1
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Portelinha A, Wang S, Parsa S, Jiang M, Gorelick AN, Mohanty S, Sharma S, de Stanchina E, Berishaj M, Zhao C, Heward J, Aryal NK, Tavana O, Wen J, Fitzgibbon J, Dogan A, Younes A, Melnick AM, Wendel HG. SETD1B mutations confer apoptosis resistance and BCL2 independence in B cell lymphoma. J Exp Med 2024; 221:e20231143. [PMID: 39235528 PMCID: PMC11380151 DOI: 10.1084/jem.20231143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 03/05/2024] [Accepted: 08/02/2024] [Indexed: 09/06/2024] Open
Abstract
The translocation t(14;18) activates BCL2 and is considered the initiating genetic lesion in most follicular lymphomas (FL). Surprisingly, FL patients fail to respond to the BCL2 inhibitor, Venetoclax. We show that mutations and deletions affecting the histone lysine methyltransferase SETD1B (KMT2G) occur in 7% of FLs and 16% of diffuse large B cell lymphomas (DLBCL). Deficiency in SETD1B confers striking resistance to Venetoclax and an experimental MCL-1 inhibitor. SETD1B also acts as a tumor suppressor and cooperates with the loss of KMT2D in lymphoma development in vivo. Consistently, loss of SETD1B in human lymphomas typically coincides with loss of KMT2D. Mechanistically, SETD1B is required for the expression of several proapoptotic BCL2 family proteins. Conversely, inhibitors of the KDM5 histone H3K4 demethylases restore BIM and BIK expression and synergize with Venetoclax in SETD1B-deficient lymphomas. These results establish SETD1B as an epigenetic regulator of cell death and reveal a pharmacological strategy to augment Venetoclax sensitivity in lymphoma.
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MESH Headings
- Animals
- Humans
- Mice
- Apoptosis/genetics
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Cell Line, Tumor
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Drug Resistance, Neoplasm/genetics
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/pathology
- Lymphoma, B-Cell/metabolism
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Mutation
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Proto-Oncogene Proteins c-bcl-2/genetics
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Sulfonamides/pharmacology
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Affiliation(s)
- Ana Portelinha
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | - Shenqiu Wang
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | - Sara Parsa
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | - Man Jiang
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | - Alexander N Gorelick
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sagarajit Mohanty
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | - Soumya Sharma
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center , New York, NY, USA
| | - Marjan Berishaj
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | - Chunying Zhao
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | | | - Neeraj K Aryal
- Bioscience, Early Oncology R&D, AstraZeneca , Waltham, MA, USA
| | - Omid Tavana
- Bioscience, Early Oncology R&D, AstraZeneca , Waltham, MA, USA
| | - Jiayu Wen
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University and Australian Research Council Centre of Excellence for the Mathematical Analysis of Cellular Systems, Canberra, Australia
| | | | - Ahmet Dogan
- Departments of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Anas Younes
- Haematology R&D, AstraZeneca , New York, NY, USA
| | - Ari M Melnick
- Hematology and Oncology Division, Medicine Department, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
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2
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Yan L, Sun H, Chen Y, Yu X, Zhang J, Li P. FOXP2 suppresses the proliferation, invasion, and aerobic glycolysis of hepatocellular carcinoma cells by regulating the KDM5A/FBP1 axis. ENVIRONMENTAL TOXICOLOGY 2024; 39:341-356. [PMID: 37713600 DOI: 10.1002/tox.23971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/04/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023]
Abstract
The Warburg effect is the preference of cancer cells to use glycolysis rather than oxidative phosphorylation to generate energy. Accumulating evidence suggests that aerobic glycolysis is widespread in hepatocellular carcinoma (HCC) and closely related to tumorigenesis. The purpose of this study was to investigate the role and mechanism of forkhead box P2 (FOXP2) in aerobic glycolysis and tumorigenesis in HCC. Here, we found that FOXP2 was lower expressed in HCC tissues and cells than in nontumor tissues and normal hepatocytes. Overexpression of FOXP2 suppressed cell proliferation and invasion of HCC cells and promoted cell apoptosis in vitro, and hindered the growth of mouse xenograft tumors in vivo. Further researches showed that FOXP2 inhibited the Warburg effect in HCC cells. Moreover, we demonstrated that FOXP2 up-regulated the expression of fructose-1, 6-diphosphatase (FBP1), and the inhibitory effect of FOXP2 on glycolysis was dependent on FBP1. Mechanistically, as a transcription factor, FOXP2 negatively regulated the transcription of lysine-specific demethylase 5A (KDM5A), and then blocked KDM5A-induced H3K4me3 demethylation in FBP1 promoter region, thereby promoting the expression of FBP1. Consistently, overexpressing KDM5A or silencing FBP1 effectively reversed the inhibitory effect of FOXP2 on HCC progression. Together, our findings revealed the mechanistic role of the FOXP2/KDM5A/FBP1 axis in glycolysis and malignant progression of HCC cells, providing a potential molecular target for the therapy of HCC.
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Affiliation(s)
- Lijing Yan
- Department of Endocrinology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huanhuan Sun
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yuling Chen
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaohui Yu
- Department of Respiratory Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jingru Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Peijie Li
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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3
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Kataria A, Tyagi S. Domain architecture and protein-protein interactions regulate KDM5A recruitment to the chromatin. Epigenetics 2023; 18:2268813. [PMID: 37838974 PMCID: PMC10578193 DOI: 10.1080/15592294.2023.2268813] [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: 05/18/2023] [Accepted: 10/01/2023] [Indexed: 10/17/2023] Open
Abstract
Tri-methylation of Histone 3 lysine 4 (H3K4) is an important epigenetic modification whose deposition and removal can affect the chromatin at structural and functional levels. KDM5A is one of the four known H3K4-specific demethylases. It is a part of the KDM5 family, which is characterized by a catalytic Jumonji domain capable of removing H3K4 di- and tri-methylation marks. KDM5A has been found to be involved in multiple cellular processes such as differentiation, metabolism, cell cycle, and transcription. Its link to various diseases, including cancer, makes KDM5A an important target for drug development. However, despite several studies outlining its significance in various pathways, our lack of understanding of its recruitment and function at the target sites on the chromatin presents a challenge in creating effective and targeted treatments. Therefore, it is essential to understand the recruitment mechanism of KDM5A to chromatin, and its activity therein, to comprehend how various roles of KDM5A are regulated. In this review, we discuss how KDM5A functions in a context-dependent manner on the chromatin, either directly through its structural domain, or through various interacting partners, to bring about a diverse range of functions.
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Affiliation(s)
- Avishek Kataria
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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4
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Cai L, Liu B, Cao Y, Sun T, Li Y. Unveiling the molecular structure and role of RBBP4/7: implications for epigenetic regulation and cancer research. Front Mol Biosci 2023; 10:1276612. [PMID: 38028543 PMCID: PMC10679446 DOI: 10.3389/fmolb.2023.1276612] [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: 08/12/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Retinoblastoma-binding protein (RBBP) family is a class of proteins that can interact with tumor suppressor retinoblastoma protein (pRb). RBBP4 and RBBP7 are the only pair of homologous proteins in this family, serving as scaffold proteins whose main function is to offer a platform to indirectly connect two proteins. This characteristic allows them to extensively participate in the binding of various proteins and epigenetic complexes, indirectly influencing the function of effector proteins. As a result, they are often highlighted in organism activities involving active epigenetic modifications, such as embryonic development and cancer activation. In this review, we summarize the structural characteristics of RBBP4/7, the complexes they are involved in, their roles in embryonic development and cancer, as well as potential future research directions, which we hope to inspire the field of epigenetic research in the future.
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Affiliation(s)
- Lize Cai
- The First Affiliated Hospital of Soochow University, Suzhou University, Suzhou, China
| | - Bin Liu
- Department of Neurosurgery, Qinghai Provincial People’s Hospital, Xining, China
| | - Yufei Cao
- The First Affiliated Hospital of Soochow University, Suzhou University, Suzhou, China
| | - Ting Sun
- The First Affiliated Hospital of Soochow University, Suzhou University, Suzhou, China
| | - Yanyan Li
- The First Affiliated Hospital of Soochow University, Suzhou University, Suzhou, China
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5
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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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6
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Zhang SM, Cao J, Yan Q. KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:113-137. [PMID: 37751138 DOI: 10.1007/978-3-031-38176-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The histone lysine demethylase 5 (KDM5) family proteins are Fe2+ and α-ketoglutarate-dependent dioxygenases, with jumonji C (JmjC) domain as their catalytic core and several plant homeodomains (PHDs) to bind different histone methylation marks. These enzymes are capable of demethylating tri-, di- and mono-methylated lysine 4 in histone H3 (H3K4me3/2/1), the key epigenetic marks for active chromatin. Thus, this H3K4 demethylase family plays critical roles in cell fate determination during development as well as malignant transformation. KDM5 demethylases have both oncogenic and tumor suppressive functions in a cancer type-dependent manner. In solid tumors, KDM5A/B are generally oncogenic, whereas KDM5C/D have tumor suppressive roles. Their involvement in de-differentiation, cancer metastasis, drug resistance, and tumor immunoevasion indicated that KDM5 family proteins are promising drug targets for cancer therapy. Significant efforts from both academia and industry have led to the development of potent and selective KDM5 inhibitors for preclinical experiments and phase I clinical trials. However, a better understanding of the roles of KDM5 demethylases in different physiological and pathological conditions is critical for further developing KDM5 modulators for clinical applications.
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Affiliation(s)
- Shang-Min Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jian Cao
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA.
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
| | - Qin Yan
- Department of Pathology, Yale Cancer Center, Yale Stem Cell Center, Yale Center for Immuno-Oncology, Yale Center for Research on Aging, Yale School of Medicine, P.O. Box 208023, New Haven, CT, 06520-8023, USA.
