1
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McCallum-Loudeac J, Moody E, Williams J, Johnstone G, Sircombe KJ, Clarkson AN, Wilson MJ. Deletion of a conserved genomic region associated with adolescent idiopathic scoliosis leads to vertebral rotation in mice. Hum Mol Genet 2024; 33:787-801. [PMID: 38280229 PMCID: PMC11031364 DOI: 10.1093/hmg/ddae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/15/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is the most common form of scoliosis, in which spinal curvature develops in adolescence, and 90% of patients are female. Scoliosis is a debilitating disease that often requires bracing or surgery in severe cases. AIS affects 2%-5.2% of the population; however, the biological origin of the disease remains poorly understood. In this study, we aimed to determine the function of a highly conserved genomic region previously linked to AIS using a mouse model generated by CRISPR-CAS9 gene editing to knockout this area of the genome to understand better its contribution to AIS, which we named AIS_CRMΔ. We also investigated the upstream factors that regulate the activity of this enhancer in vivo, whether the spatial expression of the LBX1 protein would change with the loss of AIS-CRM function, and whether any phenotype would arise after deletion of this region. We found a significant increase in mRNA expression in the developing neural tube at E10.5, and E12.5, for not only Lbx1 but also other neighboring genes. Adult knockout mice showed vertebral rotation and proprioceptive deficits, also observed in human AIS patients. In conclusion, our study sheds light on the elusive biological origins of AIS, by targeting and investigating a highly conserved genomic region linked to AIS in humans. These findings provide valuable insights into the function of the investigated region and contribute to our understanding of the underlying causes of this debilitating disease.
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Affiliation(s)
- Jeremy McCallum-Loudeac
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Edward Moody
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Jack Williams
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Georgia Johnstone
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Kathleen J Sircombe
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Andrew N Clarkson
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Megan J Wilson
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
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2
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Csergeová L, Krbušek D, Janoštiak R. CIP/KIP and INK4 families as hostages of oncogenic signaling. Cell Div 2024; 19:11. [PMID: 38561743 PMCID: PMC10985988 DOI: 10.1186/s13008-024-00115-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
CIP/KIP and INK4 families of Cyclin-dependent kinase inhibitors (CKIs) are well-established cell cycle regulatory proteins whose canonical function is binding to Cyclin-CDK complexes and altering their function. Initial experiments showed that these proteins negatively regulate cell cycle progression and thus are tumor suppressors in the context of molecular oncology. However, expanded research into the functions of these proteins showed that most of them have non-canonical functions, both cell cycle-dependent and independent, and can even act as tumor enhancers depending on their posttranslational modifications, subcellular localization, and cell state context. This review aims to provide an overview of canonical as well as non-canonical functions of CIP/KIP and INK4 families of CKIs, discuss the potential avenues to promote their tumor suppressor functions instead of tumor enhancing ones, and how they could be utilized to design improved treatment regimens for cancer patients.
