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Wang H, Helin K. Roles of H3K4 methylation in biology and disease. Trends Cell Biol 2024:S0962-8924(24)00115-6. [PMID: 38909006 DOI: 10.1016/j.tcb.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/13/2024] [Accepted: 06/03/2024] [Indexed: 06/24/2024]
Abstract
Epigenetic modifications, including posttranslational modifications of histones, are closely linked to transcriptional regulation. Trimethylated H3 lysine 4 (H3K4me3) is one of the most studied histone modifications owing to its enrichment at the start sites of transcription and its association with gene expression and processes determining cell fate, development, and disease. In this review, we focus on recent studies that have yielded insights into how levels and patterns of H3K4me3 are regulated, how H3K4me3 contributes to the regulation of specific phases of transcription such as RNA polymerase II initiation, pause-release, heterogeneity, and consistency. The conclusion from these studies is that H3K4me3 by itself regulates gene expression and its precise regulation is essential for normal development and preventing disease.
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Affiliation(s)
- Hua Wang
- Peking University International Cancer Institute, Peking University Cancer Hospital and Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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2
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Cao Y, Wu C, Ma L. Lysine demethylase 5B (KDM5B): A key regulator of cancer drug resistance. J Biochem Mol Toxicol 2024; 38:e23587. [PMID: 38014925 DOI: 10.1002/jbt.23587] [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: 07/25/2023] [Revised: 10/17/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023]
Abstract
Chemoresistance, a roadblock in the chemotherapy process, has been impeding its effective treatment. KDM5B, a member of the histone demethylase family, has been crucial in the emergence and growth of malignancies. More significantly, KDM5B has recently been linked closely to cancer's resistance to chemotherapy. In this review, we explain the biological properties of KDM5B, its function in the emergence and evolution of cancer treatment resistance, and our hopes for future drug resistance-busting combinations involving KDM5B and related targets or medications.
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Affiliation(s)
- Yaquan Cao
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, China
| | - Chunli Wu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Liying Ma
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan, China
- Key Laboratory of Cardio-Cerebrovascular Drug, China Meheco Topfond Pharmaceutical Company, Zhumadian, China
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3
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Wang D, Zhang Y, Liao Z, Ge H, Güngör C, Li Y. KDM5 family of demethylases promotes CD44-mediated chemoresistance in pancreatic adenocarcinomas. Sci Rep 2023; 13:18250. [PMID: 37880235 PMCID: PMC10600175 DOI: 10.1038/s41598-023-44536-2] [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: 05/25/2023] [Accepted: 10/10/2023] [Indexed: 10/27/2023] Open
Abstract
A growing body of evidence suggests that the histone demethylase-lysine demethylase 5 (KDM5) family is associated with drug resistance in cancer cells. However, it is still not clear whether KDM5 family members promote chemotherapy resistance in pancreatic ductal adenocarcinomas (PDAC). Comprehensive bioinformatics analysis was performed to investigate the prognostic value, and functional mechanisms of KDM5 family members in PDAC. The effects of KDM5 family members on drug resistance in PDAC cells and the relationship with CD44, as a stem cell marker, were explored by gene knockout and overexpression strategies. Finally, our findings were validated by functional experiments such as cell viability, colony formation and invasion assays. We found that the expression of KDM5A/C was significantly higher in gemcitabine-resistant cells than in sensitive cells, consistent with the analysis of the GSCALite database. The knockdown of KDM5A/C in PDAC cells resulted in diminished drug resistance, less cell colonies and reduced invasiveness, while KDM5A/C overexpression showed the opposite effect. Of note, the expression of KDM5A/C changed accordingly with the knockdown of CD44. In addition, members of the KDM5 family function in a variety of oncogenic pathways, including PI3K/AKT and Epithelial-Mesenchymal Transition. In conclusion, KDM5 family members play an important role in drug resistance and may serve as new biomarkers or potential therapeutic targets in PDAC patients.
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Affiliation(s)
- Dan Wang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yingjun Zhang
- Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Hunan Agricultural University, Changsha, China
| | - Zhouning Liao
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China
- Division of Translational Immunology, III, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Heming Ge
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cenap Güngör
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yuqiang Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
- NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, China.
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Fernandez TV, Williams ZP, Kline T, Rajendran S, Augustine F, Wright N, Sullivan CAW, Olfson E, Abdallah SB, Liu W, Hoffman EJ, Gupta AR, Singer HS. Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify KDM5B as a risk gene. PLoS One 2023; 18:e0291978. [PMID: 37788244 PMCID: PMC10547198 DOI: 10.1371/journal.pone.0291978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/10/2023] [Indexed: 10/05/2023] Open
Abstract
Motor stereotypies are common in children with autism spectrum disorder (ASD), intellectual disability, or sensory deprivation, as well as in typically developing children ("primary" stereotypies, pCMS). The precise pathophysiological mechanism for motor stereotypies is unknown, although genetic etiologies have been suggested. In this study, we perform whole-exome DNA sequencing in 129 parent-child trios with pCMS and 853 control trios (118 cases and 750 controls after quality control). We report an increased rate of de novo predicted-damaging DNA coding variants in pCMS versus controls, identifying KDM5B as a high-confidence risk gene and estimating 184 genes conferring risk. Genes harboring de novo damaging variants in pCMS probands show significant overlap with those in Tourette syndrome, ASD, and those in ASD probands with high versus low stereotypy scores. An exploratory analysis of these pCMS gene expression patterns finds clustering within the cortex and striatum during early mid-fetal development. Exploratory gene ontology and network analyses highlight functional convergence in calcium ion transport, demethylation, cell signaling, cell cycle and development. Continued sequencing of pCMS trios will identify additional risk genes and provide greater insights into biological mechanisms of stereotypies across diagnostic boundaries.
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Affiliation(s)
- Thomas V. Fernandez
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States America
| | - Zsanett P. Williams
- Department of Psychiatry, Vanderbilt University School of Nursing, Nashville, TN, United States America
| | - Tina Kline
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States America
| | - Shreenath Rajendran
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States America
| | - Farhan Augustine
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States America
| | - Nicole Wright
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
| | - Catherine A. W. Sullivan
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, United States America
| | - Emily Olfson
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
| | - Sarah B. Abdallah
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
| | - Wenzhong Liu
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
| | - Ellen J. Hoffman
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
| | - Abha R. Gupta
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, United States America
| | - Harvey S. Singer
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States America
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5
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Longbotham JE, Kelly MJS, Fujimori DG. Recognition of Histone H3 Methylation States by the PHD1 Domain of Histone Demethylase KDM5A. ACS Chem Biol 2023; 18:1915-1925. [PMID: 33621062 PMCID: PMC8380758 DOI: 10.1021/acschembio.0c00976] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PHD reader domains are chromatin binding modules often responsible for the recruitment of large protein complexes that contain histone modifying enzymes, chromatin remodelers, and DNA repair machinery. A majority of PHD domains recognize N-terminal residues of histone H3 and are sensitive to the methylation state of Lys4 in histone H3 (H3K4). Histone demethylase KDM5A, an epigenetic eraser enzyme that contains three PHD domains, is often overexpressed in various cancers, and its demethylation activity is allosterically enhanced when its PHD1 domain is bound to the H3 tail. The allosteric regulatory function of PHD1 expands roles of reader domains, suggesting unique features of this chromatin interacting module. Our previous studies determined the H3 binding site of PHD1, although it remains unclear how the H3 tail interacts with the N-terminal residues of PHD1 and how PHD1 discriminates against H3 tails with varying degrees of H3K4 methylation. Here, we have determined the solution structure of apo and H3 bound PHD1. We observe conformational changes occurring in PHD1 in order to accommodate H3, which interestingly binds in a helical conformation. We also observe differential interactions of binding residues with differently methylated H3K4 peptides (me0, me1, me2, or me3), providing a rationale for PHD1's preference for lower methylation states of H3K4. We further assessed the contributions of various H3 interacting residues in the PHD1 domain to the binding of H3 peptides. The structural details of the H3 binding site could provide useful information to aid the development of allosteric small molecule modulators of KDM5A.
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Affiliation(s)
- James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 600 16th Street, Genentech Hall, San Francisco, California 94158, United States
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, Genentech Hall, San Francisco, California 94158, United States
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 600 16th Street, Genentech Hall, San Francisco, California 94158, United States
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, Genentech Hall, San Francisco, California 94158, United States
- Quantitative Biosciences Institute, University of California San Francisco, 1700 Fourth Street, San Francisco, California 94158, United States
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6
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Zhang Z, Tan Y, Huang C, Wei X. Redox signaling in drug-tolerant persister cells as an emerging therapeutic target. EBioMedicine 2023; 89:104483. [PMID: 36827719 PMCID: PMC9982619 DOI: 10.1016/j.ebiom.2023.104483] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Drug-tolerant persister (DTP) cells have attracted significant interest, given their predominant role in treatment failure. In this respect, DTP cells reportedly survive after anticancer drug exposure, and their DNA repair mechanisms are altered to enhance adaptive mutation, accounting for the emergence of drug-resistant mutations. DTP cells resume proliferation upon treatment withdrawal and are responsible for cancer relapse. Current evidence suggests that DTP cells mediate redox signaling-mediated cellular homeostasis by developing various adaptive mechanisms, especially metabolic reprogramming that promotes mitochondrial oxidative respiration and a robust antioxidant process. There is an increasing consensus that disrupting redox homeostasis by intervening with redox signaling is theoretically a promising therapeutic strategy for targeting these sinister cells. In this review, we provide a comprehensive overview of the characteristics of DTP cells and the underlying mechanisms involved in redox signaling, aiming to provide a unique perspective on potential therapeutic applications based on their vulnerabilities to redox regulation.
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Affiliation(s)
- Zhe Zhang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, PR China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Yunhan Tan
- West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China.
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, PR China.