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7
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JMJD family proteins in cancer and inflammation. Signal Transduct Target Ther 2022; 7:304. [PMID: 36050314 PMCID: PMC9434538 DOI: 10.1038/s41392-022-01145-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/22/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022] Open
Abstract
The occurrence of cancer entails a series of genetic mutations that favor uncontrollable tumor growth. It is believed that various factors collectively contribute to cancer, and there is no one single explanation for tumorigenesis. Epigenetic changes such as the dysregulation of enzymes modifying DNA or histones are actively involved in oncogenesis and inflammatory response. The methylation of lysine residues on histone proteins represents a class of post-translational modifications. The human Jumonji C domain-containing (JMJD) protein family consists of more than 30 members. The JMJD proteins have long been identified with histone lysine demethylases (KDM) and histone arginine demethylases activities and thus could function as epigenetic modulators in physiological processes and diseases. Importantly, growing evidence has demonstrated the aberrant expression of JMJD proteins in cancer and inflammatory diseases, which might serve as an underlying mechanism for the initiation and progression of such diseases. Here, we discuss the role of key JMJD proteins in cancer and inflammation, including the intensively studied histone lysine demethylases, as well as the understudied group of JMJD members. In particular, we focused on epigenetic changes induced by each JMJD member and summarized recent research progress evaluating their therapeutic potential for the treatment of cancer and inflammatory diseases.
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8
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Putta S, Alvarez L, Lüdtke S, Sehr P, Müller GA, Fernandez SM, Tripathi S, Lewis J, Gibson TJ, Chemes LB, Rubin SM. Structural basis for tunable affinity and specificity of LxCxE-dependent protein interactions with the retinoblastoma protein family. Structure 2022; 30:1340-1353.e3. [PMID: 35716663 PMCID: PMC9444907 DOI: 10.1016/j.str.2022.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/25/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022]
Abstract
The retinoblastoma protein (Rb) and its homologs p107 and p130 are critical regulators of gene expression during the cell cycle and are commonly inactivated in cancer. Rb proteins use their "pocket domain" to bind an LxCxE sequence motif in other proteins, many of which function with Rb proteins to co-regulate transcription. Here, we present binding data and crystal structures of the p107 pocket domain in complex with LxCxE peptides from the transcriptional co-repressor proteins HDAC1, ARID4A, and EID1. Our results explain why Rb and p107 have weaker affinity for cellular LxCxE proteins compared with the E7 protein from human papillomavirus, which has been used as the primary model for understanding LxCxE motif interactions. Our structural and mutagenesis data also identify and explain differences in Rb and p107 affinities for some LxCxE-containing sequences. Our study provides new insights into how Rb proteins bind their cell partners with varying affinity and specificity.
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Affiliation(s)
- Sivasankar Putta
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Lucia Alvarez
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, Buenos Aires CP1650, Argentina
| | - Stephan Lüdtke
- Belyntic GmbH, Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - Peter Sehr
- Chemical Biology Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Gerd A Müller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Samantha M Fernandez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Joe Lewis
- Chemical Biology Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lucia B Chemes
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, Buenos Aires CP1650, Argentina.
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.
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9
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Pavlenko E, Ruengeler T, Engel P, Poepsel S. Functions and Interactions of Mammalian KDM5 Demethylases. Front Genet 2022; 13:906662. [PMID: 35899196 PMCID: PMC9309374 DOI: 10.3389/fgene.2022.906662] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/06/2022] [Indexed: 12/26/2022] Open
Abstract
Mammalian histone demethylases of the KDM5 family are mediators of gene expression dynamics during developmental, cellular differentiation, and other nuclear processes. They belong to the large group of JmjC domain containing, 2-oxoglutarate (2-OG) dependent oxygenases and target methylated lysine 4 of histone H3 (H3K4me1/2/3), an epigenetic mark associated with active transcription. In recent years, KDM5 demethylases have gained increasing attention due to their misregulation in many cancer entities and are intensively explored as therapeutic targets. Despite these implications, the molecular basis of KDM5 function has so far remained only poorly understood. Little is known about mechanisms of nucleosome recognition, the recruitment to genomic targets, as well as the local regulation of demethylase activity. Experimental evidence suggests close physical and functional interactions with epigenetic regulators such as histone deacetylase (HDAC) containing complexes, as well as the retinoblastoma protein (RB). To understand the regulation of KDM5 proteins in the context of chromatin, these interactions have to be taken into account. Here, we review the current state of knowledge on KDM5 function, with a particular emphasis on molecular interactions and their potential implications. We will discuss and outline open questions that need to be addressed to better understand histone demethylation and potential demethylation-independent functions of KDM5s. Addressing these questions will increase our understanding of histone demethylation and allow us to develop strategies to target individual KDM5 enzymes in specific biological and disease contexts.
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Affiliation(s)
- Egor Pavlenko
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Till Ruengeler
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Paulina Engel
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Simon Poepsel
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- *Correspondence: Simon Poepsel,
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10
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Diverse Functions of KDM5 in Cancer: Transcriptional Repressor or Activator? Cancers (Basel) 2022; 14:cancers14133270. [PMID: 35805040 PMCID: PMC9265395 DOI: 10.3390/cancers14133270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 11/16/2022] Open
Abstract
Epigenetic modifications are crucial for chromatin remodeling and transcriptional regulation. Post-translational modifications of histones are epigenetic processes that are fine-tuned by writer and eraser enzymes, and the disorganization of these enzymes alters the cellular state, resulting in human diseases. The KDM5 family is an enzymatic family that removes di- and tri-methyl groups (me2 and me3) from lysine 4 of histone H3 (H3K4), and its dysregulation has been implicated in cancer. Although H3K4me3 is an active chromatin marker, KDM5 proteins serve as not only transcriptional repressors but also transcriptional activators in a demethylase-dependent or -independent manner in different contexts. Notably, KDM5 proteins regulate the H3K4 methylation cycle required for active transcription. Here, we review the recent findings regarding the mechanisms of transcriptional regulation mediated by KDM5 in various contexts, with a focus on cancer, and further shed light on the potential of targeting KDM5 for cancer therapy.
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11
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KDM5A regulates the growth and gefitinib drug resistance against human lung adenocarcinoma cells. 3 Biotech 2022; 12:97. [PMID: 35371900 PMCID: PMC8934368 DOI: 10.1007/s13205-021-03018-w] [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: 11/13/2020] [Accepted: 07/09/2021] [Indexed: 11/01/2022] Open
Abstract
KDM5A, a histone demethylase, has been shown to be involved in several cancer-related process. The present study was undertaken to explore the role and therapeutic potential of KDM5A in human lung adenocarcinoma. The results of the qRT-PCR, immunohistochemistry, and western blotting showed significant upregulation of KDM5A expression in lung adenocarcinoma tissues and cell lines. The RNA interference-mediated silencing of KDM5A in lung adenocarcinoma cell line SK-LU-1 led to significant inhibition of in vitro cell proliferation via induction of apoptosis. The induction of apoptosis in SK-LU-1 lung adenocarcinoma cells was concomitant with upregulation of Bax and downregulation of Bcl-2 expression. In contrary, overexpression of KDM5A prompted the proliferation of SK-LU-1 lung adenocarcinoma cells. Interestingly, the SK-LU-1 cancer cells showed remarkably higher sensitivity to gefitinib under KDM5A transcriptional knockdown. Taken together, KDM5A is significantly upregulated in human lung adenocarcinoma and regulates the proliferation of the lung adenocarcinoma cells. These findings suggest potential of KDM5A to act as a therapeutic target for the management of human lung adenocarcinoma.
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12
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Taylor-Papadimitriou J, Burchell JM. Histone Methylases and Demethylases Regulating Antagonistic Methyl Marks: Changes Occurring in Cancer. Cells 2022; 11:1113. [PMID: 35406676 PMCID: PMC8997813 DOI: 10.3390/cells11071113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation of gene expression is crucial to the determination of cell fate in development and differentiation, and the Polycomb (PcG) and Trithorax (TrxG) groups of proteins, acting antagonistically as complexes, play a major role in this regulation. Although originally identified in Drosophila, these complexes are conserved in evolution and the components are well defined in mammals. Each complex contains a protein with methylase activity (KMT), which can add methyl groups to a specific lysine in histone tails, histone 3 lysine 27 (H3K27), by PcG complexes, and H3K4 and H3K36 by TrxG complexes, creating transcriptionally repressive or active marks, respectively. Histone demethylases (KDMs), identified later, added a new dimension to histone methylation, and mutations or changes in levels of expression are seen in both methylases and demethylases and in components of the PcG and TrX complexes across a range of cancers. In this review, we focus on both methylases and demethylases governing the methylation state of the suppressive and active marks and consider their action and interaction in normal tissues and in cancer. A picture is emerging which indicates that the changes which occur in cancer during methylation of histone lysines can lead to repression of genes, including tumour suppressor genes, or to the activation of oncogenes. Methylases or demethylases, which are themselves tumour suppressors, are highly mutated. Novel targets for cancer therapy have been identified and a methylase (KMT6A/EZH2), which produces the repressive H3K27me3 mark, and a demethylase (KDM1A/LSD1), which demethylates the active H3K4me2 mark, are now under clinical evaluation.
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13
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Hao F. Systemic Profiling of KDM5 Subfamily Signature in Non-Small-Cell Lung Cancer. Int J Gen Med 2021; 14:7259-7275. [PMID: 34737620 PMCID: PMC8558507 DOI: 10.2147/ijgm.s329733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/14/2021] [Indexed: 11/23/2022] Open
Abstract
Background Despite improvements in diagnosis and treatment, lung cancer is one of the most lethal human diseases, with a dismal 5-year relative survival rate of only 5% for patients diagnosed with advanced metastatic disease. Accumulating evidence supports that epigenetic aberration of histone demethylase-KDM5 subfamily is linked to human pan-cancer. However, the detailed functions of KDM5 proteins in lung cancer, especially in non-small-cell lung cancer (NSCLC), remain poorly understand. Methods UALCAN, GEPIA, Kaplan-Meier plotter, cBioPortal, TIMER, TISIDB, and STRING databases were utilized in this investigation. Results We detected varying degrees of gene mutations of KDM5 subfamily members and found that KDM5B/C were remarkably overexpressed in LUAD and LUSC compared to normal tissues. Different from KDM5D, positive relationship was shown between overall survival and mRNA expression of KDM5A/B/C in lung cancer. We determined that KDM5A/B/C expression levels were positively correlated with CD4+ T cells infiltration, especially immunological markers of Tregs and Th17 cells. Moreover, LUAD and LUSC were separately rich in inflammatory and wound healing subtypes after immunogenomics analyzing with respect to KDM5 subfamily overexpression. And with their 120 co-expressed genes, we revealed that nucleocytoplasmic transport and cellular protein localization-related genes were closely connected to KDM5 subfamily alterations, next to chromatin remodeling genes. Conclusion We formulated the immune-infiltrating and prognostic value of KDM5 subfamily and highlighted its promising role in immune-inflammatory interaction with tumour microenvironment in NSCLC.