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Affiliation(s)
- Lucia Csergeová
- BIOCEV-First Faculty of Medicine, Charles University, Prague, Czechia
| | - David Krbušek
- BIOCEV-First Faculty of Medicine, Charles University, Prague, Czechia
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3
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Li M, Liu D, Xue F, Zhang H, Yang Q, Sun L, Qu X, Wu X, Zhao H, Liu J, Kang Q, Wang T, An X, Chen L. Stage-specific dual function: EZH2 regulates human erythropoiesis by eliciting histone and non-histone methylation. Haematologica 2023; 108:2487-2502. [PMID: 37021526 PMCID: PMC10483364 DOI: 10.3324/haematol.2022.282016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/28/2023] [Indexed: 04/07/2023] Open
Abstract
Enhancer of zeste homolog 2 (EZH2) is the lysine methyltransferase of polycomb repressive complex 2 (PRC2) that catalyzes H3K27 tri-methylation. Aberrant expression and loss-of-function mutations of EZH2 have been demonstrated to be tightly associated with the pathogenesis of various myeloid malignancies characterized by ineffective erythropoiesis, such as myelodysplastic syndrome (MDS). However, the function and mechanism of EZH2 in human erythropoiesis still remains largely unknown. Here, we demonstrated that EZH2 regulates human erythropoiesis in a stage-specific, dual-function manner by catalyzing histone and non-histone methylation. During the early erythropoiesis, EZH2 deficiency caused cell cycle arrest in the G1 phase, which impaired cell growth and differentiation. Chromatin immunoprecipitation sequencing and RNA sequencing discovered that EZH2 knockdown caused a reduction of H3K27me3 and upregulation of cell cycle proteindependent kinase inhibitors. In contrast, EZH2 deficiency led to the generation of abnormal nuclear cells and impaired enucleation during the terminal erythropoiesis. Interestingly, EZH2 deficiency downregulated the methylation of HSP70 by directly interacting with HSP70. RNA-sequencing analysis revealed that the expression of AURKB was significantly downregulated in response to EZH2 deficiency. Furthermore, treatment with an AURKB inhibitor and small hairpin RNAmediated AURKB knockdown also led to nuclear malformation and decreased enucleation efficiency. These findings strongly suggest that EZH2 regulates terminal erythropoiesis through a HSP70 methylation-AURKB axis. Our findings have implications for improved understanding of ineffective erythropoiesis with EZH2 dysfunction.
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Affiliation(s)
- Mengjia Li
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, China 450001
| | - Donghao Liu
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, China 450001
| | - Fumin Xue
- Department of Gastroenterology, Children's Hospital affiliated to Zhengzhou University, Zhengzhou, China 450000
| | - Hengchao Zhang
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, China 450001
| | - Qianqian Yang
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, China 450001
| | - Lei Sun
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, China 450001
| | - Xiaoli Qu
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, China 450001
| | - Xiuyun Wu
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, China 450001
| | - Huizhi Zhao
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, China 450001
| | - Jing Liu
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China 410078
| | - Qiaozhen Kang
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, China 450001
| | - Ting Wang
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, China 450001
| | - Xiuli An
- Laboratory of Membrane Biology, New York Blood Center, 310 East, 67th Street, New York, NY 10065.
| | - Lixiang Chen
- School of Life Sciences, Zhengzhou University, Science Road 100, Zhengzhou, China 450001.
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4
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Farooq U, Notani D. Transcriptional regulation of INK4/ARF locus by cis and trans mechanisms. Front Cell Dev Biol 2022; 10:948351. [PMID: 36158211 PMCID: PMC9500187 DOI: 10.3389/fcell.2022.948351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/09/2022] [Indexed: 12/12/2022] Open
Abstract
9p21 locus is one of the most reproducible regions in genome-wide association studies (GWAS). The region harbors CDKN2A/B genes that code for p16INK4a, p15INK4b, and p14ARF proteins, and it also harbors a long gene desert adjacent to these genes. The polymorphisms that are associated with several diseases and cancers are present in these genes and the gene desert region. These proteins are critical cell cycle regulators whose transcriptional dysregulation is strongly linked with cellular regeneration, stemness, aging, and cancers. Given the importance of this locus, intense scientific efforts on understanding the regulation of these genes via promoter-driven mechanisms and recently, via the distal regulatory mechanism have provided major insights. In this review, we describe these mechanisms and propose the ways by which this locus can be targeted in pathologies and aging.
