospital of Essen, Universitätsstrasse 1, 45141, Essen, Germany
| | - Iris Helfrich
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Markus Kaiser
- Department of Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Schnackenburgallee 114, 22525, Hamburg, Germany
| | | | - Ivan Bogeski
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - José Neptuno Rodríguez-López
- GENZ-Group of Research on Enzymology, Department of Biochemistry and Molecular Biology-A, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, Murcia, Spain
| | - Nikolas K Haass
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
- Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Alexander Roesch
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany.
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany.
- Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
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11
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Taylor-Papadimitriou J, Burchell JM. Histone Methylases and Demethylases Regulating Antagonistic Methyl Marks: Changes Occurring in Cancer. Cells 2022; 11:cells11071113. [PMID: 35406676 PMCID: PMC8997813 DOI: 10.3390/cells11071113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation of gene expression is crucial to the determination of cell fate in development and differentiation, and the Polycomb (PcG) and Trithorax (TrxG) groups of proteins, acting antagonistically as complexes, play a major role in this regulation. Although originally identified in Drosophila, these complexes are conserved in evolution and the components are well defined in mammals. Each complex contains a protein with methylase activity (KMT), which can add methyl groups to a specific lysine in histone tails, histone 3 lysine 27 (H3K27), by PcG complexes, and H3K4 and H3K36 by TrxG complexes, creating transcriptionally repressive or active marks, respectively. Histone demethylases (KDMs), identified later, added a new dimension to histone methylation, and mutations or changes in levels of expression are seen in both methylases and demethylases and in components of the PcG and TrX complexes across a range of cancers. In this review, we focus on both methylases and demethylases governing the methylation state of the suppressive and active marks and consider their action and interaction in normal tissues and in cancer. A picture is emerging which indicates that the changes which occur in cancer during methylation of histone lysines can lead to repression of genes, including tumour suppressor genes, or to the activation of oncogenes. Methylases or demethylases, which are themselves tumour suppressors, are highly mutated. Novel targets for cancer therapy have been identified and a methylase (KMT6A/EZH2), which produces the repressive H3K27me3 mark, and a demethylase (KDM1A/LSD1), which demethylates the active H3K4me2 mark, are now under clinical evaluation.
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12
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Korn SM, Schlundt A. Structures and nucleic acid-binding preferences of the eukaryotic ARID domain. Biol Chem 2022; 403:731-747. [PMID: 35119801 DOI: 10.1515/hsz-2021-0404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/17/2022] [Indexed: 12/28/2022]
Abstract
The DNA-binding AT-rich interactive domain (ARID) exists in a wide range of proteins throughout eukaryotic kingdoms. ARID domain-containing proteins are involved in manifold biological processes, such as transcriptional regulation, cell cycle control and chromatin remodeling. Their individual domain composition allows for a sub-classification within higher mammals. ARID is categorized as binder of double-stranded AT-rich DNA, while recent work has suggested ARIDs as capable of binding other DNA motifs and also recognizing RNA. Despite a broad variability on the primary sequence level, ARIDs show a highly conserved fold, which consists of six α-helices and two loop regions. Interestingly, this minimal core domain is often found extended by helices at the N- and/or C-terminus with potential roles in target specificity and, subsequently function. While high-resolution structural information from various types of ARIDs has accumulated over two decades now, there is limited access to ARID-DNA complex structures. We thus find ourselves left at the beginning of understanding ARID domain target specificities and the role of accompanying domains. Here, we systematically summarize ARID domain conservation and compare the various types with a focus on their structural differences and DNA-binding preferences, including the context of multiple other motifs within ARID domain containing proteins.
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Affiliation(s)
- Sophie Marianne Korn
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
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13
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Yang GJ, Wu J, Miao L, Zhu MH, Zhou QJ, Lu XJ, Lu JF, Leung CH, Ma DL, Chen J. Pharmacological inhibition of KDM5A for cancer treatment. Eur J Med Chem 2021; 226:113855. [PMID: 34555614 DOI: 10.1016/j.ejmech.2021.113855] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 12/15/2022]
Abstract
Lysine-specific demethylase 5A (KDM5A, also named RBP2 or JARID1A) is a demethylase that can remove methyl groups from histones H3K4me1/2/3. It is aberrantly expressed in many cancers, where it impedes differentiation and contributes to cancer cell proliferation, cell metastasis and invasiveness, drug resistance, and is associated with poor prognosis. Pharmacological inhibition of KDM5A has been reported to significantly attenuate tumor progression in vitro and in vivo in a range of solid tumors and acute myeloid leukemia. This review will present the structural aspects of KDM5A, its role in carcinogenesis, a comparison of currently available approaches for screening KDM5A inhibitors, a classification of KDM5A inhibitors, and its potential as a drug target in cancer therapy.
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Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Jia Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao SAR, 999078, China
| | - Liang Miao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Ming-Hui Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Qian-Jin Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Xin-Jiang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Jian-Fei Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao SAR, 999078, China.
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China.
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14
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Jamshidi S, Catchpole S, Chen J, So CWE, Burchell J, Rahman KM, Taylor-Papadimitriou J. KDM5B protein expressed in viable and fertile ΔARID mice exhibit no demethylase activity. Int J Oncol 2021; 59:96. [PMID: 34713299 PMCID: PMC8562390 DOI: 10.3892/ijo.2021.5276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
Post‑translational modification of histones serve a crucial role in the control of gene transcription. Trimethylation of lysine 4 on histone 3 is associated with transcription activation. There are currently six known methylases and six known demethylases that can control the methylation status of this site. Lysine demethylase 5B (KDM5B) is one such demethylase, which can repress gene expression. In particular KDM5B has been found to be overexpressed in a number of cancer types, and small‑molecular weight inhibitors of its demethylase activity have been identified. Previous characterisation of Kdm5b knock‑out mice has revealed that this genotype leads to either embryonic or neonatal lethality. However, the ΔA‑T rich interaction domain (ΔARID)‑KDM5B strain of mice, which have the ARID domain and five amino acids within the Jumonji (Jmj)N domain spliced out from KDM5B, remain viable and fertile. In the present study, ΔARID‑KDM5B was found to have no demethylase activity as determined by in vitro demethylase assays and by immunofluorescence in transfected Cos‑1 cells. Furthermore, molecular dynamic simulations revealed conformational changes within the ΔARID‑KDM5B structure compared with that in WT‑KDM5B, particularly in the JmjC domain, which is responsible for the catalytic activity of WT‑KDM5B. This supports the experimental data that shows the loss of demethylase activity. Since Kdm5b knock‑out mice show varying degrees of lethality, these data suggest that KDM5B serves a crucial function in development in a manner that is independent of its demethylase activity.
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Affiliation(s)
- Shirin Jamshidi
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 9NN, UK
| | - Steven Catchpole
- Breast Cancer Biology, Innovation Hub, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, Guy's Hospital, London SE1 9RT, UK
| | - Jie Chen
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, Denmark Hill Campus, King's College London, London SE5 9RJ, UK
| | - Chi Wai Eric So
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, Denmark Hill Campus, King's College London, London SE5 9RJ, UK
| | - Joy Burchell
- Breast Cancer Biology, Innovation Hub, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, Guy's Hospital, London SE1 9RT, UK
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 9NN, UK
| | - Joyce Taylor-Papadimitriou
- Breast Cancer Biology, Innovation Hub, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, Guy's Hospital, London SE1 9RT, UK
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15
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Islam MT, Wang LC, Chen IJ, Lo KL, Lo WS. Arabidopsis JMJ17 promotes cotyledon greening during de-etiolation by repressing genes involved in tetrapyrrole biosynthesis in etiolated seedlings. THE NEW PHYTOLOGIST 2021; 231:1023-1039. [PMID: 33666236 DOI: 10.1111/nph.17327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Arabidopsis histone H3 lysine 4 (H3K4) demethylases play crucial roles in several developmental processes, but their involvement in seedling establishment remain unexplored. Here, we show that Arabidopsis JUMONJI DOMAIN-CONTAINING PROTEIN17 (JMJ17), an H3K4me3 demethylase, is involved in cotyledon greening during seedling establishment. Dark-grown seedlings of jmj17 accumulated a high concentration of protochlorophyllide, an intermediate metabolite in the tetrapyrrole biosynthesis (TPB) pathway that generates chlorophyll (Chl) during photomorphogenesis. Upon light irradiation, jmj17 mutants displayed decreased cotyledon greening and reduced Chl level compared with the wild-type; overexpression of JMJ17 completely rescued the jmj17-5 phenotype. Transcriptomics analysis uncovered that several genes encoding key enzymes involved in TPB were upregulated in etiolated jmj17 seedlings. Consistently, chromatin immunoprecipitation-quantitative PCR revealed elevated H3K4me3 level at the promoters of target genes. Chromatin association of JMJ17 was diminished upon light exposure. Furthermore, JMJ17 interacted with PHYTOCHROME INTERACTING FACTOR1 in the yeast two-hybrid assay. JMJ17 binds directly to gene promoters to demethylate H3K4me3 to suppress PROTOCHLOROPHYLLIDE OXIDOREDUCTASE C expression and TPB in the dark. Light results in de-repression of gene expression to modulate seedling greening during de-etiolation. Our study reveals a new role for histone demethylase JMJ17 in controlling cotyledon greening in etiolated seedlings during the dark-to-light transition.