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Affiliation(s)
- Fang Hao
- Department of Oncology, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
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14
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Tariq A, Rehman HM, Mateen RM, Ali M, Mutahir Z, Afzal MS, Sajjad M, Gul R, Saleem M. A computer aided drug discovery based discovery of lead-like compounds against KDM5A for cancers using pharmacophore modeling and high-throughput virtual screening. Proteins 2021; 90:645-657. [PMID: 34642975 DOI: 10.1002/prot.26262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/17/2021] [Accepted: 10/03/2021] [Indexed: 12/11/2022]
Abstract
KDM5A over-expression mediates cancer cell proliferation and promotes resistance toward chemotherapy through epigenetic modifications. As its complete mechanism of action is still unknown, there is no KDM5A specific drug available at clinical level. In the current study, lead compounds for KDM5A were determined through pharmacophore modeling and high-throughput virtual screening from Asinex libraries containing 0.5 million compounds. These virtual hits were further evaluated and filtered for ADMET properties. Finally, 726 compounds were used for docking analysis against KDM5A. On the basis of docking score, 10 top-ranked compounds were selected and further evaluated for non-central nervous system (CNS) and CNS drug-like properties. Among these compounds, N-{[(7-Methyl-4-oxo-1,2,3,4-tetrahydrocyclopenta [c] chromen-9-yl) oxy]acetyl}-l-phenylalanine (G-score: -11.363 kcal/mol) was estimated to exhibit non-CNS properties while 2-(3,4-Dimethoxy-phenyl)-7-methoxy-chromen-4-one (G-score: -7.977 kcal/mol) was evaluated as CNS compound. Docked complexes of both compounds were finally selected for molecular dynamic simulation to examine the stability. This study concluded that both these compounds can serve as lead compounds in the quest of finding therapeutic agents against KDM5A associated cancers.
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Affiliation(s)
- Asma Tariq
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Rana Muhammad Mateen
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Punjab, Pakistan
| | - Moazzam Ali
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Zeeshan Mutahir
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Muhammad Sohail Afzal
- Department of Life sciences, School of Science, University of Management and Technology, Lahore, Punjab, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Lahore, Punjab, Pakistan
| | - Roquyya Gul
- Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore, Punjab, Pakistan
| | - Mahjabeen Saleem
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
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15
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Basukala O, Banks L. The Not-So-Good, the Bad and the Ugly: HPV E5, E6 and E7 Oncoproteins in the Orchestration of Carcinogenesis. Viruses 2021; 13:1892. [PMID: 34696321 PMCID: PMC8541208 DOI: 10.3390/v13101892] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022] Open
Abstract
Infection with HPV starts with the access of the viral particles to basal cells in the epidermis, potentially via microtraumas to the skin. The basal cells are able to keep away these pathogens in normal circumstances through a robust immune response from the host, as HPV infections are, in general, cleared within 2 to 3 weeks. However, the rare instances of persistent infection and/or in cases where the host immune system is compromised are major risk factors for the development of lesions potentially leading to malignancy. Evolutionarily, obligatory pathogens such as HPVs would not be expected to risk exposing the host to lethal cancer, as this would entail challenging their own life cycle, but infection with these viruses is highly correlated with cancer and malignancy-as in cancer of the cervix, which is almost always associated with these viruses. Despite this key associative cause and the availability of very effective vaccines against these viruses, therapeutic interventions against HPV-induced cancers are still a challenge, indicating the need for focused translational research. In this review, we will consider the key roles that the viral proteins play in driving the host cells to carcinogenesis, mainly focusing on events orchestrated by early proteins E5, E6 and E7-the not-so-good, the bad and the ugly-and discuss and summarize the major events that lead to these viruses mechanistically corrupting cellular homeostasis, giving rise to cancer and malignancy.
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Affiliation(s)
| | - Lawrence Banks
- Tumour Virology Laboratory, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy;
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16
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Chen S, Zhao E. Development and validation of a robust epithelial-mesenchymal transition (EMT)-related prognostic signature for hepatocellular carcinoma. Clin Res Hepatol Gastroenterol 2021; 45:101587. [PMID: 33662631 DOI: 10.1016/j.clinre.2020.101587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/14/2020] [Accepted: 11/24/2020] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Epithelial-to-mesenchymal transition (EMT) is an essential biological process of cancer progression associated with increased metastatic potential and initiation. Herein, we aimed to develop and validate a robust EMT-related prognostic signature that could predict the prognosis of patients with hepatocellular carcinoma (HCC). METHODS Messenger RNA expression matrix and clinicopathological data were retrieved from The Cancer Genome Atlas (TCGA) and identified differentially expressed genes (DEGs) between HCC tissues and adjacent non-tumor samples. Univariate Cox regression analysis, least absolute shrinkage and selection operator (LASSO) Cox regression and multivariate Cox regression analysis were performed to establish a prognosis signature. Kaplan-Meier survival curve, time-dependent receiver operating characteristic (ROC), multivariate Cox regression analysis, nomogram, C-index, and decision curve analysis (DCA) were performed to investigate the prognostic performance of the signature. The prognostic performance of the new signature was further validated in an independent external cohort. A support vector machine (SVM) approach was performed to evaluate the diagnostic value of the identified genes. RESULTS A seven-gene signature was formulated to classify patients into high-risk and low-risk groups with discrepant overall survival (OS) in two cohorts (all P < 0.0001), and the former illustrated shorter survival time than the latter even stratified by various groups. The new signature has presented an excellent performance for predicting survival prognosis. Multivariate analysis showed that the signature was an independent risk factor for HCC. The SVM classifier based on the seven genes presented an excellent diagnostic power in differentiating early HCC and normal tissues. Gene Set Enrichment Analyses (GSEA) demonstrated multiple biological processes and pathways to provide novel insights into the development of HCC. CONCLUSION We established and validated a prognostic signature based on EMT-related genes with good predictive value for HCC survival. The diagnostic performance of the signature had been demonstrated to accurately distinguish early HCC from control individuals.
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Affiliation(s)
- Shimin Chen
- Department of Gastroenterology, Traditional Chinese Medical Hospital of Taihe Country, Taihe, 236600, China.
| | - Enfa Zhao
- Department of Structural Heart Disease, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
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17
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Punnia-Moorthy G, Hersey P, Emran AA, Tiffen J. Lysine Demethylases: Promising Drug Targets in Melanoma and Other Cancers. Front Genet 2021; 12:680633. [PMID: 34220955 PMCID: PMC8242339 DOI: 10.3389/fgene.2021.680633] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic dysregulation has been implicated in a variety of pathological processes including carcinogenesis. A major group of enzymes that influence epigenetic modifications are lysine demethylases (KDMs) also known as "erasers" which remove methyl groups on lysine (K) amino acids of histones. Numerous studies have implicated aberrant lysine demethylase activity in a variety of cancers, including melanoma. This review will focus on the structure, classification and functions of KDMs in normal biology and the current knowledge of how KDMs are deregulated in cancer pathogenesis, emphasizing our interest in melanoma. We highlight the current knowledge gaps of KDMs in melanoma pathobiology and describe opportunities to increases our understanding of their importance in this disease. We summarize the progress of several pre-clinical compounds that inhibit KDMs and represent promising candidates for further investigation in oncology.
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Affiliation(s)
- Gaya Punnia-Moorthy
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia
- Melanoma Epigenetics Laboratory, Centenary Institute, University of Sydney, Sydney, NSW, Australia
- Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Peter Hersey
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia
- Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Abdullah Al Emran
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia
- Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Jessamy Tiffen
- Melanoma Oncology and Immunology Group, Centenary Institute, University of Sydney, Sydney, NSW, Australia
- Melanoma Epigenetics Laboratory, Centenary Institute, University of Sydney, Sydney, NSW, Australia
- Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
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Ren J, Yao H, Hu W, Perrett S, Gong W, Feng Y. Structural basis for the DNA-binding activity of human ARID4B Tudor domain. J Biol Chem 2021; 296:100506. [PMID: 33675746 PMCID: PMC8038949 DOI: 10.1016/j.jbc.2021.100506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 11/24/2022] Open
Abstract
Human ARID4A and ARID4B are homologous proteins that are important in controlling gene expression and epigenetic regulation but have distinct functions. Previous studies have shown that the N-terminal domain of ARID4A is an unusual interdigitated double Tudor domain with DNA-binding activity. However, how the Tudor domain of ARID4B differs from that of ARID4A remains unknown. Here, we found that the ARID4B Tudor domain has significantly weaker DNA affinity than the ARID4A Tudor domain despite sharing more than 80% sequence identity. Structure determination and DNA titration analysis indicated that the ARID4B Tudor domain is also an interdigitated double Tudor domain with a DNA-binding surface similar to ARID4A. We identified a residue close to the DNA-binding site of the Tudor domain that differs between ARID4A and ARID4B. The Leu50 in ARID4A is Glu50 in ARID4B, and the latter forms salt bridges with two lysine residues at the DNA-binding surface. This causes a decrease in the strength of positive charge, thus reducing DNA-binding affinity while significantly increasing protein stability. We also found that a C-terminal extension region enhances the DNA-binding affinity of the ARID4B Tudor domain. This C-terminal extension is disordered and contains a positively charged RGR motif, providing an additional DNA-binding site. Finally, sequence and phylogenetic analyses indicated that the residue differences and the presence of the RGR extension region are conserved. These results provide new insight into the functional differences between ARID4A and ARID4B proteins, as well as elucidating the function of the disordered regions in these proteins.