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Affiliation(s)
- Umer Farooq
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
- The University of Trans-Disciplinary Health Sciences and Technology, Bangalore, India
- *Correspondence: Umer Farooq, ; Dimple Notani,
| | - Dimple Notani
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
- *Correspondence: Umer Farooq, ; Dimple Notani,
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5
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Lu S, Ding X, Wang Y, Hu X, Sun T, Wei M, Wang X, Wu H. The Relationship Between the Network of Non-coding RNAs-Molecular Targets and N6-Methyladenosine Modification in Colorectal Cancer. Front Cell Dev Biol 2021; 9:772542. [PMID: 34938735 PMCID: PMC8685436 DOI: 10.3389/fcell.2021.772542] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/11/2021] [Indexed: 12/11/2022] Open
Abstract
Recent accumulating researches implicate that non-coding RNAs (ncRNAs) including microRNA (miRNA), circular RNA (circRNA), and long non-coding RNA (lncRNAs) play crucial roles in colorectal cancer (CRC) initiation and development. Notably, N6-methyladenosine (m6A) methylation, the critical posttranscriptional modulators, exerts various functions in ncRNA metabolism such as stability and degradation. However, the interaction regulation network among ncRNAs and the interplay with m6A-related regulators has not been well documented, particularly in CRC. Here, we summarize the interaction networks and sub-networks of ncRNAs in CRC based on a data-driven approach from the publications (IF > 6) in the last quinquennium (2016–2021). Further, we extend the regulatory pattern between the core m6A regulators and m6A-related ncRNAs in the context of CRC metastasis and progression. Thus, our review will highlight the clinical potential of ncRNAs and m6A modifiers as promising biomarkers and therapeutic targets for improving the diagnostic precision and treatment of CRC.
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Affiliation(s)
- Senxu Lu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Xiangyu Ding
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Yuanhe Wang
- Department of Medical Oncology, Cancer Hospital of China Medical University, Shenyang, China
| | - Xiaoyun Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Tong Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China.,Shenyang Kangwei Medical Laboratory Analysis Co. Ltd., Liaoning, China
| | - Xiaobin Wang
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Huizhe Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
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6
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Kim J, Bordiya Y, Kathare PK, Zhao B, Zong W, Huq E, Sung S. Phytochrome B triggers light-dependent chromatin remodelling through the PRC2-associated PHD finger protein VIL1. NATURE PLANTS 2021; 7:1213-1219. [PMID: 34354260 PMCID: PMC8448934 DOI: 10.1038/s41477-021-00986-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 07/12/2021] [Indexed: 05/16/2023]
Abstract
To compensate for a sessile nature, plants have developed sophisticated mechanisms to sense varying environmental conditions. Phytochromes (phys) are light and temperature sensors that regulate downstream genes to render plants responsive to environmental stimuli1-4. Here, we show that phyB directly triggers the formation of a repressive chromatin loop by physically interacting with VERNALIZATION INSENSITIVE 3-LIKE1/VERNALIZATION 5 (VIL1/VRN5), a component of Polycomb Repressive Complex 2 (PRC2)5,6, in a light-dependent manner. VIL1 and phyB cooperatively contribute to the repression of growth-promoting genes through the enrichment of Histone H3 Lys27 trimethylation (H3K27me3), a repressive histone modification. In addition, phyB and VIL1 mediate the formation of a chromatin loop to facilitate the repression of ATHB2. Our findings show that phyB directly utilizes chromatin remodelling to regulate the expression of target genes in a light-dependent manner.
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Affiliation(s)
- Junghyun Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Yogendra Bordiya
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Praveen Kumar Kathare
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Bo Zhao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Wei Zong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Enamul Huq
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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7
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Erkek S, Johann PD, Finetti MA, Drosos Y, Chou HC, Zapatka M, Sturm D, Jones DTW, Korshunov A, Rhyzova M, Wolf S, Mallm JP, Beck K, Witt O, Kulozik AE, Frühwald MC, Northcott PA, Korbel JO, Lichter P, Eils R, Gajjar A, Roberts CWM, Williamson D, Hasselblatt M, Chavez L, Pfister SM, Kool M. Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation. Cancer Cell 2019; 35:95-110.e8. [PMID: 30595504 PMCID: PMC6341227 DOI: 10.1016/j.ccell.2018.11.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 05/30/2018] [Accepted: 11/21/2018] [Indexed: 12/27/2022]
Abstract
Biallelic inactivation of SMARCB1, encoding a member of the SWI/SNF chromatin remodeling complex, is the hallmark genetic aberration of atypical teratoid rhabdoid tumors (ATRT). Here, we report how loss of SMARCB1 affects the epigenome in these tumors. Using chromatin immunoprecipitation sequencing (ChIP-seq) on primary tumors for a series of active and repressive histone marks, we identified the chromatin states differentially represented in ATRTs compared with other brain tumors and non-neoplastic brain. Re-expression of SMARCB1 in ATRT cell lines enabled confirmation of our genome-wide findings for the chromatin states. Additional generation of ChIP-seq data for SWI/SNF and Polycomb group proteins and the transcriptional repressor protein REST determined differential dependencies of SWI/SNF and Polycomb complexes in regulation of diverse gene sets in ATRTs.