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Zhang Y, Chen J, Liu H, Mi R, Huang R, Li X, Fan F, Xie X, Ding J. The role of histone methylase and demethylase in antitumor immunity: A new direction for immunotherapy. Front Immunol 2023; 13:1099892. [PMID: 36713412 PMCID: PMC9874864 DOI: 10.3389/fimmu.2022.1099892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023] Open
Abstract
Epigenetic modifications may alter the proliferation and differentiation of normal cells, leading to malignant transformation. They can also affect normal stimulation, activation, and abnormal function of immune cells in the tissue microenvironment. Histone methylation, coordinated by histone methylase and histone demethylase to stabilize transcription levels in the promoter area, is one of the most common types of epigenetic alteration, which gained increasing interest. It can modify gene transcription through chromatin structure and affect cell fate, at the transcriptome or protein level. According to recent research, histone methylation modification can regulate tumor and immune cells affecting anti-tumor immune response. Consequently, it is critical to have a thorough grasp of the role of methylation function in cancer treatment. In this review, we discussed recent data on the mechanisms of histone methylation on factors associated with immune resistance of tumor cells and regulation of immune cell function.
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Affiliation(s)
- Yuanling Zhang
- School of Medicine, Guizhou University, Guiyang, China,Department of Gastrointestinal Surgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Junhao Chen
- Graduate School of Zunyi Medical University, Zunyi, China
| | - Hang Liu
- Department of Medical Cosmetology, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Rui Mi
- Department of General Surgery, Zhijin County People’s Hospital, Bijie, China
| | - Rui Huang
- Department of Gastrointestinal Surgery, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Xian Li
- Orthopedics Department, Dongguan Songshan Lake Tungwah Hospital, DongGuan, China
| | - Fei Fan
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Panzhihua University, Panzhihua, China
| | - Xueqing Xie
- School of Medicine, Guizhou University, Guiyang, China
| | - Jie Ding
- Department of Gastrointestinal Surgery, Guizhou Provincial People’s Hospital, Guiyang, China,*Correspondence: Jie Ding,
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8
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Hoekstra M, Ridgeway NH, Biggar KK. Characterization of KDM5 lysine demethylase family substrate preference and identification of novel substrates. J Biochem 2022; 173:31-42. [PMID: 36205465 DOI: 10.1093/jb/mvac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/21/2022] [Accepted: 10/03/2022] [Indexed: 12/29/2022] Open
Abstract
The KDM5/JARID1 sub-family are 2-oxoglutarate and Fe(II)-dependent lysine-specific histone demethylases that are characterized by their Jumonji catalytic domains. The KDM5 family is known to remove tri-/di-methyl modifications from lysine-4 of histone H3 (i.e. H3-K4me2/3), a mark associated with active gene expression. As a result, studies to date have revolved around the influence of KDM5 on disease through their ability to regulate H3-K4me2/3. Recent evidence demonstrates that KDM5 may influence disease beyond H3-K4 demethylation, making it critical to further investigate KDM5-mediated demethylation of non-histone proteins. To help identify potential non-histone substrates for the KDM5 family, we developed a library of 180 permutated peptide substrates, with sequences that are systematically altered from the wild-type H3-K4me3 substrate. From this library, we characterized recombinant KDM5A/B/C/D substrate preference and developed recognition motifs for each KDM5 demethylase. The recognition motifs developed were used to predict potential substrates for KDM5A/B/C/D and profiled to generate a list of high-ranking and medium/low-ranking substrates for further in vitro validation. Through this approach, we identified 66 high-ranking substrates in which KDM5 demethylases displayed significant in vitro activity towards.
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Affiliation(s)
- Matthew Hoekstra
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Nashira H Ridgeway
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
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Dorababu A. Pyrazolopyrimidines as attractive pharmacophores in efficient drug design: A recent update. Arch Pharm (Weinheim) 2022; 355:e2200154. [PMID: 35698212 DOI: 10.1002/ardp.202200154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 12/03/2022]
Abstract
Among the menacing diseases, cancer needs the most attention as millions of people are affected by it worldwide. Genetic and environmental factors play a pivotal role in causing cancer. Although a wide range of underlying mechanisms of cancer has been discovered, efficient treatments have not been discovered to date. Additionally, diseases caused by microbes such as viruses, bacteria, protozoa, and so forth, persistently result in several deaths. Also, inflammation is a major factor that leads to several health issues. For decades, drug design has become a major part of drug discovery and development for curing various diseases. Among the large number of pharmacological agents that have been synthesized, only very few have emerged as efficient drug molecules. Most of them are heterocyclic compounds, which are promising candidates for the design of efficient drug molecules. Furthermore, fused heterocycles showed comparatively stronger pharmacological activities than monocyclic heterocycles. The literature reveals that pyrazolopyrimidines have outstanding biological activity. Hence, here, the diverse pharmacological activities shown by pyrazolopyrimidine derivatives reported in the last 5 years are collated and reviewed systematically. This review is classified into various sections focusing on anticancer, antimicrobial, anti-inflammatory, and enzyme inhibitors. Structure-activity relationships are discussed in brief, which will help researchers design potent pharmacological agents.
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Affiliation(s)
- Atukuri Dorababu
- SRMPP Government First Grade College, Huvinahadagali, Karnataka, India
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10
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Duan Y, Du Y, Gu Z, Zheng X, Wang C. Expression, Prognostic Value, and Functional Mechanism of the KDM5 Family in Pancreatic Cancer. Front Cell Dev Biol 2022; 10:887385. [PMID: 35493099 PMCID: PMC9043291 DOI: 10.3389/fcell.2022.887385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/24/2022] [Indexed: 12/12/2022] Open
Abstract
Background: The histone lysine demethylase KDM5 family is an important epigenetic state-modifying enzyme family. Increasing evidence supports that epigenetic abnormalities in the KDM5 family are related to multiple cancers in humans. However, the role of the KDM5 family in pancreatic cancer is not clear, and related research is very scarce. Methods: R software, Kaplan–Meier Plotter, cBioPortal, TIMER, LinkedOmics, STRING, Metascape, TISIDB, and the GSCA Lite online tool were utilized for bioinformatics analysis. Results: KDM5A/B/C was significantly overexpressed in many kinds of tumor tissues, including pancreatic adenocarcinoma (PAAD), while the expression of KDM5D was significantly downregulated. The high expression of KDM5A/B/C was related to poor clinical features, such as worse treatment efficacy, higher tumor grade, and more advanced clinical stage. Patients with a family history of breast cancer and melanoma, history of drinking or history chronic pancreatitis were more likely to have KDM5A/B/C gene abnormalities, which were related to a variety of adverse clinical features. The results of gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway analyses of the KDM5 family and its 800 co-expressed genes showed that many gene terms related to cell proliferation, migration and many carcinogenic pathways. Notably, we found that the expression level of KDM5A/B/C was positively correlated with the expression of multiple key driver genes such as KRAS, BRCA1, and BRCA2 etc. In addition, PPI network analysis showed KDM5 family proteins have strong interactions with histone deacetylase family 1 (HDAC1), which could modify the lysines of histone H3, and co-act on many pathways, including the “longevity-regulating pathway” and “Notch signaling pathway”. Moreover, the upregulation of KDM5A/B/C expression was associated with an increase in the infiltration of B cells, CD8+ T cells and other infiltrating immune lymphocytes and the expression levels of immune molecules such as NT5E and CD274. Interestingly, the overexpression of KDM5A/C was also corelated with reduced sensitivity of pancreatic cancer cells to many kinds of pancreatic cancer-targeting or chemotherapeutic drugs, including axitinib and gemcitabine. Conclusion: KDM5 family members may be prognostic markers and new therapeutic targets for patients with pancreatic cancer.
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Drosophila Model for Studying Gut Microbiota in Behaviors and Neurodegenerative Diseases. Biomedicines 2022; 10:biomedicines10030596. [PMID: 35327401 PMCID: PMC8945323 DOI: 10.3390/biomedicines10030596] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/01/2022] [Indexed: 01/14/2023] Open
Abstract
Mounting evidence indicates that the gut microbiota is linked to several physiological processes and disease development in mammals; however, the underlying mechanisms remained unexplored mostly due to the complexity of the mammalian gut microbiome. The fruit fly, Drosophila melanogaster, is a valuable animal model for studying host-gut microbiota interactions in translational aspects. The availability of powerful genetic tools and resources in Drosophila allowed the scientists to unravel the mechanisms by which the gut microbes affect fitness, health, and behavior of their hosts. Drosophila models have been extensively used not only to study animal behaviors (i.e., courtship, aggression, sleep, and learning & memory), but also some human related neurodegenerative diseases (i.e., Alzheimer’s disease and Parkinson’s disease) in the past. This review comprehensively summarizes the current understanding of the gut microbiota of Drosophila and its impact on fly behavior, physiology, and neurodegenerative diseases.