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Affiliation(s)
- Jie Ren
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Hongwei Yao
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Wanhui Hu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Weibin Gong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Yingang Feng
- University of Chinese Academy of Sciences, Beijing, China; CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
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19
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Peng D, Lin B, Xie M, Zhang P, Guo Q, Li Q, Gu Q, Yang S, Sen L. Histone demethylase KDM5A promotes tumorigenesis of osteosarcoma tumor. Cell Death Discov 2021; 7:9. [PMID: 33436536 PMCID: PMC7803953 DOI: 10.1038/s41420-020-00396-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/10/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022] Open
Abstract
Osteosarcoma is a primary bone malignancy with a high rate of recurrence and poorer prognosis. Therefore, it is of vital importance to explore novel prognostic molecular biomarkers and targets for more effective therapeutic approaches. Previous studies showed that histone demethylase KDM5A can increase the proliferation and metastasis of several cancers. However, the function of KDM5A in the carcinogenesis of osteosarcoma is not clear. In the current study, KDM5A was highly expressed in osteosarcoma than adjacent normal tissue. Knockdown of KDM5A suppressed osteosarcoma cell proliferation and induced apoptosis. Moreover, knockdown of KDM5A could increase the expression level of P27 (cell-cycle inhibitor) and decrease the expression of Cyclin D1. Furthermore, after knockout of KDM5A in osteosarcoma cells by CRISPR/Cas9 system, the tumor size and growth speed were inhibited in tumor-bearing nude mice. RNA-Seq of KDM5A-KO cells indicated that interferon, epithelial–mesenchymal transition (EMT), IL6/JAK/STAT3, and TNF-α/NF-κB pathway were likely involved in the regulation of osteosarcoma cell viability. Taken together, our research established a role of KDM5A in osteosarcoma tumorigenesis and progression.
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Affiliation(s)
- Daohu Peng
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China
| | - Birong Lin
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China
| | - Mingzhong Xie
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China
| | - Ping Zhang
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China
| | - QingXi Guo
- The affiliated hospital of Southwest Medical University, 25 Taiping Street, Jiangyang District, 646015, Luzhou City, Sichuan, P. R. China
| | - Qian Li
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China
| | - Qinwen Gu
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China
| | - Sijin Yang
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China.
| | - Li Sen
- Hospital (T.C.M) Affiliated to Southwest Medical University, 182 Chunhui Road, Longmatan District, 64600, Luzhou City, Sichuan, P. R. China.
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20
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Li QM, Li JL, Feng ZH, Lin HC, Xu Q. Effect of histone demethylase KDM5A on the odontogenic differentiation of human dental pulp cells. Bioengineered 2020; 11:449-462. [PMID: 32208897 PMCID: PMC7161540 DOI: 10.1080/21655979.2020.1743536] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/13/2022] Open
Abstract
Human dental pulp cells (hDPCs) possess the capacity to differentiate into odontoblast-like cells in response to exogenous stimuli. Histone methylation is one of the most robust epigenetic marks and is essential for the regulation of multiple cellular processes. Previous studies have shown that histone methyltransferases (HMTs) and histone demethylases (HDMs) are crucial for the osteogenic differentiation of human bone marrow, adipose tissue, and tooth tissue. However, little is known about the role of histone methylation in hDPC differentiation. Here, the expression levels of HMTs and HDMs were profiled in hDPCs undergoing odontogenic induction. Among several differentially expressed enzymes, HDM KDM5A demonstrated significantly enhanced expression during cytodifferentiation. Furthermore, KDM5A expression increased during early passages and in a time-dependent manner during odontogenic induction. Using a shRNA-expressing lentivirus, KDM5A was knocked down in hDPCs. KDM5A depletion resulted in greater alkaline phosphatase activity and more mineral deposition formation. Meanwhile, the expression levels of the odontogenic markers DMP1, DSPP, OSX, and OCN were increased by KDM5A knockdown. As a histone demethylase specific for tri- and dimethylated histone H3 at lysine 4 (H3K4me3/me2), KDM5A deficiency led to a significant increment in total H3K4me3 levels, whereas no significant difference was found for H3K4 me2. H3K4me3 levels on the promoters of the odontogenic markers increased after KDM5A knockdown in hDPCs. These results demonstrated that KDM5A is present in hDPCs and inhibits the odontogenic differentiation potentiality of hDPCs by removing H3K4me3 from specific gene promoters, suggesting that KDM5A-dependent histone demethylation may play an important role in reparative dentinogenesis.
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Affiliation(s)
- Qi-Meng Li
- Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Jin-Ling Li
- Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, P.R. China
| | - Zhi-Hui Feng
- Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Huan-Cai Lin
- Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Qiong Xu
- Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
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21
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Michmerhuizen NL, Klco JM, Mullighan CG. Mechanistic insights and potential therapeutic approaches for NUP98-rearranged hematologic malignancies. Blood 2020; 136:2275-2289. [PMID: 32766874 PMCID: PMC7702474 DOI: 10.1182/blood.2020007093] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleoporin 98 (NUP98) fusion oncoproteins are observed in a spectrum of hematologic malignancies, particularly pediatric leukemias with poor patient outcomes. Although wild-type full-length NUP98 is a member of the nuclear pore complex, the chromosomal translocations leading to NUP98 gene fusions involve the intrinsically disordered and N-terminal region of NUP98 with over 30 partner genes. Fusion partners include several genes bearing homeodomains or having known roles in transcriptional or epigenetic regulation. Based on data in both experimental models and patient samples, NUP98 fusion oncoprotein-driven leukemogenesis is mediated by changes in chromatin structure and gene expression. Multiple cofactors associate with NUP98 fusion oncoproteins to mediate transcriptional changes possibly via phase separation, in a manner likely dependent on the fusion partner. NUP98 gene fusions co-occur with a set of additional mutations, including FLT3-internal tandem duplication and other events contributing to increased proliferation. To improve the currently dire outcomes for patients with NUP98-rearranged malignancies, therapeutic strategies have been considered that target transcriptional and epigenetic machinery, cooperating alterations, and signaling or cell-cycle pathways. With the development of more faithful experimental systems and continued study, we anticipate great strides in our understanding of the molecular mechanisms and therapeutic vulnerabilities at play in NUP98-rearranged models. Taken together, these studies should lead to improved clinical outcomes for NUP98-rearranged leukemia.
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Affiliation(s)
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
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22
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Venkatesh S, Baljinnyam E, Tong M, Kashihara T, Yan L, Liu T, Li H, Xie LH, Nakamura M, Oka SI, Suzuki CK, Fraidenraich D, Sadoshima J. Proteomic analysis of mitochondrial biogenesis in cardiomyocytes differentiated from human induced pluripotent stem cells. Am J Physiol Regul Integr Comp Physiol 2020; 320:R547-R562. [PMID: 33112656 DOI: 10.1152/ajpregu.00207.2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mitochondria play key roles in the differentiation and maturation of human cardiomyocytes (CMs). As human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) hold potential in the treatment of heart diseases, we sought to identify key mitochondrial pathways and regulators, which may provide targets for improving cardiac differentiation and maturation. Proteomic analysis was performed on enriched mitochondrial protein extracts isolated from hiPSC-CMs differentiated from dermal fibroblasts (dFCM) and cardiac fibroblasts (cFCM) at time points between 12 and 115 days of differentiation, and from adult and neonatal mouse hearts. Mitochondrial proteins with a twofold change at time points up to 120 days relative to 12 days were subjected to ingenuity pathway analysis (IPA). The highest upregulation was in metabolic pathways for fatty acid oxidation (FAO), the tricarboxylic acid (TCA) cycle, oxidative phosphorylation (OXPHOS), and branched chain amino acid (BCAA) degradation. The top upstream regulators predicted to be activated were peroxisome proliferator-activated receptor γ coactivator 1 α (PGC1-α), the insulin receptor (IR), and the retinoblastoma protein (Rb1) transcriptional repressor. IPA and immunoblotting showed upregulation of the mitochondrial LonP1 protease-a regulator of mitochondrial proteostasis, energetics, and metabolism. LonP1 knockdown increased FAO in neonatal rat ventricular cardiomyocytes (nRVMs). Our results support the notion that LonP1 upregulation negatively regulates FAO in cardiomyocytes to calibrate the flux between glucose and fatty acid oxidation. We discuss potential mechanisms by which IR, Rb1, and LonP1 regulate the metabolic shift from glycolysis to OXPHOS and FAO. These newly identified factors and pathways may help in optimizing the maturation of iPSC-CMs.
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Affiliation(s)
- Sundararajan Venkatesh
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Erdene Baljinnyam
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Mingming Tong
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Toshihide Kashihara
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Lin Yan
- Center for Advanced Proteomics Research and Department of Microbiology, Biochemistry and Molecular Genetics, Cancer Center, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Tong Liu
- Center for Advanced Proteomics Research and Department of Microbiology, Biochemistry and Molecular Genetics, Cancer Center, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Hong Li
- Center for Advanced Proteomics Research and Department of Microbiology, Biochemistry and Molecular Genetics, Cancer Center, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Lai-Hua Xie
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Michinari Nakamura
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Shin-Ichi Oka
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Carolyn K Suzuki
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Diego Fraidenraich
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey
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23
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Ren F, Shrestha C, Shi H, Sun F, Zhang M, Cao Y, Li G. Targeting of KDM5A by miR-421 in Human Ovarian Cancer Suppresses the Progression of Ovarian Cancer Cells. Onco Targets Ther 2020; 13:9419-9428. [PMID: 33061428 PMCID: PMC7520141 DOI: 10.2147/ott.s266211] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
PURPOSE The retinoblastoma binding protein RBP2 (KDM5A) is a histone demethylase that promotes cell growth in many human cancers. A series of functional experiments were conducted to explore the role of miR-421/KDM5A in ovarian cancer cells and their underlying molecular mechanisms. MATERIALS AND METHODS Public microarray databases were analyzed to assess KDM5A and miR-421 expression in ovarian cancer. KDM5A was predicted to be a target of miR-421 using software analysis. The expression of the miR-421/KDM5A regulatory axis in ovarian cancer and the mechanisms of its effects on proliferation, migration, and invasion of ovarian cancer cell lines were investigated. RESULTS Compared with normal ovarian tissues, the expression of KDM5A mRNA and protein was elevated (P<0.05), and miR-421 expression was reduced in ovarian cancer tissue (P<0.05). miR-421 was found to bind specifically to the KDM5A gene. Silencing KDM5A or overexpressing miR-421 significantly inhibited proliferation, migration, and invasion of OVCAR-8 and SKOV-3 cells. Similarly, compared with nude mice injected with cells transfected with empty capsids, the in vivo proliferation rate of OVCAR-8 cells after miR-421 overexpression was reduced significantly. CONCLUSION The miR-421/KDM5A regulatory axis plays an important role in the development and progression of ovarian cancer cells.