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Affiliation(s)
- Serap Erkek
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany; Izmir Biomedicine and Genome Center, 35340 Izmir, Turkey
| | - Pascal D Johann
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Martina A Finetti
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, NE2 Newcastle Upon Tyne, UK
| | - Yiannis Drosos
- Department of Oncology, St Jude Children's Research Hospital, 38105 Memphis, USA
| | - Hsien-Chao Chou
- Department of Oncology, St Jude Children's Research Hospital, 38105 Memphis, USA
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Dominik Sturm
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - David T W Jones
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marina Rhyzova
- Department of Neuropathology, Burdenko Neurosurgical Institute, 125047 Moscow, Russia
| | - Stephan Wolf
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jan-Philipp Mallm
- Genome Organization & Function Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, 69120 Heidelberg, Germany
| | - Katja Beck
- Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, 69120 Heidelberg, Germany
| | - Olaf Witt
- Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Michael C Frühwald
- University Children's Hospital Augsburg, Swabian Children's Cancer Center, 86156 Augsburg, Germany; EU-RHAB Registry Center, 86156 Augsburg, Germany
| | - Paul A Northcott
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 38105 Memphis, TN, USA
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, 69120 Heidelberg, Germany
| | - Roland Eils
- Genome Organization & Function Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Amar Gajjar
- Department of Oncology, St Jude Children's Research Hospital, 38105 Memphis, USA
| | - Charles W M Roberts
- Department of Oncology, St Jude Children's Research Hospital, 38105 Memphis, USA
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, NE2 Newcastle Upon Tyne, UK
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, 48149 Münster, Germany
| | - Lukas Chavez
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Stefan M Pfister
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Marcel Kool
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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8
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Jiang S, Zhou H, Liang J, Gerdt C, Wang C, Ke L, Schmidt SCS, Narita Y, Ma Y, Wang S, Colson T, Gewurz B, Li G, Kieff E, Zhao B. The Epstein-Barr Virus Regulome in Lymphoblastoid Cells. Cell Host Microbe 2018; 22:561-573.e4. [PMID: 29024646 DOI: 10.1016/j.chom.2017.09.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/21/2017] [Accepted: 08/30/2017] [Indexed: 01/01/2023]
Abstract
Epstein-Barr virus (EBV) transforms B cells to continuously proliferating lymphoblastoid cell lines (LCLs), which represent an experimental model for EBV-associated cancers. EBV nuclear antigens (EBNAs) and LMP1 are EBV transcriptional regulators that are essential for LCL establishment, proliferation, and survival. Starting with the 3D genome organization map of LCL, we constructed a comprehensive EBV regulome encompassing 1,992 viral/cellular genes and enhancers. Approximately 30% of genes essential for LCL growth were linked to EBV enhancers. Deleting EBNA2 sites significantly reduced their target gene expression. Additional EBV super-enhancer (ESE) targets included MCL1, IRF4, and EBF. MYC ESE looping to the transcriptional stat site of MYC was dependent on EBNAs. Deleting MYC ESEs greatly reduced MYC expression and LCL growth. EBNA3A/3C altered CDKN2A/B spatial organization to suppress senescence. EZH2 inhibition decreased the looping at the CDKN2A/B loci and reduced LCL growth. This study provides a comprehensive view of the spatial organization of chromatin during EBV-driven cellular transformation.