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12
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Cao M, Wang L, Xu D, Bi X, Guo S, Xu Z, Chen L, Zheng D, Li P, Xu J, Zheng S, Wang H, Wang B, Lu J, Li K. The synergistic interaction landscape of chromatin regulators reveals their epigenetic regulation mechanisms across five cancer cell lines. Comput Struct Biotechnol J 2022; 20:5028-5039. [PMID: 36187922 PMCID: PMC9483781 DOI: 10.1016/j.csbj.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/28/2022] [Accepted: 09/06/2022] [Indexed: 11/03/2022] Open
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13
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Hoekstra M, Biggar KK. Identification of in vitro JMJD lysine demethylase candidate substrates via systematic determination of substrate preference. Anal Biochem 2021; 633:114429. [PMID: 34678252 DOI: 10.1016/j.ab.2021.114429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/30/2021] [Accepted: 10/17/2021] [Indexed: 01/25/2023]
Abstract
A major regulatory influence over gene expression is the dynamic post translational methylation of histone proteins, with major implications from both lysine methylation and demethylation. The KDM5/JARID1 sub-family of Fe(II)/2-oxoglutarate dependent lysine-specific demethylases is, in part, responsible for the removal of tri/dimethyl modifications from lysine 4 of histone H3 (i.e., H3K4me3/2), a mark associated with active gene expression. Although the relevance of KDM5 activity to disease progression has been primarily established through its ability to regulate gene expression via histone methylation, there is evidence that these enzymes may also target non-histone proteins. To aid in the identification of new non-histone substrates, we examined KDM5A in vitro activity towards a library of 180 permutated peptide substrates derived from the H3K4me3 sequence. From this data, a recognition motif was identified and used to predict candidate KDM5A substrates from the methyllysine proteome. High-ranking candidate substrates were then validated for in vitro KDM5A activity using representative trimethylated peptides. Our approach correctly identified activity towards 90% of high-ranked substrates. Here, we have demonstrated the usefulness of our method in identifying candidate substrates that is applicable to any Fe(II)- and 2-oxoglutarate dependent demethylase.
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Affiliation(s)
- Matthew Hoekstra
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada.
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14
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Liu XY, Guo CH, Xi ZY, Xu XQ, Zhao QY, Li LS, Wang Y. Histone methylation in pancreatic cancer and its clinical implications. World J Gastroenterol 2021; 27:6004-6024. [PMID: 34629816 PMCID: PMC8476335 DOI: 10.3748/wjg.v27.i36.6004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/12/2021] [Accepted: 04/22/2021] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer (PC) is an aggressive human cancer. Appropriate methods for the diagnosis and treatment of PC have not been found at the genetic level, thus making epigenetics a promising research path in studies of PC. Histone methylation is one of the most complicated types of epigenetic modifications and has proved crucial in the development of PC. Histone methylation is a reversible process regulated by readers, writers, and erasers. Some writers and erasers can be recognized as potential biomarkers and candidate therapeutic targets in PC because of their unusual expression in PC cells compared with normal pancreatic cells. Based on the impact that writers have on the development of PC, some inhibitors of writers have been developed. However, few inhibitors of erasers have been developed and put to clinical use. Meanwhile, there is not enough research on the reader domains. Therefore, the study of erasers and readers is still a promising area. This review focuses on the regulatory mechanism of histone methylation, and the diagnosis and chemotherapy of PC based on it. The future of epigenetic modification in PC research is also discussed.
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Affiliation(s)
- Xing-Yu Liu
- The First Hospital of Jilin University, Jilin University, Changchun 130021, Jilin Province, China
| | - Chuan-Hao Guo
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Zhi-Yuan Xi
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Xin-Qi Xu
- The First Hospital of Jilin University, Jilin University, Changchun 130021, Jilin Province, China
| | - Qing-Yang Zhao
- The First Hospital of Jilin University, Jilin University, Changchun 130021, Jilin Province, China
| | - Li-Sha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Ying Wang
- The First Hospital of Jilin University, Jilin University, Changchun 130021, Jilin Province, China
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15
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Heward J, Konali L, D'Avola A, Close K, Yeomans A, Philpott M, Dunford J, Rahim T, Al Seraihi AF, Wang J, Korfi K, Araf S, Iqbal S, Bewicke-Copley F, Kumar E, Barisic D, Calaminici M, Clear A, Gribben J, Johnson P, Neve R, Cutillas P, Okosun J, Oppermann U, Melnick A, Packham G, Fitzgibbon J. KDM5 inhibition offers a novel therapeutic strategy for the treatment of KMT2D mutant lymphomas. Blood 2021; 138:370-381. [PMID: 33786580 PMCID: PMC8351530 DOI: 10.1182/blood.2020008743] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/04/2021] [Indexed: 02/07/2023] Open
Abstract
Loss-of-function mutations in KMT2D are a striking feature of germinal center (GC) lymphomas, resulting in decreased histone 3 lysine 4 (H3K4) methylation and altered gene expression. We hypothesized that inhibition of the KDM5 family, which demethylates H3K4me3/me2, would reestablish H3K4 methylation and restore the expression of genes repressed on loss of KMT2D. KDM5 inhibition increased H3K4me3 levels and caused an antiproliferative response in vitro, which was markedly greater in both endogenous and gene-edited KMT2D mutant diffuse large B-cell lymphoma cell lines, whereas tumor growth was inhibited in KMT2D mutant xenografts in vivo. KDM5 inhibition reactivated both KMT2D-dependent and -independent genes, resulting in diminished B-cell signaling and altered expression of B-cell lymphoma 2 (BCL2) family members, including BCL2 itself. KDM5 inhibition may offer an effective therapeutic strategy for ameliorating KMT2D loss-of-function mutations in GC lymphomas.
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Affiliation(s)
- James Heward
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Lola Konali
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Annalisa D'Avola
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Karina Close
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Alison Yeomans
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Martin Philpott
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - James Dunford
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Tahrima Rahim
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Ahad F Al Seraihi
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jun Wang
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Koorosh Korfi
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Shamzah Araf
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Sameena Iqbal
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Findlay Bewicke-Copley
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Emil Kumar
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Darko Barisic
- Department of Medicine, Weill Cornell Medicine, New York, NY; and
| | - Maria Calaminici
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Andrew Clear
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - John Gribben
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Peter Johnson
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | | | - Pedro Cutillas
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jessica Okosun
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Udo Oppermann
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Ari Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY; and
| | - Graham Packham
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Jude Fitzgibbon
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
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16
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Landay A, Bartley JM, Banerjee D, Hargis G, Haynes L, Keshavarzian A, Kuo CL, Kwon OS, Li S, Li S, Oh J, Ozbolat IT, Ucar D, Xu M, Yao X, Unutmaz D, Kuchel GA. Network Topology of Biological Aging and Geroscience-Guided Approaches to COVID-19. FRONTIERS IN AGING 2021; 2:695218. [PMID: 35128530 PMCID: PMC8813169 DOI: 10.3389/fragi.2021.695218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/22/2021] [Indexed: 01/08/2023]
Abstract
Aging has emerged as the greatest and most prevalent risk factor for the development of severe COVID-19 infection and death following exposure to the SARS-CoV-2 virus. The presence of multiple co-existing chronic diseases and conditions of aging further enhances this risk. Biological aging not only enhances the risk of chronic diseases, but the presence of such conditions further accelerates varied biological processes or "hallmarks" implicated in aging. Given growing evidence that it is possible to slow the rate of many biological aging processes using pharmacological compounds has led to the proposal that such geroscience-guided interventions may help enhance immune resilience and improve outcomes in the face of SARS-CoV-2 infection. Our review of the literature indicates that most, if not all, hallmarks of aging may contribute to the enhanced COVID-19 vulnerability seen in frail older adults. Moreover, varied biological mechanisms implicated in aging do not function in isolation from each other, and exhibit intricate effects on each other. With all of these considerations in mind, we highlight limitations of current strategies mostly focused on individual single mechanisms, and we propose an approach which is far more multidisciplinary and systems-based emphasizing network topology of biological aging and geroscience-guided approaches to COVID-19.
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Affiliation(s)
- Alan Landay
- Department of Medicine, Rush School of Medicine, Chicago, IL, United States
| | - Jenna M. Bartley
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Dishary Banerjee
- Engineering Science and Mechanics Department, The Huck Institutes of the Life Sciences, Penn State University, University Park, PA, United States
| | - Geneva Hargis
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Laura Haynes
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Ali Keshavarzian
- Division of Digestive Diseases, Departments of Medicine, Pharmacology, Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, IL, United States
| | - Chia-Ling Kuo
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
- Connecticut Convergence Institute for Translation in Regenerative Engineering, Storrs, CT, United States
| | - Oh Sung Kwon
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
- Department of Kinesiology, University of Connecticut, Storrs, CT, United States
| | - Sheng Li
- Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Shuzhao Li
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, United States
- Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Julia Oh
- Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Ibrahim Tarik Ozbolat
- Engineering Science and Mechanics Department, The Huck Institutes of the Life Sciences, Penn State University, University Park, PA, United States
- Biomedical Engineering Department, Neurosurgery Department, Materials Research Institute, Penn State University, University Park, PA, United States
| | - Duygu Ucar
- Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Ming Xu
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, CT, United States
| | - Derya Unutmaz
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, United States
- Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - George A. Kuchel
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
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17
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You JH, Lee J, Roh JL. Mitochondrial pyruvate carrier 1 regulates ferroptosis in drug-tolerant persister head and neck cancer cells via epithelial-mesenchymal transition. Cancer Lett 2021; 507:40-54. [PMID: 33741422 DOI: 10.1016/j.canlet.2021.03.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 02/06/2023]
Abstract
Cancer cells evolve to survive as 'persister cells' resistant to various chemotherapeutic agents. Persister cancer cells retain mesenchymal traits that are vulnerable to ferroptosis by iron-dependent accumulation of lethal lipid peroxidation. Regulation of the KDM5A-MPC1 axis might shift cancer cells to have mesenchymal traits via epithelial-mesenchymal transition process. Therefore, we examined the therapeutic potentiality of KDM5A-MPC1 axis regulation in promoting ferroptosis in erlotinib-tolerant persister head and neck cancer cells (erPCC). ErPCC acquired mesenchymal traits and disabled antioxidant program that were more vulnerable to ferroptosis inducers of RSL3, ML210, sulfasalazine, and erastin. GPX4 and xCT suppression caused increased sensitivity to ferroptosis in vivo models of GPX4 genetic silencing. KDM5A expression increased and MPC1 expression decreased in erPCC. KDM5A inhibition increased MPC1 expression and decreased sensitivity to ferroptosis inducers in erPCC. MPC1 suppression increased vulnerability to ferroptosis in vitro and in vivo by retaining mesenchymal traits and glutaminolysis. Low expression of MPC1 was associated with low overall survival from the TCGA data. Our data suggest that regulation of the KDM5A-MPC1 axis contributes to promoting cancer ferroptosis susceptibility.