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Affiliation(s)
- Fang Ren
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Christina Shrestha
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Huirong Shi
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Fangfang Sun
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Minghui Zhang
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Yuan Cao
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Gailing Li
- Department of Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
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24
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Maezawa S, Sakashita A, Yukawa M, Chen X, Takahashi K, Alavattam KG, Nakata I, Weirauch MT, Barski A, Namekawa SH. Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition. Nat Struct Mol Biol 2020; 27:978-988. [PMID: 32895557 PMCID: PMC8690596 DOI: 10.1038/s41594-020-0488-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/10/2020] [Indexed: 01/12/2023]
Abstract
Due to bursts in the expression of thousands of germline-specific genes, the testis has the most diverse and complex transcriptome of all organs. By analyzing the male germline of mice, we demonstrate that the genome-wide reorganization of super-enhancers (SEs) drives bursts in germline gene expression after the mitosis-to-meiosis transition. SE reorganization is regulated by two molecular events: the establishment of meiosis-specific SEs via A-MYB (MYBL1), a key transcription factor for germline genes, and the resolution of SEs in mitotically proliferating cells via SCML2, a germline-specific Polycomb protein required for spermatogenesis-specific gene expression. Prior to entry into meiosis, meiotic SEs are preprogrammed in mitotic spermatogonia to ensure the unidirectional differentiation of spermatogenesis. We identify key regulatory factors for both mitotic and meiotic enhancers, revealing a molecular logic for the concurrent activation of mitotic enhancers and suppression of meiotic enhancers in the somatic and/or mitotic proliferation phases.
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Affiliation(s)
- So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan. .,Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba, Japan.
| | - Akihiko Sakashita
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Masashi Yukawa
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kazuki Takahashi
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ippo Nakata
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA.
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25
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Aarthy M, Panwar U, Singh SK. Structural dynamic studies on identification of EGCG analogues for the inhibition of Human Papillomavirus E7. Sci Rep 2020; 10:8661. [PMID: 32457393 PMCID: PMC7250877 DOI: 10.1038/s41598-020-65446-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/04/2020] [Indexed: 02/04/2023] Open
Abstract
High risk human papillomaviruses are highly associated with the cervical carcinoma and the other genital tumors. Development of cervical cancer passes through the multistep process initiated from benign cyst to increasingly severe premalignant dysplastic lesions in an epithelium. Replication of this virus occurs in the fatal differentiating epithelium and involves in the activation of cellular DNA replication proteins. The oncoprotein E7 of human papillomavirus expressed in the lower epithelial layers constrains the cells into S-phase constructing an environment favorable for genome replication and cell proliferation. To date, no suitable drug molecules exist to treat HPV infection whereas anticipation of novel anti-HPV chemotherapies with distinctive mode of actions and identification of potential drugs are crucial to a greater extent. Hence, our present study focused on identification of compounds analogue to EGCG, a green tea molecule which is considered to be safe to use for mammalian systems towards treatment of cancer. A three dimensional similarity search on the small molecule library from natural product database using EGCG identified 11 potential small molecules based on their structural similarity. The docking strategies were implemented with acquired small molecules and identification of the key interactions between protein and compounds were carried out through binding free energy calculations. The conformational changes between the apoprotein and complexes were analyzed through simulation performed thrice demonstrating the dynamical and structural effects of the protein induced by the compounds signifying the domination. The analysis of the conformational stability provoked us to describe the features of the best identified small molecules through electronic structure calculations. Overall, our study provides the basis for structural insights of the identified potential identified small molecules and EGCG. Hence, the identified analogue of EGCG can be potent inhibitors against the HPV 16 E7 oncoprotein.
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Affiliation(s)
- Murali Aarthy
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630004, India
| | - Umesh Panwar
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630004, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630004, India.
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26
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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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27
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A novel KDM5A/MPC-1 signaling pathway promotes pancreatic cancer progression via redirecting mitochondrial pyruvate metabolism. Oncogene 2019; 39:1140-1151. [PMID: 31641207 DOI: 10.1038/s41388-019-1051-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 06/01/2019] [Accepted: 06/25/2019] [Indexed: 12/13/2022]
Abstract
Mitochondrial pyruvate carrier 1 (MPC-1) appears to be a tumor suppressor. In this study, we determined the regulation of MPC-1 expression by Lysine demethylase 5A (KDM5A) and critical impact of this novel KDM5A/MPC-1 signaling on PDA progression. TCGA database, paired PDA and adjacent normal pancreatic tissues, PDA tissue array and cell lines were used to determine the levels of MPC-1 and KDM5A expression, and their relationship with the clinicopathologic characteristics and overall survival (OS) of PDA patients. Both in vitro and in vivo models were used to determine biologic impacts of MPC-1 and KDM5A on PDA and mitochondrial pyruvate metabolism, and the mechanism underling reduced MPC-1 expression in PDA. The expression of MPC-1 was decreased in PDA cell lines and tissues, and negatively associated with tumor poorer differentiation, lymph nodes metastasis, higher TNM stages, and patients' overall survival (OS). Functional analysis revealed that restored expression of MPC-1 suppressed the growth, invasion, migration, stemness and tumorigenicity. Re-expression of MPC-1 stimulated the mitochondrial pyruvate metabolism and inhibited glycolysis, while MPC-1-specific inhibitor UK5099 attenuated these effects. Furthermore, KDM5A bound directly to MPC-1 promoter region and transcriptionally suppressed the expression of MPC-1 via demethylation H3K4. Consistently, KDM5A expression was elevated in PDA and promoted PDA cell proliferation in vitro and tumor growth in vivo via suppressing the expression of MPC-1. The expression of KDM5A was inversely correlated with that of MPC-1 in PDA. KDM5A/MPC-1 signaling promoted PDA growth, invasion, migration, and stemness via inhibiting mitochondrial pyruvate metabolism. Targeting KDM5A/MPC-1 signaling may be an effective therapeutic strategy for PDA.
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28
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James C, Müller M, Goldberg MW, Lenz C, Urlaub H, Kehlenbach RH. Proteomic mapping by rapamycin-dependent targeting of APEX2 identifies binding partners of VAPB at the inner nuclear membrane. J Biol Chem 2019; 294:16241-16254. [PMID: 31519755 DOI: 10.1074/jbc.ra118.007283] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 08/05/2019] [Indexed: 11/06/2022] Open
Abstract
Vesicle-associated membrane protein-associated protein B (VAPB) is a tail-anchored protein that is present at several contact sites of the endoplasmic reticulum (ER). We now show by immunoelectron microscopy that VAPB also localizes to the inner nuclear membrane (INM). Using a modified enhanced ascorbate peroxidase 2 (APEX2) approach with rapamycin-dependent targeting of the peroxidase to a protein of interest, we searched for proteins that are in close proximity to VAPB, particularly at the INM. In combination with stable isotope labeling with amino acids in cell culture (SILAC), we confirmed many well-known interaction partners at the level of the ER with a clear distinction between specific and nonspecific hits. Furthermore, we identified emerin, TMEM43, and ELYS as potential interaction partners of VAPB at the INM and the nuclear pore complex, respectively.
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Affiliation(s)
- Christina James
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center for Molecular Biosciences (GZMB), Georg August University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Marret Müller
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center for Molecular Biosciences (GZMB), Georg August University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Martin W Goldberg
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Christof Lenz
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ralph H Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center for Molecular Biosciences (GZMB), Georg August University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
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29
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Zargar ZU, Kimidi MR, Tyagi S. Dynamic site-specific recruitment of RBP2 by pocket protein p130 modulates H3K4 methylation on E2F-responsive promoters. Nucleic Acids Res 2019; 46:174-188. [PMID: 29059406 PMCID: PMC5758877 DOI: 10.1093/nar/gkx961] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 10/07/2017] [Indexed: 02/01/2023] Open
Abstract
The Histone 3 lysine 4 methylation (H3K4me3) mark closely correlates with active transcription. E2F-responsive promoters display dynamic changes in H3K4 methylation during the course of cell cycle progression. However, how and when these marks are reset, is not known. Here we show that the retinoblastoma binding protein RBP2/KDM5A, capable of removing tri-methylation marks on H3K4, associates with the E2F4 transcription factor via the pocket protein-p130-in a cell-cycle-stage specific manner. The association of RBP2 with p130 is LxCxE motif dependent. RNAi experiments reveal that p130 recruits RBP2 to E2F-responsive promoters in early G1 phase to bring about H3K4 demethylation and gene repression. A point mutation in LxCxE motif of RBP2 renders it incapable of p130-interaction and hence, repression of E2F-regulated gene promoters. We also examine how RBP2 may be recruited to non-E2F responsive promoters. Our studies provide insight into how the chromatin landscape needs to be adjusted rapidly and periodically during cell-cycle progression, concomitantly with temporal transcription, to bring about expression/repression of specific gene sets.