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Affiliation(s)
- Md Torikul Islam
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Long-Chi Wang
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - I-Ju Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Lin Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Wan-Sheng Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
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16
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Bi D, Yao J, Wang Y, Qin G, Zhang Y, Wang Y, Zhao J. CRISPR/Cas13d-mediated efficient KDM5B mRNA knockdown in porcine somatic cells and parthenogenetic embryos. Reproduction 2021; 162:149-160. [PMID: 34096883 PMCID: PMC8284906 DOI: 10.1530/rep-21-0053] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/07/2021] [Indexed: 12/26/2022]
Abstract
An efficient mRNA knockdown strategy is needed to explore gene function in cells and embryos, especially to understand the process of maternal mRNA decay during early embryo development. Cas13, a novel RNA-targeting CRISPR effector protein, could bind and cleave complementary single-strand RNA, which has been employed for mRNA knockdown in mouse and human cells and RNA-virus interference in plants. Cas13 has not yet been reported to be used in pigs. In the current study, we explored the feasibility of CRISPR/Cas13d-mediated endogenous RNA knockdown in pigs. KDM5B, a histone demethylase of H3K4me3, was downregulated at the transcriptional level by 50% with CRISPR/Cas13d in porcine fibroblast cells. Knockdown of KDM5B-induced H3K4me3 expression and decreased the abundance of H3K27me3, H3K9me3, H3K4ac, H4K8ac, and H4K12ac. These changes affected cell proliferation and cell cycle. Furthermore, stable integration of the CRISPR/Cas13d system into the porcine genome resulted in the continuous expression of Cas13d and persistent knockdown of KDM5B. Finally, the RNA-targeting potential of Cas13d was further validated in porcine parthenogenetic embryos. By microinjection of Cas13d mRNA and gRNA targeting KDM5B into porcine oocytes, the expression of KDM5B was downregulated, the abundance of H3K4me3 increased as expected, and the expression of embryonic development-related genes was changed accordingly. These results indicate that CRISPR/Cas13d provides an easily programmable platform for spatiotemporal transcriptional manipulation in pigs.
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Affiliation(s)
- Dengfeng Bi
- School of Life Sciences, University of Science and Technology of China, Hefei, China.,State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Jing Yao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guosong Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Yunting Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanfang Wang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianguo Zhao
- School of Life Sciences, University of Science and Technology of China, Hefei, China.,State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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17
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Yang GJ, Zhu MH, Lu XJ, Liu YJ, Lu JF, Leung CH, Ma DL, Chen J. The emerging role of KDM5A in human cancer. J Hematol Oncol 2021; 14:30. [PMID: 33596982 PMCID: PMC7888121 DOI: 10.1186/s13045-021-01041-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
Histone methylation is a key posttranslational modification of chromatin, and its dysregulation affects a wide array of nuclear activities including the maintenance of genome integrity, transcriptional regulation, and epigenetic inheritance. Variations in the pattern of histone methylation influence both physiological and pathological events. Lysine-specific demethylase 5A (KDM5A, also known as JARID1A or RBP2) is a KDM5 Jumonji histone demethylase subfamily member that erases di- and tri-methyl groups from lysine 4 of histone H3. Emerging studies indicate that KDM5A is responsible for driving multiple human diseases, particularly cancers. In this review, we summarize the roles of KDM5A in human cancers, survey the field of KDM5A inhibitors including their anticancer activity and modes of action, and the current challenges and potential opportunities of this field.
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Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China.,Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, People's Republic of China
| | - Ming-Hui Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Xin-Jiang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Yan-Jun Liu
- Department of Immunology and Medical Microbiology, Nanjing University of Chinese Medicine, Nanjing, 210046, People's Republic of China
| | - Jian-Fei Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Chung-Hang Leung
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, People's Republic of China.
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, People's Republic of China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China. .,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China. .,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China.
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18
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The Role of H3K4 Trimethylation in CpG Islands Hypermethylation in Cancer. Biomolecules 2021; 11:biom11020143. [PMID: 33499170 PMCID: PMC7912453 DOI: 10.3390/biom11020143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/30/2020] [Accepted: 01/15/2021] [Indexed: 01/01/2023] Open
Abstract
CpG methylation in transposons, exons, introns and intergenic regions is important for long-term silencing, silencing of parasitic sequences and alternative promoters, regulating imprinted gene expression and determining X chromosome inactivation. Promoter CpG islands, although rich in CpG dinucleotides, are unmethylated and remain so during all phases of mammalian embryogenesis and development, except in specific cases. The biological mechanisms that contribute to the maintenance of the unmethylated state of CpG islands remain elusive, but the modification of established DNA methylation patterns is a common feature in all types of tumors and is considered as an event that intrinsically, or in association with genetic lesions, feeds carcinogenesis. In this review, we focus on the latest results describing the role that the levels of H3K4 trimethylation may have in determining the aberrant hypermethylation of CpG islands in tumors.
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19
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Wang Z, Liu D, Xu B, Tian R, Zuo Y. Modular arrangements of sequence motifs determine the functional diversity of KDM proteins. Brief Bioinform 2020; 22:5912575. [PMID: 32987405 DOI: 10.1093/bib/bbaa215] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Histone lysine demethylases (KDMs) play a vital role in regulating chromatin dynamics and transcription. KDM proteins are given modular activities by its sequence motifs with obvious roles division, which endow the complex and diverse functions. In our review, according to functional features, we classify sequence motifs into four classes: catalytic motifs, targeting motifs, regulatory motifs and potential motifs. JmjC, as the main catalytic motif, combines to Fe2+ and α-ketoglutarate by residues H-D/E-H and S-N-N/Y-K-N/Y-T/S. Targeting motifs make catalytic motifs recognize specific methylated lysines, such as PHD that helps KDM5 to demethylate H3K4me3. Regulatory motifs consist of a functional network. For example, NLS, Ser-rich, TPR and JmjN motifs regulate the nuclear localization. And interactions through the CW-type-C4H2C2-SWIRM are necessary to the demethylase activity of KDM1B. Additionally, many conservative domains that have potential functions but no deep exploration are reviewed for the first time. These conservative domains are usually amino acid-rich regions, which have great research value. The arrangements of four types of sequence motifs generate that KDM proteins diversify toward modular activities and biological functions. Finally, we draw a blueprint of functional mechanisms to discuss the modular activity of KDMs.
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Affiliation(s)
- Zerong Wang
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Dongyang Liu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. He is now studying for a master's degree at the institute of botany of the Chinese Academy of Sciences. His research interests include bioinformatics and computational genomics
| | - Baofang Xu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Ruixia Tian
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Yongchun Zuo
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. His research interests include bioinformatics and integration analysis of multiomics in cell reprogramming
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20
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Fu YD, Huang MJ, Guo JW, You YZ, Liu HM, Huang LH, Yu B. Targeting histone demethylase KDM5B for cancer treatment. Eur J Med Chem 2020; 208:112760. [PMID: 32883639 DOI: 10.1016/j.ejmech.2020.112760] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023]
Abstract
KDM5B (Lysine-Specific Demethylase 5B) erases the methyl group from H3K4me2/3, which performs wide regulatory effects on chromatin structure, and represses the transcriptional function of genes. KDM5B functions as an oncogene and associates with human cancers closely. Targeting KDM5B has been a promising direction for curing cancer since the emergence of potent KDM5B inhibitor CPI-455. In this area, most reported KDM5B inhibitors are Fe (Ⅱ) chelators, which also compete with the cofactor 2-OG in the active pockets. Besides, Some KDM5B inhibitors have been identified through high throughput screening or biochemical screening. In this reviewing article, we summarized the pioneering progress in KDM5B to provide a comprehensive realization, including crystal structure, transcriptional regulation function, cancer-related functions, development of inhibitors, and SAR studies. We hope to provide a comprehensive overview of KDM5B and the development of KDM5B inhibitors.
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Affiliation(s)
- Yun-Dong Fu
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Ming-Jie Huang
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Jia-Wen Guo
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Ya-Zhen You
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Li-Hua Huang
- Green Catalysis Center, And College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China.
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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21
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Histone Demethylase KDM5B as a Therapeutic Target for Cancer Therapy. Cancers (Basel) 2020; 12:cancers12082121. [PMID: 32751840 PMCID: PMC7465382 DOI: 10.3390/cancers12082121] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 12/14/2022] Open
Abstract
Lysine-specific demethylase 5B (KDM5B/PLU1/JARID1B) is found to be overexpressed in numerous malignancies, including breast, lung, skin, liver, and prostate cancer. Identification of molecules targeting the KDM5B enzyme could be a potential lead in cancer research. Although many KDM5B inhibitors with promising outcomes have been developed so far, its further application in clinical practice is limited due to toxicity and lack of target specificity. Here, we summarize the significance of targeting KDM5B in anticancer therapy and report the molecular docking studies of some known anti-viral agents, decitabine, entecavir, abacavir, penciclovir, and 3-deazaneplanocin A in the catalytic domain JmjC of KDM5B. These studies show the repurposing potential of identified anti-viral agents in cancer therapy.