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Affiliation(s)
- Ji Hyeon You
- Department of Otorhinolaryngology-Head Neck Surgery, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Republic of Korea
| | - Jaewang Lee
- Department of Otorhinolaryngology-Head Neck Surgery, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Republic of Korea
| | - Jong-Lyel Roh
- Department of Otorhinolaryngology-Head Neck Surgery, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Republic of Korea.
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18
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Zhang Y, Rong D, Li B, Wang Y. Targeting Epigenetic Regulators with Covalent Small-Molecule Inhibitors. J Med Chem 2021; 64:7900-7925. [PMID: 33599482 DOI: 10.1021/acs.jmedchem.0c02055] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetic regulation of gene expression plays a critical role in various physiological processes, and epigenetic dysregulation is implicated in a number of diseases, prominently including cancer. Epigenetic regulators have been validated as potential therapeutic targets, and significant progress has been made in the discovery and development of epigenetic-based inhibitors. However, successful epigenetic drug discovery is still facing challenges, including moderate selectivity, limited efficacy, and acquired drug resistance. Inspired by the advantages of covalent small-molecule inhibitors, targeted covalent inhibition has attracted increasing interest in epigenetic drug discovery. In this review, we comprehensively summarize the structure-based design and characterization of covalent inhibitors targeting epigenetic writers, readers, and erasers and highlight their potential benefits in enhancing selectivity across the enzyme family and improving in vivo efficacy. We also discuss the challenges and opportunities of covalent small-molecule inhibitors and hope to shed light on future epigenetic drug discovery.
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Affiliation(s)
- Yi Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Deqin Rong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Bingbing Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yuanxiang Wang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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19
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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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20
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Wang Y, Ma J, Martinez ED, Liang D, Xie H. A UHPLC-MS/MS method for the quantification of JIB-04 in rat plasma: Development, validation and application to pharmacokinetics study. J Pharm Biomed Anal 2020; 191:113587. [PMID: 32892084 PMCID: PMC7581536 DOI: 10.1016/j.jpba.2020.113587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022]
Abstract
Methylation of lysine by histone methyltransferases can be reversed by lysine demethylases (KDMs). Different KDMs have distinct oncogenic functions based on their cellular localization, stimulating cancer cell proliferation, reducing the expression of tumor suppressors, and/or promoting the development of drug resistance. JIB-04 is a small molecule that pan-selectively inhibits KDMs, showing maximal inhibitory activity against KDM5A, and as secondary targets, KDM4D/4B/4A/6B/4C. Recently, it was found that JIB-04 also potently and selectively blocks HIV-1 Tat expression, transactivation, and virus replication in T cell lines via the inhibition of a new target, serine hydroxymethyltransferase 2. Pharmacokinetic characterization and an analytical method for the quantification of JIB-04 are necessary for the further development of this small molecule. Herein, a sensitive, specific, fast and reliable UHPLC-MS/MS method for the quantification of JIB-04 in rat plasma samples was developed and fully validated using a SCIEX 6500+ triple QUAD LC-MS system equipped with an ExionLC UHPLC unit. The chromatographic separation was achieved on a reverse phase ACE Excel 2 Super C18 column with a flow rate of 0.5 mL/min under gradient elution. The calibration curves were linear (r2 > 0.999) over concentrations from 0.5 to 1000 ng/mL. The accuracy (RE%) was between -7.4% and 3.7%, and the precision (CV%) was 10.2% or less. The stability data showed that no significant degradation occurred under the experimental conditions. This method was successfully applied to the pharmacokinetic study of JIB-04 in rat plasma after intravenous and oral administration and the oral bioavailability of JIB-04 was found to be 44.4%.
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Affiliation(s)
- Yang Wang
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Jing Ma
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Elisabeth D Martinez
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dong Liang
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Huan Xie
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA.
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21
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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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22
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Affiliation(s)
- Xiaoli Fu
- College of Public Heath, Zhengzhou University, Zhengzhou 450001, China
| | - Chao Yang
- Institute of Innovation & Application, Zhejiang Ocean University, Zhoushan 316022 Zhejiang, China
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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23
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Berry K, Wang J, Lu QR. Epigenetic regulation of oligodendrocyte myelination in developmental disorders and neurodegenerative diseases. F1000Res 2020; 9:F1000 Faculty Rev-105. [PMID: 32089836 PMCID: PMC7014579 DOI: 10.12688/f1000research.20904.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/30/2020] [Indexed: 12/16/2022] Open
Abstract
Oligodendrocytes are the critical cell types giving rise to the myelin nerve sheath enabling efficient nerve transmission in the central nervous system (CNS). Oligodendrocyte precursor cells differentiate into mature oligodendrocytes and are maintained throughout life. Deficits in the generation, proliferation, or differentiation of these cells or their maintenance have been linked to neurological disorders ranging from developmental disorders to neurodegenerative diseases and limit repair after CNS injury. Understanding the regulation of these processes is critical for achieving proper myelination during development, preventing disease, or recovering from injury. Many of the key factors underlying these processes are epigenetic regulators that enable the fine tuning or reprogramming of gene expression during development and regeneration in response to changes in the local microenvironment. These include chromatin remodelers, histone-modifying enzymes, covalent modifiers of DNA methylation, and RNA modification-mediated mechanisms. In this review, we will discuss the key components in each of these classes which are responsible for generating and maintaining oligodendrocyte myelination as well as potential targeted approaches to stimulate the regenerative program in developmental disorders and neurodegenerative diseases.
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Affiliation(s)
- Kalen Berry
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Jiajia Wang
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Q. Richard Lu
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
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24
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Hou J, Feng HQ, Chang HW, Liu Y, Li GH, Yang S, Sun CH, Zhang MZ, Yuan Y, Sun J, Zhu-Salzman K, Zhang H, Qin QM. The H3K4 demethylase Jar1 orchestrates ROS production and expression of pathogenesis-related genes to facilitate Botrytis cinerea virulence. THE NEW PHYTOLOGIST 2020; 225:930-947. [PMID: 31529514 DOI: 10.1111/nph.16200] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Histone 3 Lysine 4 (H3K4) demethylation is ubiquitous in organisms, however the roles of H3K4 demethylase JARID1(Jar1)/KDM5 in fungal development and pathogenesis remain largely unexplored. Here, we demonstrate that Jar1/KDM5 in Botrytis cinerea, the grey mould fungus, plays a crucial role in these processes. The BcJAR1 gene was deleted and its roles in fungal development and pathogenesis were investigated using approaches including genetics, molecular/cell biology, pathogenicity and transcriptomic profiling. BcJar1 regulates H3K4me3 and both H3K4me2 and H3K4me3 methylation levels during vegetative and pathogenic development, respectively. Loss of BcJAR1 impairs conidiation, appressorium formation and stress adaptation; abolishes infection cushion (IC) formation and virulence, but promotes sclerotium production in the ΔBcjar1 mutants. BcJar1 controls reactive oxygen species (ROS) production and proper assembly of Sep4, a core septin protein and virulence determinant, to initiate infection structure (IFS) formation and host penetration. Exogenous cAMP partially restored the mutant appressorium, but not IC, formation. BcJar1 orchestrates global expression of genes for ROS production, stress response, carbohydrate transmembrane transport, secondary metabolites, etc., which may be required for conidiation, IFS formation, host penetration and virulence of the pathogen. Our work systematically elucidates BcJar1 functions and provides novel insights into Jar1/KDM5-mediated H3K4 demethylation in regulating fungal development and pathogenesis.
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Affiliation(s)
- Jie Hou
- College of Plant Sciences, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
- College of Forestry, BeiHua University, Jilin, 132013, China
| | - Hui-Qiang Feng
- College of Plant Sciences, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Hao-Wu Chang
- Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China
| | - Yue Liu
- College of Plant Sciences, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Gui-Hua Li
- College of Plant Sciences, Jilin University, Changchun, 130062, China
| | - Song Yang
- College of Plant Sciences, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Chen-Hao Sun
- College of Plant Sciences, Jilin University, Changchun, 130062, China
| | - Ming-Zhe Zhang
- College of Plant Sciences, Jilin University, Changchun, 130062, China
| | - Ye Yuan
- College of Plant Sciences, Jilin University, Changchun, 130062, China
| | - Jiao Sun
- College of Plant Sciences, Jilin University, Changchun, 130062, China
| | - Keyan Zhu-Salzman
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Hao Zhang
- Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China
| | - Qing-Ming Qin
- College of Plant Sciences, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
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Karia D, Gilbert RCG, Biasutto AJ, Porcher C, Mancini EJ. The histone H3K4 demethylase JARID1A directly interacts with haematopoietic transcription factor GATA1 in erythroid cells through its second PHD domain. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191048. [PMID: 32218938 PMCID: PMC7029945 DOI: 10.1098/rsos.191048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Chromatin remodelling and transcription factors play important roles in lineage commitment and development through control of gene expression. Activation of selected lineage-specific genes and repression of alternative lineage-affiliated genes result in tightly regulated cell differentiation transcriptional programmes. However, the complex functional and physical interplay between transcription factors and chromatin-modifying enzymes remains elusive. Recent evidence has implicated histone demethylases in normal haematopoietic differentiation as well as in malignant haematopoiesis. Here, we report an interaction between H3K4 demethylase JARID1A and the haematopoietic-specific master transcription proteins SCL and GATA1 in red blood cells. Specifically, we observe a direct physical contact between GATA1 and the second PHD domain of JARID1A. This interaction has potential implications for normal and malignant haematopoiesis.