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Affiliation(s)
- Zaffer Ullah Zargar
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, India.,Graduate Studies, Manipal University, Manipal, India
| | - Mallikharjuna Rao Kimidi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, India
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30
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The cancer driver genes IDH1/2, JARID1C/ KDM5C, and UTX/ KDM6A: crosstalk between histone demethylation and hypoxic reprogramming in cancer metabolism. Exp Mol Med 2019; 51:1-17. [PMID: 31221981 PMCID: PMC6586683 DOI: 10.1038/s12276-019-0230-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/12/2018] [Indexed: 12/16/2022] Open
Abstract
Recent studies on mutations in cancer genomes have distinguished driver mutations from passenger mutations, which occur as byproducts of cancer development. The cancer genome atlas (TCGA) project identified 299 genes and 24 pathways/biological processes that drive tumor progression (Cell 173: 371-385 e318, 2018). Of the 299 driver genes, 12 genes are involved in histones, histone methylation, and demethylation. Among these 12 genes, those encoding the histone demethylases JARID1C/KDM5C and UTX/KDM6A were identified as cancer driver genes. Furthermore, gain-of-function mutations in genes encoding metabolic enzymes, such as isocitrate dehydrogenases (IDH)1/2, drive tumor progression by producing an oncometabolite, D-2-hydroxyglutarate (D-2HG), which is a competitive inhibitor of α-ketoglutarate, O2-dependent dioxygenases such as Jumonji domain-containing histone demethylases, and DNA demethylases. Studies on oncometabolites suggest that histone demethylases mediate metabolic changes in chromatin structure. We have reviewed the most recent findings regarding cancer-specific metabolic reprogramming and the tumor-suppressive roles of JARID1C/KDM5C and UTX/KDM6A. We have also discussed mutations in other isoforms such as the JARID1A, 1B, 1D of KDM5 subfamilies and the JMJD3/KDM6B of KDM6 subfamilies, which play opposing roles in tumor progression as oncogenes or tumor suppressors depending on the cancer cell type. Genes involved in the removal of methyl groups from histones associated with DNA can promote or suppress tumor growth depending on the metabolic status of the cancer cell. Hyunsung Park and colleagues at the University of Seoul, South Korea, review current knowledge of two genes encoding histone demethylases which have been identified by The Cancer Genome Atlas (TCGA) project as cancer driver genes. Because these demethylase enzymes rely on cellular metabolites to function, their effect is influenced by metabolic conditions in the tumor microenvironment such as low oxygen. The mechanisms through which changes in histone methylation affect the expression of genes involved in tumor progression remain unknown. Further understanding of how cancer metabolism affects the modification of histones will help guide the development of more effective cancer treatments.
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31
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Pippa S, Mannironi C, Licursi V, Bombardi L, Colotti G, Cundari E, Mollica A, Coluccia A, Naccarato V, La Regina G, Silvestri R, Negri R. Small Molecule Inhibitors of KDM5 Histone Demethylases Increase the Radiosensitivity of Breast Cancer Cells Overexpressing JARID1B. Molecules 2019; 24:molecules24091739. [PMID: 31060229 PMCID: PMC6540222 DOI: 10.3390/molecules24091739] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/24/2019] [Accepted: 05/01/2019] [Indexed: 12/18/2022] Open
Abstract
Background: KDM5 enzymes are H3K4 specific histone demethylases involved in transcriptional regulation and DNA repair. These proteins are overexpressed in different kinds of cancer, including breast, prostate and bladder carcinomas, with positive effects on cancer proliferation and chemoresistance. For these reasons, these enzymes are potential therapeutic targets. Methods: In the present study, we analyzed the effects of three different inhibitors of KDM5 enzymes in MCF-7 breast cancer cells over-expressing one of them, namely KDM5B/JARID1B. In particular we tested H3K4 demethylation (western blot); radio-sensitivity (cytoxicity and clonogenic assays) and damage accumulation (COMET assay and kinetics of H2AX phosphorylation). Results: we show that all three compounds with completely different chemical structures can selectively inhibit KDM5 enzymes and are capable of increasing sensitivity of breast cancer cells to ionizing radiation and radiation-induced damage. Conclusions: These findings confirm the involvement of H3K4 specific demethylases in the response to DNA damage, show a requirement of the catalytic function and suggest new strategies for the therapeutic use of their inhibitors.
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Affiliation(s)
- Simone Pippa
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Cecilia Mannironi
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Valerio Licursi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
- Institute for Systems Analysis and Computer Science "A. Ruberti", Italian National Research Council, 00185 Rome, Italy.
| | - Luca Bombardi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Enrico Cundari
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Adriano Mollica
- Department of Pharmacy, University "G. d' Annunzio" of Chieti, Via dei Vestini 31, 66100 Chieti, Italy.
| | - Antonio Coluccia
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Valentina Naccarato
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Giuseppe La Regina
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Romano Silvestri
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
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32
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Singh A, Paul MS, Dutta D, Mutsuddi M, Mukherjee A. Regulation of notch signaling by a chromatin modeling protein Hat-trick. Development 2019; 146:dev.170837. [DOI: 10.1242/dev.170837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 05/16/2019] [Indexed: 01/08/2023]
Abstract
Notch signaling plays pleiotropic role in astounding variety of cellular processes including cell fate determination, differentiation, proliferation and apoptosis. The increasingly complex regulatory mechanisms of Notch signaling account for the multitude of functions exhibited by Notch during development. We identified Hat-trick (Htk), a DNA binding protein, as an interacting partner of Notch-ICD in a yeast two-hybrid screen and their physical interaction was further validated by co-immunoprecipitation experiments. htk genetically interacts with Notch pathway components in trans-heterozygous combinations. Loss of htk function in htk mutant somatic clones showed down-regulation of Notch targets, whereas over-expression of htk caused ectopic expression of Notch target, without affecting the level of Notch protein. Immunocytochemical analysis has demonstrated that Htk co-localizes with over-expressed Notch-ICD in the same nuclear compartment. We have shown here that Htk cooperates with Notch-ICD and Suppressor of Hairless to form activation complex and binds to the regulatory sequences of Notch downstream targets, Enhancer of Split complex genes to direct their expression. Taken together, our results suggest a novel mode of regulation of Notch signaling by a chromatin modeling protein Htk.
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Affiliation(s)
- Ankita Singh
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
| | - Maimuna S. Paul
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
| | - Debdeep Dutta
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
| | - Mousumi Mutsuddi
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
| | - Ashim Mukherjee
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
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33
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Ilicic M, Zakar T, Paul JW. Epigenetic regulation of progesterone receptors and the onset of labour. Reprod Fertil Dev 2019; 31:1035-1048. [DOI: 10.1071/rd18392] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/29/2019] [Indexed: 01/09/2023] Open
Abstract
Progesterone plays a crucial role in maintaining pregnancy by promoting myometrial quiescence. The withdrawal of progesterone action signals the end of pregnancy and, in most mammalian species, this is achieved by a rapid fall in progesterone concentrations. However, in humans circulating progesterone concentrations remain high up to and during labour. Efforts to understand this phenomenon led to the ‘functional progesterone withdrawal’ hypothesis, whereby the pro-gestation actions of progesterone are withdrawn, despite circulating concentrations remaining elevated. The exact mechanism of functional progesterone withdrawal is still unclear and in recent years has been the focus of intense research. Emerging evidence now indicates that epigenetic regulation of progesterone receptor isoform expression may be the crucial mechanism by which functional progesterone withdrawal is achieved, effectively precipitating human labour despite high concentrations of circulating progesterone. This review examines current evidence that epigenetic mechanisms play a role in determining whether the pro-gestation or pro-contractile isoform of the progesterone receptor is expressed in the pregnant human uterus. We explore the mechanism by which these epigenetic modifications are achieved and, importantly, how these underlying epigenetic mechanisms are influenced by known regulators of uterine physiology, such as prostaglandins and oestrogens, in order to phenotypically transform the pregnant uterus and initiate labour.
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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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Xhabija B, Kidder BL. KDM5B is a master regulator of the H3K4-methylome in stem cells, development and cancer. Semin Cancer Biol 2018; 57:79-85. [PMID: 30448242 DOI: 10.1016/j.semcancer.2018.11.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 12/12/2022]
Abstract
Epigenetic regulation of chromatin plays a critical role in controlling stem cell function and tumorigenesis. The histone lysine demethylase, KDM5B, which catalyzes the demethylation of histone 3 lysine 4 (H3K4), is important for embryonic stem (ES) cell differentiation, and is a critical regulator of the H3K4-methylome during early mouse embryonic pre-implantation stage development. KDM5B is also overexpressed, amplified, or mutated in many cancer types. In cancer cells, KDM5B regulates expression of oncogenes and tumor suppressors by modulating H3K4 methylation levels. In this review, we examine how KDM5B regulates gene expression and cellular fates of stem cells and cancer cells by temporally and spatially controlling H3K4 methylation levels.
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Affiliation(s)
- Besa Xhabija
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
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36
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Liu H, Wang J, Liu Y, Hu L, Zhang C, Xing B, Du X. Human U3 protein14a is a novel type ubiquitin ligase that binds RB and promotes RB degradation depending on a leucine-rich region. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1611-1620. [DOI: 10.1016/j.bbamcr.2018.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 11/16/2022]
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Endoplasmic Reticulum Homeostasis Is Modulated by the Forkhead Transcription Factor FKH-9 During Infection of Caenorhabditis elegans. Genetics 2018; 210:1329-1337. [PMID: 30287474 DOI: 10.1534/genetics.118.301450] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/25/2018] [Indexed: 12/29/2022] Open
Abstract
Animals have evolved critical mechanisms to maintain cellular and organismal proteostasis during development, disease, and exposure to environmental stressors. The Unfolded Protein Response (UPR) is a conserved pathway that senses and responds to the accumulation of misfolded proteins in the endoplasmic reticulum (ER) lumen. We have previously demonstrated that the IRE-1-XBP-1 branch of the UPR is required to maintain Caenorhabditis elegans ER homeostasis during larval development in the presence of pathogenic Pseudomonas aeruginosa In this study, we identify loss-of-function mutations in four conserved transcriptional regulators that suppress the larval lethality of xbp-1 mutant animals caused by immune activation in response to infection by pathogenic bacteria: FKH-9, a forkhead family transcription factor; ARID-1, an ARID/Bright domain-containing transcription factor; HCF-1, a transcriptional regulator that associates with histone modifying enzymes; and SIN-3, a subunit of a histone deacetylase complex. Further characterization of FKH-9 suggests that loss of FKH-9 enhances resistance to the ER toxin tunicamycin and results in enhanced ER-associated degradation (ERAD). Increased ERAD activity of fkh-9 loss-of-function mutants is accompanied by a diminished capacity to degrade cytosolic proteasomal substrates and a corresponding increased sensitivity to the proteasomal inhibitor bortezomib. Our data underscore how the balance between ER and cytosolic proteostasis can be influenced by compensatory activation of ERAD during the physiological ER stress of infection and immune activation.