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Affiliation(s)
- Sizun Jiang
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Hufeng Zhou
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Liang
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Catherine Gerdt
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Chong Wang
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Liangru Ke
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Nasopharyngeal Carcinoma, Sun Yat-Sen Cancer Center, Sun Yat-Sen University, Guangzhou 510060, China
| | - Stefanie C S Schmidt
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Yohei Narita
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Yijie Ma
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Shuangqi Wang
- National Key Laboratory of Crop Genetic Improvement, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Tyler Colson
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin Gewurz
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Elliott Kieff
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Bo Zhao
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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9
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Herviou L, Cavalli G, Moreaux J. [EZH2 is therapeutic target for personalized treatment in multiple myeloma]. Bull Cancer 2018; 105:804-819. [PMID: 30041976 DOI: 10.1016/j.bulcan.2018.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 12/30/2022]
Abstract
Enhancer of zeste homolog 2 (EZH2) is a histone methyltransferase that functions as the catalytic subunit of the polycomb repressive complex 2 (PRC2). PRC2 represses gene transcription through tri-methylation of lysine 27 of histone 3 (H3K27me3) by its catalytic subunit EZH2. EZH2 is also involved in normal B cell differentiation. EZH2 deregulation has been described in many cancer types including hematological malignancies. The oncogenic addiction of tumor cells to EZH2 represents a therapeutic target in several hematological malignancies and solid cancers. Specific small molecules have been recently developed to target cancer cells with EZH2 overexpression or activating mutation. Their therapeutic potential is currently under evaluation. In particular, EZH2 is overexpressed in multiple myeloma (MM), a neoplasia characterized by the accumulation of clonal plasma cells within the bone marrow, with biological functions in the pathophysiology. This review summarizes the roles of EZH2 in B cell differentiation and pathologic hematological processes with a particular focus in multiple myeloma. We also discuss recent advances in the development of EZH2 inhibitors for the personalized treatment of patients with hematological malignancies.
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Affiliation(s)
- Laurie Herviou
- IGH, CNRS, université Montpellier, 141, rue de la Cardonille, 34090 Montpellier, France
| | - Giacomo Cavalli
- IGH, CNRS, université Montpellier, 141, rue de la Cardonille, 34090 Montpellier, France
| | - Jerome Moreaux
- IGH, CNRS, université Montpellier, 141, rue de la Cardonille, 34090 Montpellier, France; CHU de Montpellier, department of biological hematology, 80, avenue Augustin-Fliche, 34090 Montpellier, France; Université Montpellier, UFR de médecine, 2, rue École de Médecine, CS 59001, 34060 Montpellier cedex 2, France.
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10
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Chen G, Subedi K, Chakraborty S, Sharov A, Lu J, Kim J, Mi X, Wersto R, Sung MH, Weng NP. Ezh2 Regulates Activation-Induced CD8 + T Cell Cycle Progression via Repressing Cdkn2a and Cdkn1c Expression. Front Immunol 2018; 9:549. [PMID: 29632530 PMCID: PMC5879148 DOI: 10.3389/fimmu.2018.00549] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/05/2018] [Indexed: 12/22/2022] Open
Abstract
Transition from resting to cell cycle in response to antigenic stimulation is an essential step for naïve CD8+ T cells to differentiate to effector and memory cells. Leaving the resting state requires dramatic changes of chromatin status in the key cell cycle inhibitors but the details of these concerted events are not fully elucidated. Here, we showed that Ezh2, an enzymatic component of polycomb repressive complex 2 (PRC2) catalyzing the trimethylation of lysine 27 on histone 3 (H3K27me3), regulates activation induced naïve CD8+ T cells proliferation and apoptosis. Upon deletion of Ezh2 during thymocyte development (Ezh2fl/flCd4Cre+ mice), naive CD8+ T cells displayed impaired proliferation and increased apoptosis in response to antigen stimulation. However, naive CD8+ T cells only had impaired proliferation but no increase in apoptosis when Ezh2 was deleted after activation (Ezh2fl/flGzmBCre+ mice), suggesting cell cycle and apoptosis are temporally separable events controlled by Ezh2. We then showed that deletion of Ezh2 resulted in the increase in expression of cyclin-dependent kinase inhibitors Cdkn2a (p16 and Arf) and Cdkn1c (p57) in activated naïve CD8+ T cells as the consequence of reduced levels of H3K27me3 at these two gene loci. Finally, with real time imaging, we observed prolonged cell division times of naïve CD8+ T cells in the absence of Ezh2 post in vitro stimulation. Together, these findings reveal that repression of Cdkn1c and Cdkn2a by Ezh2 plays a critical role in execution of activation-induced CD8+ T cell proliferation.