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22
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Zhang N, Jiang T, Wang Y, Hu L, Bu Y. BTG4 is A Novel p53 Target Gene That Inhibits Cell Growth and Induces Apoptosis. Genes (Basel) 2020; 11:genes11020217. [PMID: 32093041 PMCID: PMC7074044 DOI: 10.3390/genes11020217] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 01/09/2023] Open
Abstract
BTG4 is the last cloned and poorly studied member of BTG/Tob family. Studies have suggested that BTG4 is critical for the degradation of maternal mRNAs in mice during the process of maternal-to-zygotic transition, and downregulated in cancers, such as gastric cancer. However, the regulatory mechanism of BTG4 and its function in cancers remain elusive. In this study, we have for the first time identified the promoter region of the human BTG4 gene. Serial luciferase reporter assay demonstrated that the core promoter of BTG4 is mainly located within the 388 bp region near its transcription initiation site. Transcription factor binding site analysis revealed that the BTG4 promoter contains binding sites for canonical transcription factors, such as Sp1, whereas its first intron contains two overlapped consensus p53 binding sites. However, overexpression of Sp1 has negligible effects on BTG4 promoter activity, and site-directed mutagenesis assay further suggested that Sp1 is not a critical transcription factor for the transcriptional regulation of BTG4. Of note, luciferase assay revealed that one of the intronic p53 binding sites is highly responsive to p53. Both exogenous p53 overexpression and adriamycin-mediated endogenous p53 activation result in the transcriptional upregulation of BTG4. In addition, BTG4 is downregulated in lung and colorectal cancers, and overexpression of BTG4 inhibits cell growth and induces apoptosis in cancer cells. Taken together, our results strongly suggest that BTG4 is a novel p53-regulated gene and probably functions as a tumor suppressor in lung and colorectal cancers.
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Affiliation(s)
- Na Zhang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; (N.Z.); (T.J.); (Y.W.); (L.H.)
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Tinghui Jiang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; (N.Z.); (T.J.); (Y.W.); (L.H.)
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yitao Wang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; (N.Z.); (T.J.); (Y.W.); (L.H.)
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Lanyue Hu
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; (N.Z.); (T.J.); (Y.W.); (L.H.)
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Youquan Bu
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; (N.Z.); (T.J.); (Y.W.); (L.H.)
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
- Correspondence: ; Tel.: +86-23-68485991
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23
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Bamodu O, Chao TY. Dissecting the functional pleiotropism of lysine demethylase 5B in physiology and pathology. JOURNAL OF CANCER RESEARCH AND PRACTICE 2020. [DOI: 10.4103/jcrp.jcrp_5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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24
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Yuan X, Liu Y, Li G, Lan Z, Ma M, Li H, Kong J, Sun J, Hou G, Hou X, Ma Y, Ren F, Zhou F, Gao S. Blockade of Immune-Checkpoint B7-H4 and Lysine Demethylase 5B in Esophageal Squamous Cell Carcinoma Confers Protective Immunity against P. gingivalis Infection. Cancer Immunol Res 2019; 7:1440-1456. [PMID: 31350278 DOI: 10.1158/2326-6066.cir-18-0709] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/14/2019] [Accepted: 07/22/2019] [Indexed: 11/16/2022]
Abstract
Pathogens are capable of hijacking immune defense mechanisms, thereby creating a tolerogenic environment for hypermutated malignant cells that arise within the site of infection. Immune checkpoint-oriented immunotherapies have shown considerable promise. Equally important, the epigenetic reprogramming of an immune-evasive phenotype that activates the immune system in a synergistic manner can improve immunotherapy outcomes. These advances have led to combinations of epigenetic- and immune-based therapeutics. We previously demonstrated that Porphyromonas gingivalis isolated from esophageal squamous cell carcinoma (ESCC) lesions represents a major pathogen associated with this deadly disease. In this study, we examined the mechanisms associated with host immunity during P. gingivalis infection and demonstrated that experimentally infected ESCC responds by increasing the expression of B7-H4 and lysine demethylase 5B, which allowed subsequent in vivo analysis of the immunotherapeutic effects of anti-B7-H4 and histone demethylase inhibitors in models of chronic infection and immunity against xenografted human tumors. Using three different preclinical mouse models receiving combined therapy, we showed that mice mounted strong resistance against P. gingivalis infection and tumor challenge. This may have occurred via generation of a T cell-mediated response in the microenvironment and formation of immune memory. In ESCC subjects, coexpression of B7-H4 and KDM5B correlated more significantly with bacterial load than with the expression of either molecule alone. These results highlight the unique ability of P. gingivalis to evade immunity and define potential targets that can be exploited therapeutically to improve the control of P. gingivalis infection and the development of associated neoplasia.
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Affiliation(s)
- Xiang Yuan
- Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China.,Department of Medical Oncology, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China
| | - Yiwen Liu
- Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China
| | - Guifang Li
- Department of Pulmonary Tumor Surgery, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China
| | - Zijun Lan
- Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China
| | - Mingyang Ma
- Department of Pulmonary Tumor Surgery, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China
| | - Huaxu Li
- Queen Mary College, Medical College of Nanchang University, Nanchang, China
| | - Jinyu Kong
- Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China
| | - Jiangtao Sun
- Department of Pulmonary Tumor Surgery, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China
| | - Gaochao Hou
- Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China
| | - Xurong Hou
- Department of Medical Oncology, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China
| | - Yingjian Ma
- Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China
| | - Feng Ren
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Fuyou Zhou
- Department of Thoracic Surgery, Anyang Tumor Hospital, Anyang, Henan, China.
| | - Shegan Gao
- Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China. .,Department of Medical Oncology, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, China
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25
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The cancer driver genes IDH1/2, JARID1C/ KDM5C, and UTX/ KDM6A: crosstalk between histone demethylation and hypoxic reprogramming in cancer metabolism. Exp Mol Med 2019; 51:1-17. [PMID: 31221981 PMCID: PMC6586683 DOI: 10.1038/s12276-019-0230-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/12/2018] [Indexed: 12/16/2022] Open
Abstract
Recent studies on mutations in cancer genomes have distinguished driver mutations from passenger mutations, which occur as byproducts of cancer development. The cancer genome atlas (TCGA) project identified 299 genes and 24 pathways/biological processes that drive tumor progression (Cell 173: 371-385 e318, 2018). Of the 299 driver genes, 12 genes are involved in histones, histone methylation, and demethylation. Among these 12 genes, those encoding the histone demethylases JARID1C/KDM5C and UTX/KDM6A were identified as cancer driver genes. Furthermore, gain-of-function mutations in genes encoding metabolic enzymes, such as isocitrate dehydrogenases (IDH)1/2, drive tumor progression by producing an oncometabolite, D-2-hydroxyglutarate (D-2HG), which is a competitive inhibitor of α-ketoglutarate, O2-dependent dioxygenases such as Jumonji domain-containing histone demethylases, and DNA demethylases. Studies on oncometabolites suggest that histone demethylases mediate metabolic changes in chromatin structure. We have reviewed the most recent findings regarding cancer-specific metabolic reprogramming and the tumor-suppressive roles of JARID1C/KDM5C and UTX/KDM6A. We have also discussed mutations in other isoforms such as the JARID1A, 1B, 1D of KDM5 subfamilies and the JMJD3/KDM6B of KDM6 subfamilies, which play opposing roles in tumor progression as oncogenes or tumor suppressors depending on the cancer cell type. Genes involved in the removal of methyl groups from histones associated with DNA can promote or suppress tumor growth depending on the metabolic status of the cancer cell. Hyunsung Park and colleagues at the University of Seoul, South Korea, review current knowledge of two genes encoding histone demethylases which have been identified by The Cancer Genome Atlas (TCGA) project as cancer driver genes. Because these demethylase enzymes rely on cellular metabolites to function, their effect is influenced by metabolic conditions in the tumor microenvironment such as low oxygen. The mechanisms through which changes in histone methylation affect the expression of genes involved in tumor progression remain unknown. Further understanding of how cancer metabolism affects the modification of histones will help guide the development of more effective cancer treatments.
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26
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Sun X, Li Z, Niu Y, Zhao L, Huang Y, Li Q, Zhang S, Chen T, Fu T, Yang T, An X, Jiang Y, Zhang J. Jarid1b promotes epidermal differentiation by mediating the repression of Ship1 and activation of the AKT/Ovol1 pathway. Cell Prolif 2019; 52:e12638. [PMID: 31152465 PMCID: PMC6797505 DOI: 10.1111/cpr.12638] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 12/13/2022] Open
Abstract
Objectives Terminally differentiated stratified squamous epithelial cells play an important role in barrier protection of the skin. The integrity of epidermal cells is maintained by tight regulation of proliferation and differentiation. The aim of this study was to investigate the role of epigenetic regulator H3K4me3 and its demethylase Jarid1b in the control of epithelial cell differentiation. Materials and methods RT‐qPCR, Western blotting and IHC were used to detect mRNA and protein levels. We analysed cell proliferation by CCK8 assay and cell migration by wound healing assay. ChIP was used to measure H3K4me3 enrichment. A chamber graft model was established for epidermal development. Results Our studies showed that H3K4me3 was decreased during epidermal differentiation. The H3K4me3 demethylase Jarid1b positively controlled epidermal cell differentiation in vitro and in vivo. Mechanistically, we found that Jarid1b substantially increased the expression of mesenchymal‐epithelial transition (MET)‐related genes, among which Ovol1 positively regulated differentiation gene expression. In addition, Ovol1 expression was repressed by PI3K‐AKT pathway inhibitors and overexpression (O/E) of the PI3K‐AKT pathway suppressor Ship1. Knockdown (KD) of Ship1 activated downstream PI3K‐AKT pathway and enhanced Ovol1 expression in HaCaT. Importantly, we found that Jarid1b negatively regulated Ship1 expression, but not that of Pten, by directly binding to its promoter to modulate H3K4me3 enrichment. Conclusion Our results identify an essential role of Jarid1b in the regulation of the Ship1/AKT/Ovol1 pathway to promote epithelial cell differentiation.