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Affiliation(s)
- Dimple Karia
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Robert C. G. Gilbert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Antonio J. Biasutto
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Department of Biochemistry, University of Oxford, 3 S Parks Road, Oxford OX1 3QU, UK
| | - Catherine Porcher
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Erika J. Mancini
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RH, UK
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Sex Determination Using RNA-Sequencing Analyses in Early Prenatal Pig Development. Genes (Basel) 2019; 10:genes10121010. [PMID: 31817322 PMCID: PMC6947224 DOI: 10.3390/genes10121010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022] Open
Abstract
Sexual dimorphism is a relevant factor in animal science, since it can affect the gene expression of economically important traits. Eventually, the interest in the prenatal phase in a transcriptome study may not comprise the period of development in which male and female conceptuses are phenotypically divergent. Therefore, it would be interesting if sex differentiation could be performed using transcriptome data, with no need for extra techniques. In this study, the sex of pig conceptuses (embryos at 25 days-old and fetuses at 35 days-old) was determined by reads counts per million (CPM) of Y chromosome-linked genes that were discrepant among samples. Thus, ten genes were used: DDX3Y, KDM5D, ZFY, EIF2S3Y, EIF1AY, LOC110255320, LOC110257894, LOC396706, LOC100625207, and LOC110255257. Conceptuses that presented reads CPM sum for these genes (ΣCPMchrY) greater than 400 were classified as males and those with ΣCPMchrY below 2 were classified as females. It was demonstrated that the sex identification can be performed at early stages of pig development from RNA-sequencing analysis of genes mapped on Y chromosome. Additionally, these results reinforce that sex determination is a mechanism conserved across mammals, highlighting the importance of using pigs as an animal model to study sex determination during human prenatal development.
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Montano MM, Yeh IJ, Chen Y, Hernandez C, Kiselar JG, de la Fuente M, Lawes AM, Nieman MT, Kiser PD, Jacobberger J, Exner AA, Lawes MC. Inhibition of the histone demethylase, KDM5B, directly induces re-expression of tumor suppressor protein HEXIM1 in cancer cells. Breast Cancer Res 2019; 21:138. [PMID: 31805991 PMCID: PMC6896798 DOI: 10.1186/s13058-019-1228-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/14/2019] [Indexed: 01/07/2023] Open
Abstract
Background The tumor suppressor actions of hexamethylene bis-acetamide (HMBA)-inducible protein 1 (HEXIM1) in the breast, prostate, melanomas, and AML have been reported by our group and others. Increased HEXIM1 expression caused differentiation and inhibited proliferation and metastasis of cancer cells. Historically, HEXIM1 has been experimentally induced with the hybrid polar compound HMBA, but HMBA is a poor clinical candidate due to lack of a known target, poor pharmacological properties, and unfavorable ADMETox characteristics. Thus, HEXIM1 induction is an intriguing therapeutic approach to cancer treatment, but requires better chemical tools than HMBA. Methods We identified and verified KDM5B as a target of HEXIM1 inducers using a chemical proteomics approach, biotin–NeutrAvidin pull-down assays, surface plasmon resonance, and molecular docking. The regulation of HEXIM1 by KDM5B and KDM5B inhibitors was assessed using chromatin immunoprecipitation assays, RT-PCR, western blotting, and depletion of KDM5B with shRNAs. The regulation of breast cancer cell phenotype by KDM5B inhibitors was assessed using western blots, differentiation assays, proliferation assays, and a mouse model of breast cancer metastasis. The relative role of HEXIM1 in the action of KDM5B inhibitors was determined by depleting HEXIM1 using shRNAs followed by western blots, differentiation assays, and proliferation assays. Results We have identified a highly druggable target, KDM5B, which is inhibited by small molecule inducers of HEXIM1. RNAi knockdown of KDM5B induced HEXIM1 expression, thus validating the specific negative regulation of tumor suppressor HEXIM1 by the H3K4me3/2 demethylase KDM5B. Known inhibitors of KDM5B were also able to induce HEXIM1 expression, inhibit cell proliferation, induce differentiation, potentiate sensitivity to cancer chemotherapy, and inhibit breast tumor metastasis. Conclusion HMBA and 4a1 induce HEXIM1 expression by inhibiting KDM5B. Upregulation of HEXIM1 expression levels plays a critical role in the inhibition of proliferation of breast cancer cells using KDM5B inhibitors. Based on the novel molecular scaffolds that we identified which more potently induced HEXIM1 expression and data in support that KDM5B is a target of these compounds, we have opened up new lead discovery and optimization directions.
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Affiliation(s)
- Monica M Montano
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA. .,Oncostatyx, 11000 Cedar Avenue Suite 26, Cleveland, OH, 44106, USA.
| | - I-Ju Yeh
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Yinghua Chen
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Chris Hernandez
- General Medical Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Janna G Kiselar
- Department of Radiology, and Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Maria de la Fuente
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Adriane M Lawes
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Marvin T Nieman
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Philip D Kiser
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - James Jacobberger
- General Medical Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Agata A Exner
- Department of Radiology, and Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Matthew C Lawes
- Oncostatyx, 11000 Cedar Avenue Suite 26, Cleveland, OH, 44106, USA
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Le Bihan YV, Lanigan RM, Atrash B, McLaughlin MG, Velupillai S, Malcolm AG, England KS, Ruda GF, Mok NY, Tumber A, Tomlin K, Saville H, Shehu E, McAndrew C, Carmichael L, Bennett JM, Jeganathan F, Eve P, Donovan A, Hayes A, Wood F, Raynaud FI, Fedorov O, Brennan PE, Burke R, van Montfort RLM, Rossanese OW, Blagg J, Bavetsias V. C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur J Med Chem 2019; 177:316-337. [PMID: 31158747 PMCID: PMC6580095 DOI: 10.1016/j.ejmech.2019.05.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 12/25/2022]
Abstract
Residues in the histone substrate binding sites that differ between the KDM4 and KDM5 subfamilies were identified. Subsequently, a C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one series was designed to rationally exploit these residue differences between the histone substrate binding sites in order to improve affinity for the KDM4-subfamily over KDM5-subfamily enzymes. In particular, residues E169 and V313 (KDM4A numbering) were targeted. Additionally, conformational restriction of the flexible pyridopyrimidinone C8-substituent was investigated. These approaches yielded potent and cell-penetrant dual KDM4/5-subfamily inhibitors including 19a (KDM4A and KDM5B Ki = 0.004 and 0.007 μM, respectively). Compound cellular profiling in two orthogonal target engagement assays revealed a significant reduction from biochemical to cell-based activity across multiple analogues; this decrease was shown to be consistent with 2OG competition, and suggests that sub-nanomolar biochemical potency will be required with C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one compounds to achieve sub-micromolar target inhibition in cells.
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Affiliation(s)
- Yann-Vaï Le Bihan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Rachel M Lanigan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Butrus Atrash
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Mark G McLaughlin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Srikannathasan Velupillai
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Andrew G Malcolm
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Katherine S England
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Gian Filippo Ruda
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - N Yi Mok
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Anthony Tumber
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Kathy Tomlin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Harry Saville
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Erald Shehu
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Craig McAndrew
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - LeAnne Carmichael
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - James M Bennett
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Fiona Jeganathan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Paul Eve
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Adam Donovan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Angela Hayes
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Francesca Wood
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Florence I Raynaud
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Oleg Fedorov
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Paul E Brennan
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Rosemary Burke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Rob L M van Montfort
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Olivia W Rossanese
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
| | - Vassilios Bavetsias
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
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29
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Berry KP, Lu QR. Chromatin modification and epigenetic control in functional nerve regeneration. Semin Cell Dev Biol 2019; 97:74-83. [PMID: 31301357 DOI: 10.1016/j.semcdb.2019.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022]
Abstract
The repair and functional recovery of the nervous system is a highly regulated process that requires the coordination of many different components including the proper myelination of regenerated axons. Dysmyelination and remyelination failures after injury result in defective nerve conduction, impairing normal nervous system functions. There are many convergent regulatory networks and signaling mechanisms between development and regeneration. For instance, the regulatory mechanisms required for oligodendrocyte lineage progression could potentially play fundamental roles in myelin repair. In recent years, epigenetic chromatin modifications have been implicated in CNS myelination and functional nerve restoration. The pro-regenerative transcriptional program is likely silenced or repressed in adult neural cells including neurons and myelinating cells in the central and peripheral nervous systems limiting the capacity for repair after injury. In this review, we will discuss the roles of epigenetic mechanisms, including histone modifications, chromatin remodeling, and DNA methylation, in the maintenance and establishment of the myelination program during normal oligodendrocyte development and regeneration. We also discuss how these epigenetic processes impact myelination and axonal regeneration, and facilitate the improvement of current preclinical therapeutics for functional nerve regeneration in neurodegenerative disorders or after injury.
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Affiliation(s)
- Kalen P Berry
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Q Richard Lu
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
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Abstract
KDM5 family members (A, B, C and D) that demethylate H3K4me3 have been shown to be involved in human cancers. Here we performed screening for KDM5A inhibitors from chemical libraries using the AlphaScreen method and identified a battery of screening hits that inhibited recombinant KDM5A. These compounds were further subjected to cell-based screening using a reporter gene that responded to KDM5A inhibition and 6 compounds were obtained as candidate inhibitors. When further confirmation of their inhibition activity on cellular KDM5A was made by immunostaining H3K4me3 in KDM5A-overexpressing cells, ryuvidine clearly repressed H3K4me3 demethylation. Ryuvidine prevented generation of gefitinib-tolerant human small-cell lung cancer PC9 cells and also inhibited the growth of the drug-tolerant cells at concentrations that did not affect the growth of parental PC9 cells. Ryuvidine inhibited not only KDM5A but also recombinant KDM5B and C; KDM5B was the most sensitive to the inhibitor. These results warrant that ryuvidine may serve as a lead compound for KDM5 targeted therapeutics.