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Autochthonous tumors driven by Rb1 loss have an ongoing requirement for the RBP2 histone demethylase. Proc Natl Acad Sci U S A 2018; 115:E3741-E3748. [PMID: 29610306 DOI: 10.1073/pnas.1716029115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inactivation of the retinoblastoma gene (RB1) product, pRB, is common in many human cancers. Targeting downstream effectors of pRB that are central to tumorigenesis is a promising strategy to block the growth of tumors harboring loss-of-function RB1 mutations. One such effector is retinoblastoma-binding protein 2 (RBP2, also called JARID1A or KDM5A), which encodes an H3K4 demethylase. Binding of pRB to RBP2 has been linked to the ability of pRB to promote senescence and differentiation. Importantly, genetic ablation of RBP2 is sufficient to phenocopy pRB's ability to induce these cellular changes in cell culture experiments. Moreover, germline Rbp2 deletion significantly impedes tumorigenesis in Rb1+/- mice. The value of RBP2 as a therapeutic target in cancer, however, hinges on whether loss of RBP2 could block the growth of established tumors as opposed to simply delaying their onset. Here we show that conditional, systemic ablation of RBP2 in tumor-bearing Rb1+/- mice is sufficient to slow tumor growth and significantly extend survival without causing obvious toxicity to the host. These findings show that established Rb1-null tumors require RBP2 for growth and further credential RBP2 as a therapeutic target in human cancers driven by RB1 inactivation.
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Pleiotropic Functions of the Chromodomain-Containing Protein Hat-trick During Oogenesis in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2018; 8:1067-1077. [PMID: 29367451 PMCID: PMC5844294 DOI: 10.1534/g3.117.300526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chromatin-remodeling proteins have a profound role in the transcriptional regulation of gene expression during development. Here, we have shown that the chromodomain-containing protein Hat-trick is predominantly expressed within the oocyte nucleus, specifically within the heterochromatinized karyosome, and that a mild expression is observed in follicle cells. Colocalization of Hat-trick with Heterochromatin Protein 1 and synaptonemal complex component C(3)G along with the diffused karyosome after hat-trick downregulation shows the role of this protein in heterochromatin clustering and karyosome maintenance. Germline mosaic analysis reveals that hat-trick is required for maintaining the dorso-ventral patterning of eggs by regulating the expression of Gurken. The increased incidence of double-strand breaks (DSBs), delayed DSB repair, defects in karyosome formation, altered Vasa mobility, and, consequently, misexpression and altered localization of Gurken in hat-trick mutant egg chambers clearly suggest a putative involvement of Hat-trick in the early stages of oogenesis. In addition, based on phenotypic observations in hat-trick mutant egg chambers, we speculate a substantial role of hat-trick in cystoblast proliferation, oocyte determination, nurse cell endoreplication, germ cell positioning, cyst encapsulation, and nurse cell migration. Our results demonstrate that hat-trick has profound pleiotropic functions during oogenesis in Drosophila melanogaster.
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Lei M, Feng Y, Zhou M, Yang Y, Loppnau P, Li Y, Yang Y, Liu Y. Crystal structure of chromo barrel domain of RBBP1. Biochem Biophys Res Commun 2018; 496:1344-1348. [DOI: 10.1016/j.bbrc.2018.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 02/02/2018] [Indexed: 01/28/2023]
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Dai B, Huang H, Guan F, Zhu G, Xiao Z, Mao B, Su H, Hu Z. Histone demethylase KDM5A inhibits glioma cells migration and invasion by down regulating ZEB1. Biomed Pharmacother 2018; 99:72-80. [PMID: 29324315 DOI: 10.1016/j.biopha.2018.01.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 01/01/2018] [Accepted: 01/03/2018] [Indexed: 01/16/2023] Open
Abstract
Malignant gliomas are highly lethal cancers worldwide as tumor cells infiltrate to healthy brain tissue invariably. Histone demethylase KDM5A as an oncogene or tumor suppressor in cancer still has been controversial. KDM5A may have a different function in different type cancer cells. However, the specific roles of KDM5A in the progression of glioma remain undiscovered. In this study, we found that compared with primary glioma, metastasis glioma had low KDM5A levels. Besides, lower KDM5A levels were linked to poor survival in glioma cancer patients, indicating that KDM5A is a new prognostic marker for glioma cancer. KDM5A knockdown increases the invasive abilities of glioma cancer cells and changes the EMT markers. A mechanism, KDM5A suppressing the expression of ZEB1, and its catalytic activity is indispensable for anti-invasive function. Our study revealed that histone demethylase KDM5A exerts anti-invasiveness function partly through repressing oncogenic ZEB1 expression by mediating H3K4 demethylation. We also demonstrate that ZEB1 play a crucial role in KDM5A induced function. In summary, in this study, we showed that KDM5A has a crucial role in glioma and therefore may serve as a novel therapeutic target and prognostic marker in glioma.
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Affiliation(s)
- Bin Dai
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Hui Huang
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Feng Guan
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Guangtong Zhu
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Zhiyong Xiao
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Beibei Mao
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Haiyang Su
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China
| | - Zhiqiang Hu
- Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Rd., Yangfangdian, Haidian District, Beijing 100038, PR China.
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Choi HJ, Joo HS, Won HY, Min KW, Kim HY, Son T, Oh YH, Lee JY, Kong G. Role of RBP2-Induced ER and IGF1R-ErbB Signaling in Tamoxifen Resistance in Breast Cancer. J Natl Cancer Inst 2017; 110:4443110. [DOI: 10.1093/jnci/djx207] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/30/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
- Hee-Joo Choi
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Hyeong-Seok Joo
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Hee-Young Won
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Kyueng-Whan Min
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Hyung-Yong Kim
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Taekwon Son
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Young-Ha Oh
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Jeong-Yeon Lee
- Institute for Bioengineering and Biopharmaceutical Research (IBBR), Hanyang University, Seoul, Republic of Korea
| | - Gu Kong
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Republic of Korea
- Institute for Bioengineering and Biopharmaceutical Research (IBBR), Hanyang University, Seoul, Republic of Korea
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Harmeyer KM, Facompre ND, Herlyn M, Basu D. JARID1 Histone Demethylases: Emerging Targets in Cancer. Trends Cancer 2017; 3:713-725. [PMID: 28958389 DOI: 10.1016/j.trecan.2017.08.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 01/04/2023]
Abstract
JARID1 proteins are histone demethylases that both regulate normal cell fates during development and contribute to the epigenetic plasticity that underlies malignant transformation. This H3K4 demethylase family participates in multiple repressive transcriptional complexes at promoters and has broader regulatory effects on chromatin that remain ill-defined. There is growing understanding of the oncogenic and tumor suppressive functions of JARID1 proteins, which are contingent on cell context and the protein isoform. Their contributions to stem cell-like dedifferentiation, tumor aggressiveness, and therapy resistance in cancer have sustained interest in the development of JARID1 inhibitors. Here we review the diverse and context-specific functions of the JARID1 proteins that may impact the utilization of emerging targeted inhibitors of this histone demethylase family in cancer therapy.
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Affiliation(s)
- Kayla M Harmeyer
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicole D Facompre
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Devraj Basu
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104, USA; The Wistar Institute, Philadelphia, PA 19104, USA; Philadelphia VA Medical Center, Philadelphia, PA 19104, USA.
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44
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Lopez CK, Malinge S, Gaudry M, Bernard OA, Mercher T. Pediatric Acute Megakaryoblastic Leukemia: Multitasking Fusion Proteins and Oncogenic Cooperations. Trends Cancer 2017; 3:631-642. [PMID: 28867167 DOI: 10.1016/j.trecan.2017.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/10/2017] [Accepted: 07/17/2017] [Indexed: 02/06/2023]
Abstract
Pediatric leukemia presents specific clinical and genetic features from adult leukemia but the underpinning mechanisms of transformation are still unclear. Acute megakaryoblastic leukemia (AMKL) is the malignant accumulation of progenitors of the megakaryocyte lineage that normally produce blood platelets. AMKL is diagnosed de novo, in patients showing a poor prognosis, or in Down syndrome (DS) patients with a better prognosis. Recent data show that de novo AMKL is primarily associated with chromosomal alterations leading to the expression of fusions between transcriptional regulators. This review highlights the most recurrent genetic events found in de novo pediatric AMKL patients and, based on recent functional analyses, proposes a mechanism of leukemogenesis common to de novo and DS-AMKL.
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MESH Headings
- Age Factors
- Animals
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- Cell Differentiation/genetics
- Cell Lineage/genetics
- Child
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Megakaryoblastic, Acute/drug therapy
- Leukemia, Megakaryoblastic, Acute/etiology
- Leukemia, Megakaryoblastic, Acute/metabolism
- Leukemia, Megakaryoblastic, Acute/pathology
- Megakaryocytes/metabolism
- Megakaryocytes/pathology
- Molecular Targeted Therapy
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Signal Transduction
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Affiliation(s)
- Cécile K Lopez
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France; Université Paris-Sud, 91405 Orsay, France
| | - Sébastien Malinge
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France; Université Paris Diderot, 75013 Paris, France
| | - Muriel Gaudry
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France; Université Paris-Sud, 91405 Orsay, France
| | - Olivier A Bernard
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France; Université Paris-Sud, 91405 Orsay, France
| | - Thomas Mercher
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France; Université Paris-Sud, 91405 Orsay, France; Université Paris Diderot, 75013 Paris, France.