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Affiliation(s)
- Xuewei Sun
- Department of Otolaryngology-Head and Neck Surgery, Key Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Zhiyuan Li
- Department of Otolaryngology-Head and Neck Surgery, Key Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yanfang Niu
- Department of Otolaryngology-Head and Neck Surgery, Key Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Lijuan Zhao
- Department of Otolaryngology-Head and Neck Surgery, Key Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yichuan Huang
- Department of Otolaryngology-Head and Neck Surgery, Key Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Qiang Li
- Department of Andrology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Shengnan Zhang
- Department of Otolaryngology-Head and Neck Surgery, Key Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Ting Chen
- Department of Otolaryngology-Head and Neck Surgery, Key Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Tao Fu
- Department of Otolaryngology-Head and Neck Surgery, Key Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Tao Yang
- Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Xiaofei An
- Department of Endocrinology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Yan Jiang
- Department of Otolaryngology-Head and Neck Surgery, Key Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Jisheng Zhang
- Department of Otolaryngology-Head and Neck Surgery, Key Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Shandong Key Laboratory of Digital Medicine and Computer Assisted Surgery, Qingdao, China.,Shandong College Collaborative Innovation Center of Digital Medicine in Clinical Treatment and Nutrition Health, Qingdao, China
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27
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Mocavini I, Pippa S, Licursi V, Paci P, Trisciuoglio D, Mannironi C, Presutti C, Negri R. JARID1B expression and its function in DNA damage repair are tightly regulated by miRNAs in breast cancer. Cancer Sci 2019; 110:1232-1243. [PMID: 30588710 PMCID: PMC6447846 DOI: 10.1111/cas.13925] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 12/13/2018] [Accepted: 12/16/2018] [Indexed: 12/18/2022] Open
Abstract
JARID1B/KDM5B histone demethylase's mRNA is markedly overexpressed in breast cancer tissues and cell lines and the protein has been shown to have a prominent role in cancer cell proliferation and DNA repair. However, the mechanism of its post‐transcriptional regulation in cancer cells remains elusive. We performed a computational analysis of transcriptomic data from a set of 103 breast cancer patients, which, along with JARID1B upregulation, showed a strong downregulation of 2 microRNAs (miRNAs), mir‐381 and mir‐486, potentially targeting its mRNA. We showed that both miRNAs can target JARID1B 3′UTR and reduce luciferase's activity in a complementarity‐driven repression assay. Moreover, MCF7 breast cancer cells overexpressing JARID1B showed a strong protein reduction when transfected with mir‐486. This protein's decrease is accompanied by accumulation of DNA damage, enhanced radiosensitivity and increase of BRCA1 mRNA, 3 features previously correlated with JARID1B silencing. These results enlighten an important role of a miRNA’s circuit in regulating JARID1B's activity and suggest new perspectives for epigenetic therapies.
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Affiliation(s)
| | - Simone Pippa
- Department of Biology and Biotechnology "C. Darwin,", "Sapienza" - University of Rome, Rome, Italy
| | - Valerio Licursi
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Daniela Trisciuoglio
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Cecilia Mannironi
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Carlo Presutti
- Department of Biology and Biotechnology "C. Darwin,", "Sapienza" - University of Rome, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin,", "Sapienza" - University of Rome, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
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28
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Dorosz J, Kristensen LH, Aduri NG, Mirza O, Lousen R, Bucciarelli S, Mehta V, Sellés-Baiget S, Solbak SMØ, Bach A, Mesa P, Hernandez PA, Montoya G, Nguyen TTTN, Rand KD, Boesen T, Gajhede M. Molecular architecture of the Jumonji C family histone demethylase KDM5B. Sci Rep 2019; 9:4019. [PMID: 30858420 PMCID: PMC6411775 DOI: 10.1038/s41598-019-40573-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/19/2019] [Indexed: 12/02/2022] Open
Abstract
The full length human histone 3 lysine 4 demethylase KDM5B (PLU-1/Jarid1B) has been studied using Hydrogen/Deuterium exchange mass spectrometry, homology modelling, sequence analysis, small angle X-ray scattering and electron microscopy. This first structure on an intact multi-domain Jumonji histone demethylase reveal that the so-called PLU region, in the central region of KDM5B, has a curved α-helical three-dimensional structure, that acts as a rigid linker between the catalytic core and a region comprising four α-helices, a loop comprising the PHD2 domain, two large intrinsically disordered loops and the PHD3 domain in close proximity. The dumbbell shaped and curved KDM5B architecture observed by electron microscopy is complementary to the nucleosome surface and has a striking overall similarity to that of the functionally related KDM1A/CoREST complex. This could suggest that there are similarities between the demethylation mechanisms employed by the two histone 3 lysine 4 demethylases at the molecular level.
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Affiliation(s)
- Jerzy Dorosz
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Line Hyltoft Kristensen
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Nanda G Aduri
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Osman Mirza
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Rikke Lousen
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Saskia Bucciarelli
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Ved Mehta
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Selene Sellés-Baiget
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Sara Marie Øie Solbak
- Medicinal Chemistry Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Anders Bach
- Medicinal Chemistry Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Pablo Mesa
- Protein Structure & Function Programme, Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
| | - Pablo Alcon Hernandez
- Protein Structure & Function Programme, Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
| | - Guillermo Montoya
- Protein Structure & Function Programme, Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
| | - Tam T T N Nguyen
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Kasper D Rand
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Thomas Boesen
- Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Michael Gajhede
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark.
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29
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Xhabija B, Kidder BL. KDM5B is a master regulator of the H3K4-methylome in stem cells, development and cancer. Semin Cancer Biol 2018; 57:79-85. [PMID: 30448242 DOI: 10.1016/j.semcancer.2018.11.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 12/12/2022]
Abstract
Epigenetic regulation of chromatin plays a critical role in controlling stem cell function and tumorigenesis. The histone lysine demethylase, KDM5B, which catalyzes the demethylation of histone 3 lysine 4 (H3K4), is important for embryonic stem (ES) cell differentiation, and is a critical regulator of the H3K4-methylome during early mouse embryonic pre-implantation stage development. KDM5B is also overexpressed, amplified, or mutated in many cancer types. In cancer cells, KDM5B regulates expression of oncogenes and tumor suppressors by modulating H3K4 methylation levels. In this review, we examine how KDM5B regulates gene expression and cellular fates of stem cells and cancer cells by temporally and spatially controlling H3K4 methylation levels.
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Affiliation(s)
- Besa Xhabija
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
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30
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Histone demethylase JARID1B regulates proliferation and migration of pulmonary arterial smooth muscle cells in mice with chronic hypoxia-induced pulmonary hypertension via nuclear factor-kappa B (NFkB). Cardiovasc Pathol 2018; 37:8-14. [DOI: 10.1016/j.carpath.2018.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/14/2018] [Accepted: 07/27/2018] [Indexed: 01/05/2023] Open
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Sapienza MR, Abate F, Melle F, Orecchioni S, Fuligni F, Etebari M, Tabanelli V, Laginestra MA, Pileri A, Motta G, Rossi M, Agostinelli C, Sabattini E, Pimpinelli N, Truni M, Falini B, Cerroni L, Talarico G, Piccioni R, Amente S, Indio V, Tarantino G, Brundu F, Paulli M, Berti E, Facchetti F, Dellino GI, Bertolini F, Tripodo C, Rabadan R, Pileri SA. Blastic plasmacytoid dendritic cell neoplasm: genomics mark epigenetic dysregulation as a primary therapeutic target. Haematologica 2018; 104:729-737. [PMID: 30381297 PMCID: PMC6442957 DOI: 10.3324/haematol.2018.202093] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/30/2018] [Indexed: 01/01/2023] Open
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and aggressive hematologic malignancy for which there is still no effective therapy. In order to identify genetic alterations useful for a new treatment design, we used whole-exome sequencing to analyze 14 BPDCN patients and the patient-derived CAL-1 cell line. The functional enrichment analysis of mutational data reported the epigenetic regulatory program to be the most significantly undermined (P<0.0001). In particular, twenty-five epigenetic modifiers were found mutated (e.g. ASXL1, TET2, SUZ12, ARID1A, PHF2, CHD8); ASXL1 was the most frequently affected (28.6% of cases). To evaluate the impact of the identified epigenetic mutations at the gene-expression and Histone H3 lysine 27 trimethylation/acetylation levels, we performed additional RNA and pathology tissue-chromatin immunoprecipitation sequencing experiments. The patients displayed enrichment in gene signatures regulated by methylation and modifiable by decitabine administration, shared common H3K27-acetylated regions, and had a set of cell-cycle genes aberrantly up-regulated and marked by promoter acetylation. Collectively, the integration of sequencing data showed the potential of a therapy based on epigenetic agents. Through the adoption of a preclinical BPDCN mouse model, established by CAL-1 cell line xenografting, we demonstrated the efficacy of the combination of the epigenetic drugs 5’-azacytidine and decitabine in controlling disease progression in vivo.