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31
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Kumar A, Kumari N, Sharma U, Ram S, Singh SK, Kakkar N, Kaushal K, Prasad R. Reduction in H3K4me patterns due to aberrant expression of methyltransferases and demethylases in renal cell carcinoma: prognostic and therapeutic implications. Sci Rep 2019; 9:8189. [PMID: 31160694 PMCID: PMC6546756 DOI: 10.1038/s41598-019-44733-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 05/09/2019] [Indexed: 12/13/2022] Open
Abstract
Renal cell carcinoma (RCC) is the leading cause among cancer-related deaths due to urological cancers, which results in response to combination of genetic and epigenetic factors. Histone methylations have been implicated in renal tumorigenesis but their clinical significance and underlying pathology are unexplored. Here, we elucidated the histone 3 lysine 4 (H3K4) methylation patterns in clear cell RCC and its underlying pathology. Lower cellular levels of H3K4 mono-methylation, -dimethylation and -tri-methylation were fraternized with higher TNM staging and Fuhrman grading as well as tumor metastasis. Further, the expression profile of 20 H3K4 modifiers revealed the significant over-expression of histone demethylases compared to methyltransferases, indicating their role in the reduction of H3K4 methylation levels. In view of above facts, the role of LSD2 and KDM5A demethylases in RCC pathogenesis were explored using respective siRNAs. The RCC cells exhibited reduced cell viability after knockdown of LSD2 and KDM5A genes with concomitant induction of apoptosis. In addition, propidium iodide staining demonstrated an arrest of RCC cells at S-phase and sub-G1 phase of the cell cycle. Taken together, these observations provide new pathological insights behind the alterations of H3K4 methylation patterns in ccRCC with their prognostic and therapeutic implications.
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Affiliation(s)
- Aman Kumar
- Department of Biochemistry, Post Graduate Institute of Medical Educational and Research, Chandigarh, India
| | - Niti Kumari
- Department of Biochemistry, Post Graduate Institute of Medical Educational and Research, Chandigarh, India
| | - Ujjawal Sharma
- Department of Biochemistry, Post Graduate Institute of Medical Educational and Research, Chandigarh, India
| | - Sant Ram
- Department of Biochemistry, Post Graduate Institute of Medical Educational and Research, Chandigarh, India
| | - Shrawan Kumar Singh
- Department of Urology, Post Graduate Institute of Medical Educational and Research, Chandigarh, India
| | - Nandita Kakkar
- Department of Histopathology, Post Graduate Institute of Medical Educational and Research, Chandigarh, India
| | - Karanvir Kaushal
- Department of Biochemistry, Post Graduate Institute of Medical Educational and Research, Chandigarh, India
| | - Rajendra Prasad
- Department of Biochemistry, Post Graduate Institute of Medical Educational and Research, Chandigarh, India.
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32
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Zhang ZG, Zhang HS, Sun HL, Liu HY, Liu MY, Zhou Z. KDM5B promotes breast cancer cell proliferation and migration via AMPK-mediated lipid metabolism reprogramming. Exp Cell Res 2019; 379:182-190. [DOI: 10.1016/j.yexcr.2019.04.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/24/2019] [Accepted: 04/05/2019] [Indexed: 12/24/2022]
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Abstract
Histone lysine demethylase 5 enzymes (KDM5s) have recently been proposed as crucial oncogenic drivers. In this issue of Cell Chemical Biology, Horton et al. (2016) describe results of an extensive structural analysis that reveals how distinct inhibitor chemotypes bind KDM5 and suggest avenues for improving KDM5 inhibitory potency and selectivity.
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Affiliation(s)
- Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy.
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
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Metwally NH, Mohamed MS, Ragb EA. Design, synthesis, anticancer evaluation, molecular docking and cell cycle analysis of 3-methyl-4,7-dihydropyrazolo[1,5-a]pyrimidine derivatives as potent histone lysine demethylases (KDM) inhibitors and apoptosis inducers. Bioorg Chem 2019; 88:102929. [PMID: 31015179 DOI: 10.1016/j.bioorg.2019.102929] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 04/11/2019] [Accepted: 04/15/2019] [Indexed: 01/07/2023]
Abstract
A novel series of pyrazolo[1,5-a]pyrimidines were synthesized and proved by their spectral and elemental analysis, some elected of the newly synthesized compounds were examined for their cytotoxic activity employing MTT assay on two cancer cell lines (Breast and Hela cancers). Compounds 5, 7e and 7i showed the higher cytotoxicity against two cancer cell lines with (IC50 = 13.91 ± 1.4 and 22.37 ± 1.8 μM/L), (IC50 = 6.56 ± 0.5 and 8.72 ± 0.9 μM/L) and (IC50 = 4.17 ± 0.2 and 5.57 ± 0.4 μM/L) for two cancer cell lines breast and hela respectively, using doxorubicin as a reference drug. The most potent cytotoxic active compounds 5, 7e and 7i presented inhibitory activity against KDM (histone lysine demethylases) with IC50 = 4.05, 1.91 and 2.31 μM, respectively. The most potent KDM inhibitor 7e (IC50 = 1.91 μM) showed to cause cell cycle arrest at G2/M phase by 4 folds than control and induce total apoptotic effect by 10 folds more than control. In silico studies performed on the more potent cytotoxic active compounds 5, 7e and 7i included lipinisk's rule of five. Moreover, molecular docking study was utilized to explore the binding mode of the most active compounds to the target enzyme (PDB-ID: 5IVE). Also, some bioinformatics studies were carried out for compounds 7e and 7i using Swiss ADME (Swiss Institute of bioinformatics 2018).
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Affiliation(s)
| | - Mona Said Mohamed
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt
| | - Eman Ali Ragb
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt
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35
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Research update and opportunity of non-hormonal male contraception: Histone demethylase KDM5B-based targeting. Pharmacol Res 2019; 141:1-20. [DOI: 10.1016/j.phrs.2018.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/29/2018] [Accepted: 12/09/2018] [Indexed: 12/28/2022]
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36
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Mascaró C, Ortega A, Carceller E, Ruiz Rodriguez R, Ciceri F, Lunardi S, Yu L, Hilbert M, Maes T. Chemoprobe-based assays of histone lysine demethylase 1A target occupation enable in vivo pharmacokinetics and pharmacodynamics studies of KDM1A inhibitors. J Biol Chem 2019; 294:8311-8322. [PMID: 30804215 DOI: 10.1074/jbc.ra118.006980] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/19/2019] [Indexed: 12/22/2022] Open
Abstract
Screening of cellular activity for inhibitors of histone lysine modifiers is most frequently performed indirectly by analyzing changes in the total levels of histone marks targeted by lysine methylases/demethylases. However, inhibition of histone lysine modifiers often leads to local rather than total changes in histone marks. Also, because histone modifications can be modulated by more than one cellular enzyme, it is not always clear whether changes in histone marks are a direct or indirect consequence of the inhibitor treatment applied. Direct assessment of target occupation can provide a useful tool to quantify the fraction of an epigenetic modifier that is bound to a pharmacological inhibitor (target engagement). Here, we developed and used a novel chemoprobe-based immunoassay to quantify target engagement in cells. Quantification of the fraction of free KDM1A was made possible, in an immune-based assay, by coupling a biotinylated chemoprobe to a warhead capable of selectively and irreversibly binding to the free active form of KDM1A. The results obtained confirmed that this approach is able to determine the degree of target engagement in a dose-dependent manner. Furthermore, the assay can be also used on tissue extracts to analyze the in vivo pharmacokinetics and pharmacodynamics relationship of KDM1A inhibitors, as has been exemplified with ORY-1001 (iadademstat), a potent and irreversible inhibitor of KDM1A. The principle of this assay may be applied to other targets, and the KDM1A probe may be employed in chemoproteomic analyses.
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Affiliation(s)
- Cristina Mascaró
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain
| | - Alberto Ortega
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain
| | - Elena Carceller
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain
| | - Raquel Ruiz Rodriguez
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain
| | - Filippo Ciceri
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain
| | - Serena Lunardi
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain
| | - Li Yu
- Roche Innovation Center New York, New York, New York 10016
| | - Manuel Hilbert
- Roche Innovation Center Basel, Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Tamara Maes
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain.
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Jiang Z, You Q, Zhang X. Medicinal chemistry of metal chelating fragments in metalloenzyme active sites: A perspective. Eur J Med Chem 2019; 165:172-197. [PMID: 30684796 DOI: 10.1016/j.ejmech.2019.01.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/22/2018] [Accepted: 01/08/2019] [Indexed: 12/25/2022]
Abstract
Numerous metal-containing enzymes (metalloenzymes) have been considered as drug targets related to diseases such as cancers, diabetes, anemia, AIDS, malaria, bacterial infection, fibrosis, and neurodegenerative diseases. Inhibitors of the metalloenzymes have been developed independently, most of which are mimics of substrates of the corresponding enzymes. However, little attention has been paid to the interactions between inhibitors and active site metal ions. This review is focused on different metal binding fragments and their chelating properties in the metal-containing active binding pockets of metalloenzymes. We have enumerated over one hundred of inhibitors targeting various metalloenzymes and identified over ten kinds of fragments with different binding patterns. Furthermore, we have investigated the inhibitors that are undergoing clinical evaluation in order to help looking for more potential scaffolds bearing metal binding fragments. This review will provide deep insights for the rational design of novel inhibitors targeting the metal-containing binding sites of specific proteins.
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Affiliation(s)
- Zhensheng Jiang
- Sate Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Sate Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Xiaojin Zhang
- Sate Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Chemistry, School of Science, China Pharmaceutical University, Nanjing, 211198, China.