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45
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Feng T, Wang Y, Lang Y, Zhang Y. KDM5A promotes proliferation and EMT in ovarian cancer and closely correlates with PTX resistance. Mol Med Rep 2017; 16:3573-3580. [PMID: 28714030 DOI: 10.3892/mmr.2017.6960] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 04/27/2017] [Indexed: 11/06/2022] Open
Abstract
The authors initially performed reverse transcription‑quantitative polymerase chain reaction to determine the expression profile of KDM5A in ovarian cancer tissues and adjacent normal tissue. Compared with adjacent normal tissue, it was identified that KDM5A was highly expressed in ovarian cancer tissues. Moreover, human ovarian cell lines also confirmed that KDM5A was highly expressed in ovarian cancer. KDM5A was especially highly expressed in SKOV3/paclitaxel (PTX) cells, which are resistant to PTX. Previous studies demonstrated that chemoresistance in cancer cells facilitates epithelial‑to‑mesenchymal transition (EMT). Following this, whether KDM5A influenced EMT and metastasis was investigated. The expression of KDM5A and N‑cadherin were obviously higher in SKOV3/PTX cells than in SKOV3 cells. The expression of E‑cadherin was decreased and the expression of N‑cadherin was increased following ectopic expression of KDM5A, while the expression of E‑cadherin was increased and the expression of N‑cadherin was decreased following KDM5A depletion. Transwell and wound healing assays were used to explore the function of KMD5A in metastasis. The present results indicated that KDM5A facilitated EMT and metastasis in ovarian cells. Moreover, it was identified that P‑glycoprotein was increased while KDM5A was expressed ectopically in SKOV3 cells. Following fluorescence‑activated cell sorting flow cytometry analysis and CCK‑8 assay all revealed that KDM5A regulated the PTX sensitivity in SKOV3 and SKOV3/PTX cells. In brief, KDM5A is a crucial oncogene that is significantly upregulated in ovarian cancer. Its expression is closely correlated with cancer cell proliferation, EMT and metastasis. KDM5A suppresses ovarian cancer cell apoptosis under PTX treatment.
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Affiliation(s)
- Tongfu Feng
- Center of Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yan Wang
- Department of Gynecology, Hubei Maternal and Children's Hospital, Wuhan, Hubei 430070, P.R. China
| | - Yan Lang
- Department of Gynecology, Hubei Maternal and Children's Hospital, Wuhan, Hubei 430070, P.R. China
| | - Yuanzhen Zhang
- Center of Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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Abstract
![]()
Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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Maggi EC, Crabtree JS. Novel targets in the treatment of neuroendocrine tumors: RBP2. INTERNATIONAL JOURNAL OF ENDOCRINE ONCOLOGY 2017. [DOI: 10.2217/ije-2016-0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Retinoblastoma binding protein 2, also known as RBP2, JARID1A or KDM5A, is an H3K4 demethylase implicated in a variety of non-neuroendocrine, and more recently, neuroendocrine tumors (NETs). NETs are tumors that form from neuroendocrine cells in tissues of the GI tract, endocrine pancreas, lung, skin and other tissues. RBP2 is expressed at abnormally high levels in NETs and recent work demonstrates that modulation of RBP2 in vitro and in vivo impacts end points of tumorigenesis. Interestingly, the demethylase activity of RBP2 is not exclusively responsible for these changes, as RBP2's binding partners may mediate its activity in a tissue- or context-dependent manner. Here, we discuss the features of RBP2 and its role in cell cycle regulation, angiogenesis and drug resistance in cancer.
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Affiliation(s)
- Elaine C Maggi
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Judy S Crabtree
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, USA
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48
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Wei L, Zhao X. Roles of SUMO in Replication Initiation, Progression, and Termination. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:371-393. [PMID: 29357067 PMCID: PMC6643980 DOI: 10.1007/978-981-10-6955-0_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Accurate genome duplication during cell division is essential for life. This process is accomplished by the close collaboration between replication factors and many additional proteins that provide assistant roles. Replication factors establish the replication machineries capable of copying billions of nucleotides, while regulatory proteins help to achieve accuracy and efficiency of replication. Among regulatory proteins, protein modification enzymes can bestow fast and reversible changes to many targets, leading to coordinated effects on replication. Recent studies have begun to elucidate how one type of protein modification, sumoylation, can modify replication proteins and regulate genome duplication through multiple mechanisms. This chapter summarizes these new findings, and how they can integrate with the known regulatory circuitries of replication. As this area of research is still at its infancy, many outstanding questions remain to be explored, and we discuss these issues in light of the new advances.
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Affiliation(s)
- Lei Wei
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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49
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Aiello KA, Alter O. Platform-Independent Genome-Wide Pattern of DNA Copy-Number Alterations Predicting Astrocytoma Survival and Response to Treatment Revealed by the GSVD Formulated as a Comparative Spectral Decomposition. PLoS One 2016; 11:e0164546. [PMID: 27798635 PMCID: PMC5087864 DOI: 10.1371/journal.pone.0164546] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/27/2016] [Indexed: 01/07/2023] Open
Abstract
We use the generalized singular value decomposition (GSVD), formulated as a comparative spectral decomposition, to model patient-matched grades III and II, i.e., lower-grade astrocytoma (LGA) brain tumor and normal DNA copy-number profiles. A genome-wide tumor-exclusive pattern of DNA copy-number alterations (CNAs) is revealed, encompassed in that previously uncovered in glioblastoma (GBM), i.e., grade IV astrocytoma, where GBM-specific CNAs encode for enhanced opportunities for transformation and proliferation via growth and developmental signaling pathways in GBM relative to LGA. The GSVD separates the LGA pattern from other sources of biological and experimental variation, common to both, or exclusive to one of the tumor and normal datasets. We find, first, and computationally validate, that the LGA pattern is correlated with a patient's survival and response to treatment. Second, the GBM pattern identifies among the LGA patients a subtype, statistically indistinguishable from that among the GBM patients, where the CNA genotype is correlated with an approximately one-year survival phenotype. Third, cross-platform classification of the Affymetrix-measured LGA and GBM profiles by using the Agilent-derived GBM pattern shows that the GBM pattern is a platform-independent predictor of astrocytoma outcome. Statistically, the pattern is a better predictor (corresponding to greater median survival time difference, proportional hazard ratio, and concordance index) than the patient's age and the tumor's grade, which are the best indicators of astrocytoma currently in clinical use, and laboratory tests. The pattern is also statistically independent of these indicators, and, combined with either one, is an even better predictor of astrocytoma outcome. Recurring DNA CNAs have been observed in astrocytoma tumors' genomes for decades, however, copy-number subtypes that are predictive of patients' outcomes were not identified before. This is despite the growing number of datasets recording different aspects of the disease, and due to an existing fundamental need for mathematical frameworks that can simultaneously find similarities and dissimilarities across the datasets. This illustrates the ability of comparative spectral decompositions to find what other methods miss.
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Affiliation(s)
- Katherine A. Aiello
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah, Salt Lake City, Utah, United States of America
| | - Orly Alter
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah, Salt Lake City, Utah, United States of America
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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Zhang J, Loyd MR, Randall MS, Morris JJ, Shah JG, Ney PA. Repression by RB1 characterizes genes involved in the penultimate stage of erythroid development. Cell Cycle 2016; 14:3441-53. [PMID: 26397180 DOI: 10.1080/15384101.2015.1090067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Retinoblastoma-1 (RB1), and the RB1-related proteins p107 and p130, are key regulators of the cell cycle. Although RB1 is required for normal erythroid development in vitro, it is largely dispensable for erythropoiesis in vivo. The modest phenotype caused by RB1 deficiency in mice raises questions about redundancy within the RB1 family, and the role of RB1 in erythroid differentiation. Here we show that RB1 is the major pocket protein that regulates terminal erythroid differentiation. Erythroid cells lacking all pocket proteins exhibit the same cell cycle defects as those deficient for RB1 alone. RB1 has broad repressive effects on gene transcription in erythroid cells. As a group, RB1-repressed genes are generally well expressed but downregulated at the final stage of erythroid development. Repression correlates with E2F binding, implicating E2Fs in the recruitment of RB1 to repressed genes. Merging differential and time-dependent changes in expression, we define a group of approximately 800 RB1-repressed genes. Bioinformatics analysis shows that this list is enriched for terms related to the cell cycle, but also for terms related to terminal differentiation. Some of these have not been previously linked to RB1. These results expand the range of processes potentially regulated by RB1, and suggest that a principal role of RB1 in development is coordinating the events required for terminal differentiation.
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Affiliation(s)
- Ji Zhang
- a Department of Biochemistry ; St. Jude Children's Research Hospital ; Memphis , TN USA.,b Current address: Cancer Biology & Genetics; Memorial Sloan-Kettering Cancer Center ; New York , NY USA
| | - Melanie R Loyd
- a Department of Biochemistry ; St. Jude Children's Research Hospital ; Memphis , TN USA.,c Hartwell Center for Bioinformatics and Biotechnology; St. Jude Children's Research Hospital ; Memphis , TN USA
| | - Mindy S Randall
- a Department of Biochemistry ; St. Jude Children's Research Hospital ; Memphis , TN USA
| | - John J Morris
- c Hartwell Center for Bioinformatics and Biotechnology; St. Jude Children's Research Hospital ; Memphis , TN USA
| | - Jayesh G Shah
- d Cell & Molecular Biology; Lindsley F. Kimball Research Institute; New York Blood Center ; New York , NY USA
| | - Paul A Ney
- a Department of Biochemistry ; St. Jude Children's Research Hospital ; Memphis , TN USA.,d Cell & Molecular Biology; Lindsley F. Kimball Research Institute; New York Blood Center ; New York , NY USA.,e Current address: 1735 York Ave., New York , NY USA
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