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Affiliation(s)
- Maria Rosaria Sapienza
- Hematopathology Unit, Department of Experimental, Diagnostic, and Specialty Medicine, S. Orsola-Malpighi Hospital, University of Bologna, Italy
| | - Francesco Abate
- Department of Systems Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA.,Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Federica Melle
- Division of Haematopathology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Stefania Orecchioni
- Laboratory of Hematology-Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Fabio Fuligni
- Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Maryam Etebari
- Hematopathology Unit, Department of Experimental, Diagnostic, and Specialty Medicine, S. Orsola-Malpighi Hospital, University of Bologna, Italy
| | - Valentina Tabanelli
- Division of Haematopathology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Maria Antonella Laginestra
- Hematopathology Unit, Department of Experimental, Diagnostic, and Specialty Medicine, S. Orsola-Malpighi Hospital, University of Bologna, Italy
| | - Alessandro Pileri
- Dermatology Unit, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy.,Division of Dermatology, Department of Surgery and Translational Medicine, University of Florence, Italy
| | - Giovanna Motta
- Division of Haematopathology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Maura Rossi
- Hematopathology Unit, Department of Experimental, Diagnostic, and Specialty Medicine, S. Orsola-Malpighi Hospital, University of Bologna, Italy
| | - Claudio Agostinelli
- Hematopathology Unit, Department of Experimental, Diagnostic, and Specialty Medicine, S. Orsola-Malpighi Hospital, University of Bologna, Italy
| | - Elena Sabattini
- Hematopathology Unit, Department of Experimental, Diagnostic, and Specialty Medicine, S. Orsola-Malpighi Hospital, University of Bologna, Italy
| | - Nicola Pimpinelli
- Division of Dermatology, Department of Surgery and Translational Medicine, University of Florence, Italy
| | - Mauro Truni
- Pathological Anatomy Histology & Cytogenetics, Niguarda Cancer Center, Niguarda-Ca' Granda Hospital, Milan, Italy
| | - Brunangelo Falini
- Institute of Hematology and Center for Hemato-Oncology Research (CREO), University and Hospital of Perugia, Italy
| | - Lorenzo Cerroni
- Universitätsklinik für Dermatologie und Venerologie, LKH-Universitatsklinikum Graz, Austria
| | - Giovanna Talarico
- Laboratory of Hematology-Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Rossana Piccioni
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples 'Federico II', Italy
| | - Valentina Indio
- "Giorgio Prodi" Cancer Research Center, University of Bologna, Italy
| | | | - Francesco Brundu
- Department of Systems Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Marco Paulli
- Unit of Anatomic Pathology, Department of Molecular Medicine, University of Pavia and Fondazione IRCCS San Matteo Policlinic, Pavia, Italy
| | - Emilio Berti
- Department of Dermatology, Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinic and Milan University, Milan, Italy
| | - Fabio Facchetti
- Pathology Section, Department of Molecular and Translational Medicine, University of Brescia, Italy
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Italy
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Health Science, Human Pathology Section, University of Palermo School of Medicine, Italy
| | - Raul Rabadan
- Department of Systems Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA.,Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Stefano A Pileri
- Division of Haematopathology, IEO European Institute of Oncology IRCCS, Milan, Italy
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Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Nat Commun 2018; 9:3815. [PMID: 30232459 PMCID: PMC6145927 DOI: 10.1038/s41467-018-05729-w] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 07/24/2018] [Indexed: 01/03/2023] Open
Abstract
Intratumoral heterogeneity in cancers arises from genomic instability and epigenomic plasticity and is associated with resistance to cytotoxic and targeted therapies. We show here that cell-state heterogeneity, defined by differentiation-state marker expression, is high in triple-negative and basal-like breast cancer subtypes, and that drug tolerant persister (DTP) cell populations with altered marker expression emerge during treatment with a wide range of pathway-targeted therapeutic compounds. We show that MEK and PI3K/mTOR inhibitor-driven DTP states arise through distinct cell-state transitions rather than by Darwinian selection of preexisting subpopulations, and that these transitions involve dynamic remodeling of open chromatin architecture. Increased activity of many chromatin modifier enzymes, including BRD4, is observed in DTP cells. Co-treatment with the PI3K/mTOR inhibitor BEZ235 and the BET inhibitor JQ1 prevents changes to the open chromatin architecture, inhibits the acquisition of a DTP state, and results in robust cell death in vitro and xenograft regression in vivo. Resistance to therapy can be driven by intratumoral heterogeneity. Here, the authors show that drug tolerant persistent cell populations emerge during treatment, and these emergent populations arise through epigenetically mediated cell state transitions rather than sub population selection.
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Lebrun N, Mehler-Jacob C, Poirier K, Zordan C, Lacombe D, Carion N, Billuart P, Bienvenu T. Novel KDM5B splice variants identified in patients with developmental disorders: Functional consequences. Gene 2018; 679:305-313. [PMID: 30217758 DOI: 10.1016/j.gene.2018.09.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/28/2018] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
Histone lysine methylation influences processes such as gene expression and DNA repair. Thirty Jumonji C (JmjC) domain-containing proteins have been identified and phylogenetically clustered into seven subfamilies. Most JmjC domain-containing proteins have been shown to possess histone demethylase activity toward specific histone methylation marks. One of these subfamilies, the KDM5 family, is characterized by five conserved domains and includes four members. Interestingly, de novo loss-of-function and missense variants in KDM5B were identified in patients with intellectual disability (ID) and autism spectrum disorder (ASD) but also in unaffected individuals. Here, we report two novel de novo splice variants in the KDM5B gene in three patients with ID and ASD. The c.808 + 1G > A variant was identified in a boy with mild ID and autism traits and is associated with a significant reduced KDM5B mRNA expression without alteration of its H3K4me3 pattern. In contrast, the c.576 + 2T > C variant was found in twins with global delay in developmental milestones, poor language and ASD. This variant causes the production of an abnormal transcript which may produce an altered protein with the loss of the ARID1B domain with an increase in global gene H3K4me3. Our data reinforces the recent observation that the KDM5B haploinsufficiency is not a mechanism involved in intellectual disability and that KDM5B disorder associated with LOF variants is a recessive disorder. However, some variants may also cause gain of function, and need to be interpreted with caution, and functional studies should be performed to identify the molecular consequences of these different rare variants.
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Affiliation(s)
- Nicolas Lebrun
- Inserm, U1016, Institut Cochin, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; CNRS, UMR8104, Paris, France; Institut de Psychiatrie et de Neurosciences de Paris, 102 rue de la santé, 75014 Paris, France
| | - Claire Mehler-Jacob
- Service de Neuropédiatrie, HU-Paris Sud site Bicêtre AP-HP, 78 rue du Général Leclerc, 94270 Le Kremlin-Bicêtre, France
| | - Karine Poirier
- Inserm, U1016, Institut Cochin, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; CNRS, UMR8104, Paris, France
| | - Cecile Zordan
- Service de Génétique Médicale, Hôpital Pellegrin, Place Amélie Raba-Léon, CHU de Bordeaux, 33076 Bordeaux Cedex, France
| | - Didier Lacombe
- Service de Génétique Médicale, Hôpital Pellegrin, Place Amélie Raba-Léon, CHU de Bordeaux, 33076 Bordeaux Cedex, France
| | - Nathalie Carion
- Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, AP-HP, Paris, France
| | - Pierre Billuart
- Inserm, U1016, Institut Cochin, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; CNRS, UMR8104, Paris, France; Institut de Psychiatrie et de Neurosciences de Paris, 102 rue de la santé, 75014 Paris, France
| | - Thierry Bienvenu
- Inserm, U1016, Institut Cochin, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; CNRS, UMR8104, Paris, France; Institut de Psychiatrie et de Neurosciences de Paris, 102 rue de la santé, 75014 Paris, France; Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, AP-HP, Paris, France.
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Abstract
Differentiation of stem cells into highly specialised cells requires gene expression changes brought about by remodelling of the chromatin architecture. During this lineage-commitment process, the majority of DNA needs to be packaged into inactive heterochromatin, allowing only a subset of regulatory elements to remain open and functionally required genes to be expressed. Epigenetic mechanisms such as DNA methylation, post-translational modifications to histone tails, and nucleosome positioning all potentially contribute to the changes in higher order chromatin structure during differentiation. The mammary gland is a particularly useful model to study these complex epigenetic processes since the majority of its development is postnatal, the gland is easily accessible, and development occurs in a highly reproducible manner. Inappropriate epigenetic remodelling can also drive tumourigenesis; thus, insights into epigenetic remodelling during mammary gland development advance our understanding of breast cancer aetiology. We review the current literature surrounding DNA methylation and histone modifications in the developing mammary gland and its implications for breast cancer.
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Affiliation(s)
- Holly Holliday
- The Kinghorn Cancer Centre, Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia
| | - Laura A Baker
- The Kinghorn Cancer Centre, Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia
| | - Simon R Junankar
- The Kinghorn Cancer Centre, Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia
| | - Susan J Clark
- St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia.,Epigenetics Research Program, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Alexander Swarbrick
- The Kinghorn Cancer Centre, Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia. .,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia.
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35
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Shen X, Cheng G, Xu L, Wu W, Chen Z, Du P. Jumonji AT-rich interactive domain 1B promotes the growth of pancreatic tumors via the phosphatase and tensin homolog/protein kinase B signaling pathway. Oncol Lett 2018; 16:267-275. [PMID: 29928411 PMCID: PMC6006380 DOI: 10.3892/ol.2018.8618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 01/10/2018] [Indexed: 02/06/2023] Open
Abstract
Jumonji AT-rich interactive domain 1B (JARID1B) has been revealed to remove methyl residues from methylated lysine 4 on histone H3 (H3K4) and has also been reported to be associated with the progression of numerous types of tumor. However, its roles and mechanisms in pancreatic cancer (PC) remain unknown. The present study demonstrated that JARID1B is elevated in PC and is associated with the growth of pancreatic tumors. Overexpression of JARID1B significantly promoted the proliferation in vitro and tumor formation in vivo of PC cells. Furthermore, silencing the expression of JARID1B in other PC cells revealed opposite effects. Further research revealed that JARID1B exerted its function through modulation of H3K4me3 at the phosphatase and tensin homolog (PTEN) gene promoter which was associated with inactive PTEN transcription. To the best of our knowledge, the present study was the first to demonstrate that JARID1B promotes the growth of PC and that targeting JARID1B may be a useful strategy to suppress the progression of PC.