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Horton JR, Woodcock CB, Chen Q, Liu X, Zhang X, Shanks J, Rai G, Mott BT, Jansen DJ, Kales SC, Henderson MJ, Cyr M, Pohida K, Hu X, Shah P, Xu X, Jadhav A, Maloney DJ, Hall MD, Simeonov A, Fu H, Vertino PM, Cheng X. Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A. J Med Chem 2018; 61:10588-10601. [PMID: 30392349 PMCID: PMC6467790 DOI: 10.1021/acs.jmedchem.8b01219] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The active sites of hundreds of human α-ketoglutarate (αKG) and Fe(II)-dependent dioxygenases are exceedingly well preserved, which challenges the design of selective inhibitors. We identified a noncatalytic cysteine (Cys481 in KDM5A) near the active sites of KDM5 histone H3 lysine 4 demethylases, which is absent in other histone demethylase families, that could be explored for interaction with the cysteine-reactive electrophile acrylamide. We synthesized analogs of a thienopyridine-based inhibitor chemotype, namely, 2-((3-aminophenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2- b]pyridine-7-carboxylic acid (N70) and a derivative containing a (dimethylamino)but-2-enamido)phenyl moiety (N71) designed to form a covalent interaction with Cys481. We characterized the inhibitory and binding activities against KDM5A and determined the cocrystal structures of the catalytic domain of KDM5A in complex with N70 and N71. Whereas the noncovalent inhibitor N70 displayed αKG-competitive inhibition that could be reversed after dialysis, inhibition by N71 was dependent on enzyme concentration and persisted even after dialysis, consistent with covalent modification.
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Affiliation(s)
- John R. Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Clayton B. Woodcock
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Qin Chen
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - John Shanks
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Bryan T. Mott
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Daniel J. Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Stephen C. Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Mark J. Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew Cyr
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Katherine Pohida
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Pranav Shah
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - David J. Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Haian Fu
- Departments of Pharmacology, Emory University, Atlanta, Georgia 30322, United States
- Hematology and Medical Oncology, Emory University, Atlanta, Georgia 30322, United States
- Emory Chemical Biology Discovery Center, Emory University, Atlanta, Georgia 30322, United States
- The Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
| | - Paula M. Vertino
- The Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
- Department of Radiation Oncology, Emory University, Atlanta, Georgia 30322, United States
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
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Plch J, Hrabeta J, Eckschlager T. KDM5 demethylases and their role in cancer cell chemoresistance. Int J Cancer 2018; 144:221-231. [PMID: 30246379 DOI: 10.1002/ijc.31881] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 09/03/2018] [Accepted: 09/13/2018] [Indexed: 12/28/2022]
Abstract
Histone methylation is important in the regulation of genes expression, and thus its dysregulation has been observed in various cancers. KDM5 enzymes are capable of removing tri- and di- methyl marks from lysine 4 on histone H3 (H3K4) which makes them potential players in the downregulation of tumor suppressors, but could also suggest that their activity repress oncogenes. Depending on the methylation site, their effect on transcription can be either activating or repressing. There is emerging evidence for deregulation of KDM5A/B/C/D and important phenotypic consequences in various types of cancer. It has been suggested that the KDM5 family of demethylases plays a role in the appearance of drug tolerance. Drug resistance remains a challenge to successful cancer treatment. This review summarizes recent advances in understanding the functions of KDM5 histone demethylases in cancer chemoresistance and potential therapeutic targeting of these enzymes, which seems to prevent the emergence of a drug-resistant population.
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Affiliation(s)
- Johana Plch
- Department of Pediatric Hematology and Oncology, 2nd Medical Faculty and University Hospital Motol, Prague, Czech Republic
| | - Jan Hrabeta
- Department of Pediatric Hematology and Oncology, 2nd Medical Faculty and University Hospital Motol, Prague, Czech Republic
| | - Tomas Eckschlager
- Department of Pediatric Hematology and Oncology, 2nd Medical Faculty and University Hospital Motol, Prague, Czech Republic
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40
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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: 64] [Impact Index Per Article: 10.7] [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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41
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Sun Y, Zhou B, Mao F, Xu J, Miao H, Zou Z, Phuc Khoa LT, Jang Y, Cai S, Witkin M, Koche R, Ge K, Dressler GR, Levine RL, Armstrong SA, Dou Y, Hess JL. HOXA9 Reprograms the Enhancer Landscape to Promote Leukemogenesis. Cancer Cell 2018; 34:643-658.e5. [PMID: 30270123 PMCID: PMC6179449 DOI: 10.1016/j.ccell.2018.08.018] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 06/07/2018] [Accepted: 08/29/2018] [Indexed: 12/19/2022]
Abstract
Aberrant expression of HOXA9 is a prominent feature of acute leukemia driven by diverse oncogenes. Here we show that HOXA9 overexpression in myeloid and B progenitor cells leads to significant enhancer reorganizations with prominent emergence of leukemia-specific de novo enhancers. Alterations in the enhancer landscape lead to activation of an ectopic embryonic gene program. We show that HOXA9 functions as a pioneer factor at de novo enhancers and recruits CEBPα and the MLL3/MLL4 complex. Genetic deletion of MLL3/MLL4 blocks histone H3K4 methylation at de novo enhancers and inhibits HOXA9/MEIS1-mediated leukemogenesis in vivo. These results suggest that therapeutic targeting of HOXA9-dependent enhancer reorganization can be an effective therapeutic strategy in acute leukemia with HOXA9 overexpression.
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Affiliation(s)
- Yuqing Sun
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Bo Zhou
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Fengbiao Mao
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jing Xu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Hongzhi Miao
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zhenhua Zou
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Le Tran Phuc Khoa
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Younghoon Jang
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sheng Cai
- Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew Witkin
- Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Richard Koche
- Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Kai Ge
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gregory R Dressler
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ross L Levine
- Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Scott A Armstrong
- Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Yali Dou
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Jay L Hess
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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Yang G, Wang W, Mok SWF, Wu C, Law BYK, Miao X, Wu K, Zhong H, Wong C, Wong VKW, Ma D, Leung C. Selective Inhibition of Lysine‐Specific Demethylase 5A (KDM5A) Using a Rhodium(III) Complex for Triple‐Negative Breast Cancer Therapy. Angew Chem Int Ed Engl 2018; 57:13091-13095. [DOI: 10.1002/anie.201807305] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Guan‐Jun Yang
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese MedicineUniversity of Macau Macao China
| | - Wanhe Wang
- Department of ChemistryHong Kong Baptist University Kowloon Tong, Hong Kong China
| | - Simon Wing Fai Mok
- State Key Laboratory of Quality Research in Chinese MedicineMacau University of Science and Technology, Avenida Wai Long Taipa, Macao China
| | - Chun Wu
- Department of ChemistryHong Kong Baptist University Kowloon Tong, Hong Kong China
| | - Betty Yuen Kwan Law
- State Key Laboratory of Quality Research in Chinese MedicineMacau University of Science and Technology, Avenida Wai Long Taipa, Macao China
| | - Xiang‐Min Miao
- School of Life ScienceJiangsu Normal University Xuzhou 221116 P. R. China
| | - Ke‐Jia Wu
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese MedicineUniversity of Macau Macao China
| | - Hai‐Jing Zhong
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese MedicineUniversity of Macau Macao China
| | - Chun‐Yuen Wong
- Department of ChemistryCity University of Hong Kong Tat Chee Avenue Hong Kong SAR P. R. China
| | - Vincent Kam Wai Wong
- State Key Laboratory of Quality Research in Chinese MedicineMacau University of Science and Technology, Avenida Wai Long Taipa, Macao China
| | - Dik‐Lung Ma
- Department of ChemistryHong Kong Baptist University Kowloon Tong, Hong Kong China
| | - Chung‐Hang Leung
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese MedicineUniversity of Macau Macao China
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43
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Kuo KT, Huang WC, Bamodu OA, Lee WH, Wang CH, Hsiao M, Wang LS, Yeh CT. Histone demethylase JARID1B/KDM5B promotes aggressiveness of non-small cell lung cancer and serves as a good prognostic predictor. Clin Epigenetics 2018; 10:107. [PMID: 30092824 PMCID: PMC6085612 DOI: 10.1186/s13148-018-0533-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Background Lung cancer is the leading cause of cancer death worldwide. Recently, epigenetic dysregulation has been known to promote tumor progression and therefore may be a therapeutic target for anticancer therapy. JARID1B, a member of histone demethylases, has been found to be related to tumorigenesis in certain kinds of cancers. However, its biological roles in non-small cell lung cancer (NSCLC) remain largely unclear. Methods We firstly examined the expression of JARID1B in surgical specimens and six NSCLC cell lines. Then, we evaluated the relationship between JARID1B expression and clinicopathologic parameters in 72 NSCLC patients, thereby established its prognostic importance. We subsequently studied the functional roles of JARID1B in tumorigenesis to verify its clinicopathologic significance. Results Our results showed that JARID1B was overexpressed in NSCLC cells and JARID1B overexpression was associated with tumor size, lymph node metastasis, advanced stages, and poor overall survival in NSCLC patients. JARID1B overexpression resulted in increased cell proliferation and formation of tumorspheres and correlated positively with the expression of cancer stem cells (CSCs) and epithelial-mesenchymal transition (EMT) markers, while the c-Met signaling pathway was actively involved. It also correlated with the strength of resistance to cisplatin and doxorubicin. On the contrary, downregulation of JARID1B expression by applying shRNA or JARID1B inhibitor PBIT reversed these phenomena. Conclusions JARID1B worsens prognosis of NSCLC patients by promotion of tumor aggressiveness through multiple biological facets which were associated with activation of the c-Met signaling, and can be a novel prognostic biomarker and therapeutic target for NSCLC. Electronic supplementary material The online version of this article (10.1186/s13148-018-0533-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kuang-Tai Kuo
- Division of Thoracic Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Thoracic Surgery, Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wen-Chien Huang
- Division of Thoracic Surgery, Department of Surgery, MacKay Memorial Hospital, Taipei, Taiwan.,MacKay Medical College, Taipei, Taiwan
| | - Oluwaseun Adebayo Bamodu
- Department of Medical Research and Education, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Hematology/Oncology, Department of Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Wei-Hwa Lee
- Department of Pathology, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Chun-Hua Wang
- Department of Dermatology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan.,School of Medicine, Buddhist Tzu Chi University, Hualien, Taiwan
| | - M Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Liang-Shun Wang
- Division of Thoracic Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.
| | - Chi-Tai Yeh
- Department of Medical Research and Education, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan. .,Division of Hematology/Oncology, Department of Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.