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Affiliation(s)
- Xudong Shen
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Guilian Cheng
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Liming Xu
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Wei Wu
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Zhengrong Chen
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Peng Du
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China,Correspondence to: Mr. Peng Du, Department of General Surgery, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, Jiangsu 215004, P.R. China, E-mail:
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36
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Cui Y, Zhang Y, Wei Z, Gao J, Yu T, Chen R, Lv X, Pan C. Pig KDM5B: mRNA expression profiles of different tissues and testicular cells and association analyses with testicular morphology traits. Gene 2018; 650:27-33. [DOI: 10.1016/j.gene.2018.01.092] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/18/2018] [Accepted: 01/29/2018] [Indexed: 12/31/2022]
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37
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Histone demethylase lysine demethylase 5B in development and cancer. Oncotarget 2018; 8:8980-8991. [PMID: 27974677 PMCID: PMC5352456 DOI: 10.18632/oncotarget.13858] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/08/2016] [Indexed: 12/25/2022] Open
Abstract
Histone methylation is one of the most important chromatin posttranslational modifications. It has a range of influences on nuclear functions including epigenetic inheritance, transcriptional regulation and the maintenance of genome integrity. Changes in histone methylation status take part in various physiological and pathological processes. KDM5B (lysine demethylase 5B, also called JARID1B or PLU-1) encodes the histone H3 lysine4 (H3K4) demethylase and exhibits a strong transcriptional repression activity. KDM5B plays a role in cell differentiation, stem cell self-renewal and other developmental progresses. Recent studies showed that KDM5B expression was increased in breast, bladder, lung, prostate and many other tumors and promotes tumor initiation, invasion and metastasis. Given its association with tumor progression and prognosis of cancer patients, KDM5B was proposed to be a novel target for the prevention and treatment of human cancers. In this review, we will summarize recent advances in our understanding of the regulation and function of KDM5B in development and cancer.
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38
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Kuźbicki Ł, Lange D, Stanek-Widera A, Chwirot BW. Prognostic significance of RBP2-H1 variant of JARID1B in melanoma. BMC Cancer 2017; 17:854. [PMID: 29246117 PMCID: PMC5731204 DOI: 10.1186/s12885-017-3836-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 11/23/2017] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Histone demethylase JARID1B plays several context dependent roles in epigenetic regulation of cellular differentiation in normal development and is highly expressed in multiple human cancers. The protein is a strong transcriptional repressor capable of downregulating numerous genes. There are three splicing isoforms of JARID1B, however the links between the protein structure and function are not clear. The expression pattern of JARID1B in human melanoma seems to be different from observed in other cancers. Moreover, up to now no data on the impact of JARID1B expression in cutaneous melanoma on the patients' prognosis have been reported. METHODS We investigated immunohistochemically the association of intratumoral expression of total JARID1B protein and its RBP2-H1 isoform in primary and metastatic melanomas with prognosis for the patients. RESULTS Expression of both total JARID1B protein and its RBP2-H1 variant was found in all the melanomas investigated. Our results indicate, however, that only high (above 90% of the cells) intratumoral expression of RBP2-H1 can be considered prognostic factor associated with worse overall survival of the patients. CONCLUSIONS Such results if considered together with data demonstrating a switch to enhanced expression of RBP2-H1 at early stages of malignant transformation of melanocytes are in agreement with hypothetical crucial role of JARID1B in the course of melanoma development and progression and suggest that altered splicing of JARID1B may be important factor increasing melanoma aggressiveness.
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Affiliation(s)
- Łukasz Kuźbicki
- Department of Medical Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - Dariusz Lange
- Department of Tumor Pathology, Oncology Center - Maria Skłodowska-Curie Institute, Wybrzeże Armii Krajowej 15, 44-101, Gliwice, Poland
| | - Agata Stanek-Widera
- Department of Tumor Pathology, Oncology Center - Maria Skłodowska-Curie Institute, Wybrzeże Armii Krajowej 15, 44-101, Gliwice, Poland
| | - Barbara W Chwirot
- Department of Medical Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland.
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Ahsendorf T, Müller FJ, Topkar V, Gunawardena J, Eils R. Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant. PLoS One 2017; 12:e0186324. [PMID: 29216191 PMCID: PMC5720766 DOI: 10.1371/journal.pone.0186324] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/28/2017] [Indexed: 11/30/2022] Open
Abstract
The DNA microstates that regulate transcription include sequence-specific transcription factors (TFs), coregulatory complexes, nucleosomes, histone modifications, DNA methylation, and parts of the three-dimensional architecture of genomes, which could create an enormous combinatorial complexity across the genome. However, many proteins and epigenetic marks are known to colocalize, suggesting that the information content encoded in these marks can be compressed. It has so far proved difficult to understand this compression in a systematic and quantitative manner. Here, we show that simple linear models can reliably predict the data generated by the ENCODE and Roadmap Epigenomics consortia. Further, we demonstrate that a small number of marks can predict all other marks with high average correlation across the genome, systematically revealing the substantial information compression that is present in different cell lines. We find that the linear models for activating marks are typically cell line-independent, while those for silencing marks are predominantly cell line-specific. Of particular note, a nuclear receptor corepressor, transducin beta-like 1 X-linked receptor 1 (TBLR1), was highly predictive of other marks in two hematopoietic cell lines. The methodology presented here shows how the potentially vast complexity of TFs, coregulators, and epigenetic marks at eukaryotic genes is highly redundant and that the information present can be compressed onto a much smaller subset of marks. These findings could be used to efficiently characterize cell lines and tissues based on a small number of diagnostic marks and suggest how the DNA microstates, which regulate the expression of individual genes, can be specified.
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Affiliation(s)
- Tobias Ahsendorf
- Division of Theoretical Bioinformatics, German Cancer Research Center, Heidelberg, Baden-Württemberg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Baden-Württemberg, Germany
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Ved Topkar
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard College, Boston, Massachusetts, United States of America
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center, Heidelberg, Baden-Württemberg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Heidelberg, Baden-Württemberg, Germany
- * E-mail:
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Krizkova S, Kepinska M, Emri G, Eckschlager T, Stiborova M, Pokorna P, Heger Z, Adam V. An insight into the complex roles of metallothioneins in malignant diseases with emphasis on (sub)isoforms/isoforms and epigenetics phenomena. Pharmacol Ther 2017; 183:90-117. [PMID: 28987322 DOI: 10.1016/j.pharmthera.2017.10.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Metallothioneins (MTs) belong to a group of small cysteine-rich proteins that are ubiquitous throughout all kingdoms. The main function of MTs is scavenging of free radicals and detoxification and homeostating of heavy metals. In humans, 16 genes localized on chromosome 16 have been identified to encode four MT isoforms labelled by numbers (MT-1-MT-4). MT-2, MT-3 and MT-4 proteins are encoded by a single gene. MT-1 comprises many (sub)isoforms. The known active MT-1 genes are MT-1A, -1B, -1E, -1F, -1G, -1H, -1M and -1X. The rest of the MT-1 genes (MT-1C, -1D, -1I, -1J and -1L) are pseudogenes. The expression and localization of individual MT (sub)isoforms and pseudogenes vary at intra-cellular level and in individual tissues. Changes in MT expression are associated with the process of carcinogenesis of various types of human malignancies, or with a more aggressive phenotype and therapeutic resistance. Hence, MT (sub)isoform profiling status could be utilized for diagnostics and therapy of tumour diseases. This review aims on a comprehensive summary of methods for analysis of MTs at (sub)isoforms levels, their expression in single tumour diseases and strategies how this knowledge can be utilized in anticancer therapy.
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Affiliation(s)
- Sona Krizkova
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic; Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Marta Kepinska
- Department of Biomedical and Environmental Analysis, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland
| | - Gabriella Emri
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Nagyerdei krt 98, H-4032 Debrecen, Hungary
| | - Tomas Eckschlager
- Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, V Uvalu 84, CZ-150 06 Prague 5, Czech Republic
| | - Marie Stiborova
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, CZ-128 40 Prague 2, Czech Republic
| | - Petra Pokorna
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, CZ-128 40 Prague 2, Czech Republic; Department of Oncology, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, V Uvalu 84, CZ-150 06 Prague 5, Czech Republic
| | - Zbynek Heger
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic; Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Vojtech Adam
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic; Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic.
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41
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Harmeyer KM, Facompre ND, Herlyn M, Basu D. JARID1 Histone Demethylases: Emerging Targets in Cancer. Trends Cancer 2017; 3:713-725. [PMID: 28958389 DOI: 10.1016/j.trecan.2017.08.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 01/04/2023]
Abstract
JARID1 proteins are histone demethylases that both regulate normal cell fates during development and contribute to the epigenetic plasticity that underlies malignant transformation. This H3K4 demethylase family participates in multiple repressive transcriptional complexes at promoters and has broader regulatory effects on chromatin that remain ill-defined. There is growing understanding of the oncogenic and tumor suppressive functions of JARID1 proteins, which are contingent on cell context and the protein isoform. Their contributions to stem cell-like dedifferentiation, tumor aggressiveness, and therapy resistance in cancer have sustained interest in the development of JARID1 inhibitors. Here we review the diverse and context-specific functions of the JARID1 proteins that may impact the utilization of emerging targeted inhibitors of this histone demethylase family in cancer therapy.
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Affiliation(s)
- Kayla M Harmeyer
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicole D Facompre
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Devraj Basu
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104, USA; The Wistar Institute, Philadelphia, PA 19104, USA; Philadelphia VA Medical Center, Philadelphia, PA 19104, USA.
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42
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Nanashima N, Horie K, Chiba M, Nakano M, Maeda H, Nakamura T. Anthocyanin-rich blackcurrant extract inhibits proliferation of the MCF10A healthy human breast epithelial cell line through induction of G0/G1 arrest and apoptosis. Mol Med Rep 2017; 16:6134-6141. [DOI: 10.3892/mmr.2017.7391] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 05/15/2017] [Indexed: 11/06/2022] Open
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43
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Brier ASB, Loft A, Madsen J, Rosengren T, Nielsen R, Schmidt SF, Liu Z, Yan Q, Gronemeyer H, Mandrup S. The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation. Nucleic Acids Res 2017; 45:1743-1759. [PMID: 27899593 PMCID: PMC5389521 DOI: 10.1093/nar/gkw1156] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 11/01/2016] [Accepted: 11/05/2016] [Indexed: 12/23/2022] Open
Abstract
The KDM5 family of histone demethylases removes the H3K4 tri-methylation (H3K4me3) mark frequently found at promoter regions of actively transcribed genes and is therefore generally considered to contribute to corepression. In this study, we show that knockdown (KD) of all expressed members of the KDM5 family in white and brown preadipocytes leads to deregulated gene expression and blocks differentiation to mature adipocytes. KDM5 KD leads to a considerable increase in H3K4me3 at promoter regions; however, these changes in H3K4me3 have a limited effect on gene expression per se. By contrast, genome-wide analyses demonstrate that KDM5A is strongly enriched at KDM5-activated promoters, which generally have high levels of H3K4me3 and are associated with highly expressed genes. We show that KDM5-activated genes include a large set of cell cycle regulators and that the KDM5s are necessary for mitotic clonal expansion in 3T3-L1 cells, indicating that KDM5 KD may interfere with differentiation in part by impairing proliferation. Notably, the demethylase activity of KDM5A is required for activation of at least a subset of pro-proliferative cell cycle genes. In conclusion, the KDM5 family acts as dual modulators of gene expression in preadipocytes and is required for early stage differentiation and activation of pro-proliferative cell cycle genes.
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Affiliation(s)
- Ann-Sofie B. Brier
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Anne Loft
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jesper G. S. Madsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Thomas Rosengren
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ronni Nielsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Søren F. Schmidt
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Zongzhi Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Hinrich Gronemeyer
- Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, Illkirch, France
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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44
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Facompre ND, Harmeyer KM, Sole X, Kabraji S, Belden Z, Sahu V, Whelan K, Tanaka K, Weinstein GS, Montone KT, Roesch A, Gimotty PA, Herlyn M, Rustgi AK, Nakagawa H, Ramaswamy S, Basu D. JARID1B Enables Transit between Distinct States of the Stem-like Cell Population in Oral Cancers. Cancer Res 2016; 76:5538-49. [PMID: 27488530 PMCID: PMC5026599 DOI: 10.1158/0008-5472.can-15-3377] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 06/15/2016] [Indexed: 01/01/2023]
Abstract
The degree of heterogeneity among cancer stem cells (CSC) remains ill-defined and may hinder effective anti-CSC therapy. Evaluation of oral cancers for such heterogeneity identified two compartments within the CSC pool. One compartment was detected using a reporter for expression of the H3K4me3 demethylase JARID1B to isolate a JARID1B(high) fraction of cells with stem cell-like function. JARID1B(high) cells expressed oral CSC markers including CD44 and ALDH1 and showed increased PI3K pathway activation. They were distinguished from a fraction in a G0-like cell-cycle state characterized by low reactive oxygen species and suppressed PI3K/AKT signaling. G0-like cells lacked conventional CSC markers but were primed to acquire stem cell-like function by upregulating JARID1B, which directly mediated transition to a state expressing known oral CSC markers. The transition was regulated by PI3K signals acting upstream of JARID1B expression, resulting in PI3K inhibition depleting JARID1B(high) cells but expanding the G0-like subset. These findings define a novel developmental relationship between two cell phenotypes that may jointly contribute to CSC maintenance. Expansion of the G0-like subset during targeted depletion of JARID1B(high) cells implicates it as a candidate therapeutic target within the oral CSC pool. Cancer Res; 76(18); 5538-49. ©2016 AACR.
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Affiliation(s)
- Nicole D Facompre
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kayla M Harmeyer
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xavier Sole
- Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sheheryar Kabraji
- Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Zachary Belden
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Varun Sahu
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kelly Whelan
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Koji Tanaka
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gregory S Weinstein
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kathleen T Montone
- Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Phyllis A Gimotty
- Department of Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Anil K Rustgi
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hiroshi Nakagawa
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sridhar Ramaswamy
- Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Devraj Basu
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, Pennsylvania. The Wistar Institute, Philadelphia, Pennsylvania. VA Medical Center, Philadelphia, Pennsylvania.
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45
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Horton JR, Liu X, Gale M, Wu L, Shanks JR, Zhang X, Webber PJ, Bell JSK, Kales SC, Mott BT, Rai G, Jansen DJ, Henderson MJ, Urban DJ, Hall MD, Simeonov A, Maloney DJ, Johns MA, Fu H, Jadhav A, Vertino PM, Yan Q, Cheng X. Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds. Cell Chem Biol 2016; 23:769-781. [PMID: 27427228 PMCID: PMC4958579 DOI: 10.1016/j.chembiol.2016.06.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/15/2016] [Accepted: 06/04/2016] [Indexed: 12/12/2022]
Abstract
The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases removes methyl groups from methylated lysine 4 of histone H3. Accumulating evidence supports a role for KDM5 family members as oncogenic drivers. We compare the in vitro inhibitory properties and binding affinity of ten diverse compounds with all four family members, and present the crystal structures of the KDM5A-linked Jumonji domain in complex with eight of these inhibitors in the presence of Mn(II). All eight inhibitors structurally examined occupy the binding site of α-ketoglutarate, but differ in their specific binding interactions, including the number of ligands involved in metal coordination. We also observed inhibitor-induced conformational changes in KDM5A, particularly those residues involved in the binding of α-ketoglutarate, the anticipated peptide substrate, and intramolecular interactions. We discuss how particular chemical moieties contribute to inhibitor potency and suggest strategies that might be utilized in the successful design of selective and potent epigenetic inhibitors.
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Affiliation(s)
- John R Horton
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Xu Liu
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Molly Gale
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Lizhen Wu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - John R Shanks
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Philip J Webber
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA
| | - Joshua S K Bell
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Bryan T Mott
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Daniel J Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Daniel J Urban
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - David J Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Margaret A Johns
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA
| | - Haian Fu
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Paula M Vertino
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA.
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA.
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46
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Tang B, Qi G, Tang F, Yuan S, Wang Z, Liang X, Li B, Yu S, Liu J, Huang Q, Wei Y, Zhai R, Lei B, Yu H, Jiao X, He S. JARID1B promotes metastasis and epithelial-mesenchymal transition via PTEN/AKT signaling in hepatocellular carcinoma cells. Oncotarget 2016; 6:12723-39. [PMID: 25909289 PMCID: PMC4494969 DOI: 10.18632/oncotarget.3713] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 03/10/2015] [Indexed: 01/02/2023] Open
Abstract
JARID1B is a member of the family of JmjC domain-containing proteins that removes methyl residues from methylated lysine 4 on histone H3 lysine 4 (H3K4). JARID1B has been proposed as an oncogene in many types of tumors; however, its role and underlying mechanisms in hepatocellular carcinoma (HCC) remain unknown. Here we show that JARID1B is elevated in HCC and its expression level is positively correlated with metastasis. In addition Kaplan-Meier survival analysis showed that high expression of JARID1B was associated with decreased overall survival of HCC patients. Overexpression of JARID1B in HCC cells increased proliferation, epithelial-mesenchymal transition, migration and invasion in vitro, and enhanced tumorigenic and metastatic capacities in vivo. In contrast, silencing JARID1B in aggressive and invasive HCC cells inhibited these processes. Mechanistically, we found JARID1B exerts its function through modulation of H3K4me3 at the PTEN gene promoter, which was associated with inactive PTEN transcription. PTEN overexpression blocked JARID1B-driven proliferation, EMT, and metastasis. Our results, for the first time, portray a pivotal role of JARID1B in stimulating metastatic behaviors of HCC cells. Targeting JARID1B may thus be a useful strategy to impede HCC cell invasion and metastasis.