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Yang Q, Yang Y, Zhou N, Tang K, Lau WB, Lau B, Wang W, Xu L, Yang Z, Huang S, Wang X, Yi T, Zhao X, Wei Y, Wang H, Zhao L, Zhou S. Epigenetics in ovarian cancer: premise, properties, and perspectives. Mol Cancer 2018; 17:109. [PMID: 30064416 PMCID: PMC6069741 DOI: 10.1186/s12943-018-0855-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 07/11/2018] [Indexed: 01/04/2023] Open
Abstract
Malignant ovarian tumors bear the highest mortality rate among all gynecological cancers. Both late tumor diagnosis and tolerance to available chemical therapy increase patient mortality. Therefore, it is both urgent and important to identify biomarkers facilitating early identification and novel agents preventing recurrence. Accumulating evidence demonstrates that epigenetic aberrations (particularly histone modifications) are crucial in tumor initiation and development. Histone acetylation and methylation are respectively regulated by acetyltransferases-deacetylases and methyltransferases-demethylases, both of which are implicated in ovarian cancer pathogenesis. In this review, we summarize the most recent discoveries pertaining to ovarian cancer development arising from the imbalance of histone acetylation and methylation, and provide insight into novel therapeutic interventions for the treatment of ovarian carcinoma.
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Affiliation(s)
- Qilian Yang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Yuqing Yang
- Nanchang University, Nanchang, People's Republic of China
| | - Nianxin Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Kexin Tang
- Sichuan Normal University Affiliated Middle School, Chengdu, People's Republic of China
| | - Wayne Bond Lau
- Department of Emergency Medicine, Thomas Jefferson University Hospital, Philadelphia, USA
| | - Bonnie Lau
- Department of Surgery, Emergency Medicine, Kaiser Santa Clara Medical Center, Affiliate of Stanford University, Stanford, USA
| | - Wei Wang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China
| | - Lian Xu
- Department of Pathology, West China Second University Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Zhengnan Yang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Shuang Huang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China
| | - Tao Yi
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Xia Zhao
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Yuquan Wei
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Hongjing Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China.
| | - Linjie Zhao
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China.
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China.
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45
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Yang G, Wang W, Mok SWF, Wu C, Law BYK, Miao X, Wu K, Zhong H, Wong C, Wong VKW, Ma D, Leung C. Selective Inhibition of Lysine‐Specific Demethylase 5A (KDM5A) Using a Rhodium(III) Complex for Triple‐Negative Breast Cancer Therapy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807305] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Guan‐Jun Yang
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese MedicineUniversity of Macau Macao China
| | - Wanhe Wang
- Department of ChemistryHong Kong Baptist University Kowloon Tong, Hong Kong China
| | - Simon Wing Fai Mok
- State Key Laboratory of Quality Research in Chinese MedicineMacau University of Science and Technology, Avenida Wai Long Taipa, Macao China
| | - Chun Wu
- Department of ChemistryHong Kong Baptist University Kowloon Tong, Hong Kong China
| | - Betty Yuen Kwan Law
- State Key Laboratory of Quality Research in Chinese MedicineMacau University of Science and Technology, Avenida Wai Long Taipa, Macao China
| | - Xiang‐Min Miao
- School of Life ScienceJiangsu Normal University Xuzhou 221116 P. R. China
| | - Ke‐Jia Wu
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese MedicineUniversity of Macau Macao China
| | - Hai‐Jing Zhong
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese MedicineUniversity of Macau Macao China
| | - Chun‐Yuen Wong
- Department of ChemistryCity University of Hong Kong Tat Chee Avenue Hong Kong SAR P. R. China
| | - Vincent Kam Wai Wong
- State Key Laboratory of Quality Research in Chinese MedicineMacau University of Science and Technology, Avenida Wai Long Taipa, Macao China
| | - Dik‐Lung Ma
- Department of ChemistryHong Kong Baptist University Kowloon Tong, Hong Kong China
| | - Chung‐Hang Leung
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese MedicineUniversity of Macau Macao China
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Bhushan B, Erdmann A, Zhang Y, Belle R, Johannson C, Oppermann U, Hopkinson RJ, Schofield CJ, Kawamura A. Investigations on small molecule inhibitors targeting the histone H3K4 tri-methyllysine binding PHD-finger of JmjC histone demethylases. Bioorg Med Chem 2018; 26:2984-2991. [PMID: 29764755 PMCID: PMC6380468 DOI: 10.1016/j.bmc.2018.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/10/2018] [Accepted: 03/18/2018] [Indexed: 12/12/2022]
Abstract
Plant homeodomain (PHD) containing proteins are important epigenetic regulators and are of interest as potential drug targets. Inspired by the amiodarone derivatives reported to inhibit the PHD finger 3 of KDM5A (KDM5A(PHD3)), a set of compounds were synthesised. Amiodarone and its derivatives were observed to weakly disrupt the interactions of a histone H3K4me3 peptide with KDM5A(PHD3). Selected amiodarone derivatives inhibited catalysis of KDM5A, but in a PHD-finger independent manner. Amiodarone derivatives also bind to H3K4me3-binding PHD-fingers from the KDM7 subfamily. Further work is required to develop potent and selective PHD finger inhibitors.
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Affiliation(s)
- Bhaskar Bhushan
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Alexandre Erdmann
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Yijia Zhang
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Roman Belle
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Catrine Johannson
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, United Kingdom
| | - Udo Oppermann
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, United Kingdom
| | - Richard J Hopkinson
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Akane Kawamura
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.
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47
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Nie Z, Shi L, Lai C, O'Connell SM, Xu J, Stansfield RK, Hosfield DJ, Veal JM, Stafford JA. Structure-based design and discovery of potent and selective KDM5 inhibitors. Bioorg Med Chem Lett 2018; 28:1490-1494. [DOI: 10.1016/j.bmcl.2018.03.083] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 12/16/2022]
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Lin H, Li Q, Li Q, Zhu J, Gu K, Jiang X, Hu Q, Feng F, Qu W, Chen Y, Sun H. Small molecule KDM4s inhibitors as anti-cancer agents. J Enzyme Inhib Med Chem 2018; 33:777-793. [PMID: 29651880 PMCID: PMC6010108 DOI: 10.1080/14756366.2018.1455676] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Histone demethylation is a vital process in epigenetic regulation of gene expression. A number of histone demethylases are present to control the methylated states of histone. Among these enzymes, KDM4s are one subfamily of JmjC KDMs and play important roles in both normal and cancer cells. The discovery of KDM4s inhibitors is a potential therapeutic strategy against different diseases including cancer. Here, we summarize the development of KDM4s inhibitors and some related pharmaceutical information to provide an update of recent progress in KDM4s inhibitors.
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Affiliation(s)
- Hongzhi Lin
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qihang Li
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qi Li
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Jie Zhu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Kai Gu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Xueyang Jiang
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qianqian Hu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Feng Feng
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Wei Qu
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Yao Chen
- c School of Pharmacy , Nanjing University of Chinese Medicine , Nanjing , China
| | - Haopeng Sun
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
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Horton JR, Liu X, Wu L, Zhang K, Shanks J, Zhang X, Rai G, Mott BT, Jansen DJ, Kales SC, Henderson MJ, Pohida K, Fang Y, Hu X, Jadhav A, Maloney DJ, Hall MD, Simeonov A, Fu H, Vertino PM, Yan Q, Cheng X. Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A. J Med Chem 2018; 61:3193-3208. [PMID: 29537847 PMCID: PMC6322411 DOI: 10.1021/acs.jmedchem.8b00261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Isomers of chiral drugs can exhibit marked differences in biological activities. We studied the binding and inhibitory activities of 12 compounds against KDM5A. Among them are two pairs of enantiomers representing two distinct inhibitor chemotypes, namely, ( R)- and ( S)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1 H-pyrrolo[3,2- b]pyridine-7-carboxylic acid (compounds N51 and N52) and ( R) - and ( S) -N-(1-(3-isopropyl-1 H-pyrazole-5-carbonyl)pyrrolidin-3-yl)cyclopropanecarboxamide (compounds N54 and N55). In vitro, the S enantiomer of the N51/N52 pair (N52) and the R enantiomer of the N54/N55 pair (N54) exhibited about 4- to 5-fold greater binding affinity. The more potent enzyme inhibition of KDM5A by the R-isoform for the cell-permeable N54/N55 pair translated to differences in growth inhibitory activity. We determined structures of the KDM5A catalytic domain in complex with all 12 inhibitors, which revealed the interactions (or lack thereof) responsible for the differences in binding affinity. These results provide insights to guide improvements in binding potency and avenues for development of cell permeable inhibitors of the KDM5 family.
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Affiliation(s)
- John R. Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Lizhen Wu
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Kai Zhang
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - John Shanks
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Bryan T. Mott
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Daniel J. Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Stephen C. Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Mark J. Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Katherine Pohida
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - David J. Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Haian Fu
- Department of Pharmacology, Emory University, Atlanta, Georgia 30322, United States
- Department of Hematology and Medical Oncology, Emory University, Atlanta, Georgia 30322, United States
- Emory Chemical Biology Discovery Center, Emory University, Atlanta, Georgia 30322, United States
- The Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
| | - Paula M. Vertino
- The Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
- Department of Radiation Oncology, Emory University, Atlanta, Georgia 30322, United States
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
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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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