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Affiliation(s)
- Bo Tang
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Guangying Qi
- Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China.,Department of Pathology and Physiopathology, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Fang Tang
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Shengguang Yuan
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Zhenran Wang
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Xingsi Liang
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Bo Li
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Shuiping Yu
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Jie Liu
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Qi Huang
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Yangchao Wei
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Run Zhai
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Biao Lei
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Hongping Yu
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical College, Guilin, Guangxi, People's Republic of China
| | - Xingyuan Jiao
- Department of General Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Songqing He
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi, People's Republic of China.,Laboratory of Liver Injury and Repair Molecular Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
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Bamodu OA, Huang WC, Lee WH, Wu A, Wang LS, Hsiao M, Yeh CT, Chao TY. Aberrant KDM5B expression promotes aggressive breast cancer through MALAT1 overexpression and downregulation of hsa-miR-448. BMC Cancer 2016; 16:160. [PMID: 26917489 PMCID: PMC4768424 DOI: 10.1186/s12885-016-2108-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 02/01/2016] [Indexed: 12/17/2022] Open
Abstract
Background Triple negative breast cancers (TNBC) possess cell dedifferentiation characteristics, carry out activities connate to those of cancer stem cells (CSCs) and are associated with increased metastasis, as well as, poor clinical prognosis. The regulatory mechanism of this highly malignant phenotype is still poorly characterized. Accruing evidence support the role of non-coding RNAs (ncRNAs) as potent regulators of CSC and metastatic gene expression, with their dysregulation implicated in tumorigenesis and disease progression. Methods In this study, we investigated TNBC metastasis, metastasis-associated genes and potential inhibitory mechanisms using bioinformatics, tissue microarray analyses, immunoblotting, polymerase chain reaction, loss and gain of gene function assays and comparative analyses of data obtained. Results Compared with other breast cancer types, the highly metastatic MDA-MB-231 cells concurrently exhibited increased expression levels of Lysine-specific demethylase 5B protein (KDM5B) and long non-coding RNA (lncRNA), MALAT1, suggesting their functional association. KDM5B-silencing in the TNBC cells correlated with the upregulation of hsa-miR-448 and led to suppression of MALAT1 expression with decreased migration, invasion and clonogenic capacity in vitro, as well as, poor survival in vivo. This projects MALAT1 as a mediator of KDM5B oncogenic potential and highlights the critical role of this microRNA, lncRNA and histone demethylase in cancer cell motility and metastatic colonization. Increased expression of KDM5B correlating with disease progression and poor clinical outcome in breast cancer was reversed by hsa-miR-448. Conclusions Our findings demonstrate the critical role of KDM5B and its negative regulator hsa-miR-448 in TNBC metastasis and progression. Hsa-miR-448 disrupting KDM5B-MALAT1 signalling axis and associated activities in TNBC cells, projects it as a putative therapeutic factor for selective eradication of TNBC cells. KDM5B, MALAT1 and hsa-miR-448 are active looped components of the epigenetic poculo mortis in aggressive breast cancer. ![]()
Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2108-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oluwaseun Adebayo Bamodu
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei City, Taiwan. .,Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan.
| | - Wen-Chien Huang
- Department of Thoracic Surgery, Mackay Memorial Hospital, Taipei, 10449, Taiwan.
| | - Wei-Hwa Lee
- Department of Pathology, Taipei Medical University-Shuang Ho Hospital, Taipei, Taiwan.
| | - Alexander Wu
- Graduate Institute of Translational Medicine, Taipei Medical University, Taipei City, Taiwan. .,The PhD Program of Translational Medicine, Academia Sinica, Nankang, Taipei, Taiwan.
| | - Liang Shun Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei City, Taiwan. .,Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan.
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
| | - Chi-Tai Yeh
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei City, Taiwan. .,Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan.
| | - Tsu-Yi Chao
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei City, Taiwan. .,Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan. .,Tri-Service General Hospital, Neihu District, Taipei City, Taiwan.
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48
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Horton JR, Engstrom A, Zoeller EL, Liu X, Shanks JR, Zhang X, Johns MA, Vertino PM, Fu H, Cheng X. Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases. J Biol Chem 2016; 291:2631-46. [PMID: 26645689 PMCID: PMC4742734 DOI: 10.1074/jbc.m115.698449] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 11/17/2015] [Indexed: 12/18/2022] Open
Abstract
The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases remove methyl groups from tri- and dimethylated lysine 4 of histone H3. Accumulating evidence from primary tumors and model systems supports a role for KDM5A (JARID1A/RBP2) and KDM5B (JARID1B/PLU1) as oncogenic drivers. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC). Here we demonstrate that internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes. We present a crystal structure of the linked JmjN-JmjC domain from KDM5A, which reveals that the linked domain fully reconstitutes the cofactor (metal ion and α-ketoglutarate) binding characteristics of other structurally characterized Jumonji domain demethylases. Docking studies with GSK-J1, a selective inhibitor of the KDM6/KDM5 subfamilies, identify critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain. Further, we found that GSK-J1 inhibited the demethylase activity of KDM5C with 8.5-fold increased potency compared with that of KDM5B at 1 mm α-ketoglutarate. In contrast, JIB-04 (a pan-inhibitor of the Jumonji demethylase superfamily) had the opposite effect and was ~8-fold more potent against KDM5B than against KDM5C. Interestingly, the relative selectivity of JIB-04 toward KDM5B over KDM5C in vitro translates to a ~10-50-fold greater growth-inhibitory activity against breast cancer cell lines. These data define the minimal requirements for enzymatic activity of the KDM5 family to be the linked JmjN-JmjC domain coupled with the immediate C-terminal helical zinc-binding domain and provide structural characterization of the linked JmjN-JmjC domain for the KDM5 family, which should prove useful in the design of KDM5 demethylase inhibitors with improved potency and selectivity.
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Affiliation(s)
| | - Amanda Engstrom
- the Graduate Program in Biochemistry, Cell and Developmental Biology
| | | | - Xu Liu
- From the Departments of Biochemistry
| | | | | | | | - Paula M Vertino
- Radiation Oncology, the Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Haian Fu
- the Winship Cancer Institute, Emory University, Atlanta, Georgia 30322 Radiation Oncology, the Emory Chemical Biology Discovery Center, and Hematology and Medical Oncology, and
| | - Xiaodong Cheng
- From the Departments of Biochemistry, the Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
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49
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Gajan A, Barnes VL, Liu M, Saha N, Pile LA. The histone demethylase dKDM5/LID interacts with the SIN3 histone deacetylase complex and shares functional similarities with SIN3. Epigenetics Chromatin 2016; 9:4. [PMID: 26848313 PMCID: PMC4740996 DOI: 10.1186/s13072-016-0053-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/14/2016] [Indexed: 01/01/2023] Open
Abstract
Background Regulation of gene expression by histone-modifying enzymes is essential to control cell fate decisions and developmental processes. Two histone-modifying enzymes, RPD3, a deacetylase, and dKDM5/LID, a demethylase, are present in a single complex, coordinated through the SIN3 scaffold protein. While the SIN3 complex has been demonstrated to have functional histone deacetylase activity, the role of the demethylase dKDM5/LID as part of the complex has not been investigated. Results Here, we analyzed the developmental and transcriptional activities of dKDM5/LID in relation to SIN3. Knockdown of either Sin3A or lid resulted in decreased cell proliferation in S2 cells and wing imaginal discs. Conditional knockdown of either Sin3A or lid resulted in flies that displayed wing developmental defects. Interestingly, overexpression of dKDM5/LID rescued the wing developmental defect due to reduced levels of SIN3 in female flies, indicating a major role for dKDM5/LID in cooperation with SIN3 during development. Together, these observed phenotypes strongly suggest that dKDM5/LID as part of the SIN3 complex can impact previously uncharacterized transcriptional networks. Transcriptome analysis revealed that SIN3 and dKDM5/LID regulate many common genes. While several genes implicated in cell cycle and wing developmental pathways were affected upon altering the level of these chromatin factors, a significant affect was also observed on genes required to mount an effective stress response. Further, under conditions of induced oxidative stress, reduction of SIN3 and/or dKDM5/LID altered the expression of a greater number of genes involved in cell cycle-related processes relative to normal conditions. This highlights an important role for SIN3 and dKDM5/LID proteins to maintain proper progression through the cell cycle in environments of cellular stress. Further, we find that target genes are bound by both SIN3 and dKDM5/LID, however, histone acetylation, not methylation, plays a predominant role in gene regulation by the SIN3 complex. Conclusions We have provided genetic evidence to demonstrate functional cooperation between the histone demethylase dKDM5/LID and SIN3. Biochemical and transcriptome data further support functional links between these proteins. Together, the data provide a solid framework for analyzing the gene regulatory pathways through which SIN3 and dKDM5/LID control diverse biological processes in the organism. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0053-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ambikai Gajan
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Valerie L Barnes
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Mengying Liu
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Nirmalya Saha
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
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Vallianatos CN, Iwase S. Disrupted intricacy of histone H3K4 methylation in neurodevelopmental disorders. Epigenomics 2015; 7:503-19. [PMID: 26077434 DOI: 10.2217/epi.15.1] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Methylation of histone H3 lysine 4 (H3K4me) is an intricately regulated posttranslational modification, which is broadly associated with enhancers and promoters of actively transcribed genomic loci. Recent advances in next-generation sequencing have identified a number of H3K4me regulators mutated in neurodevelopmental disorders including intellectual disabilities, autism spectrum disorders, and schizophrenia. Here, we aim to summarize the molecular function of H3K4me-regulating enzymes in brain development and function. We describe four H3K4me methyltransferases (KMT2A, KMT2C, KMT2D, KMT2F), four demethylases (KDM1A, KDM5A, KDM5B, KDM5C), and two reader proteins (PHF21A, PHF8) mutated in neurodevelopmental disorders. Understanding the role of these chromatin regulators in the development and maintenance of neural connections will advance therapeutic opportunities for prevention and treatment of these lifelong neurodevelopmental disorders.
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Affiliation(s)
- Christina N Vallianatos
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA.,Predoctoral Training Program in Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
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