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Affiliation(s)
- Guobing Chen
- Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging (NIH), Baltimore, MD, United States
| | - Kalpana Subedi
- Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging (NIH), Baltimore, MD, United States
| | - Sayantan Chakraborty
- Transcription Systems Dynamics and Biology Unit, Laboratory of Molecular Biology and Immunology, National Institute on Aging (NIH), Baltimore, MD, United States
| | - Alexie Sharov
- Laboratory of Genetics and Genomics, National Institute on Aging (NIH), Baltimore, MD, United States
| | - Jian Lu
- Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging (NIH), Baltimore, MD, United States
| | - Jaekwan Kim
- Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging (NIH), Baltimore, MD, United States
| | - Xiaofan Mi
- Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging (NIH), Baltimore, MD, United States
| | - Robert Wersto
- Flow Cytometry Unit, National Institute on Aging (NIH), Baltimore, MD, United States
| | - Myong-Hee Sung
- Transcription Systems Dynamics and Biology Unit, Laboratory of Molecular Biology and Immunology, National Institute on Aging (NIH), Baltimore, MD, United States
| | - Nan-Ping Weng
- Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging (NIH), Baltimore, MD, United States
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11
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12
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Park M, Min B, Jeon K, Cho S, Park JS, Kim J, Jeon J, Song J, Kim S, Jeong S, Seo H, Kang YK. Age-associated chromatin relaxation is enhanced in Huntington's disease mice. Aging (Albany NY) 2017; 9:803-822. [PMID: 28288000 PMCID: PMC5391233 DOI: 10.18632/aging.101193] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 02/26/2017] [Indexed: 12/13/2022]
Abstract
Expansion of polyglutamine stretch in the huntingtin (HTT) protein is a major cause of Huntington's disease (HD). The polyglutamine part in HTT interacts with various proteins implicated in epigenetic regulation of genes, suggesting that mutant HTT may disturb the integrity of the epigenetic system. Here, we used a PCRseq-based method to examine expression profile of 395 exonic segments from 260 “epi-driver” genes in splenic T lymphocytes from aged HD mice. We identified 67 exonic segments differentially expressed between young and aged HD mice, most of them upregulated in the aged. Polycomb-repressive complex (PRC)-regulated genes (PRGs) were markedly upregulated in aged HD mice, consistent with downregulation of PRC genes. Epi-driver gene categories of lysine-methylation, lysine-demethylation, arginine-methylation, and PRG showed differential age-associated changes between HD and control. Analyzing the pattern of change in epi-driver gene expressions hinted at an enhanced shift in HD chromatin to a more accessible state with age, which was experimentally demonstrated by DNase-I-hypersensitivity sequencing showing increased chromatin accessibility in HD cells compared to control. We suggest the global change can potentially relieve chromatin-induced repression of many genes, and the unintended expressions of some detrimental proteins could alter T cell function to a greater degree in aged HD mice.
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Affiliation(s)
- Myungsun Park
- Development and Differentiation Research Center, KRIBB, Yuseong-gu, Daejeon, 305-806, South Korea
| | - Byungkuk Min
- Development and Differentiation Research Center, KRIBB, Yuseong-gu, Daejeon, 305-806, South Korea
| | - Kyuheum Jeon
- Development and Differentiation Research Center, KRIBB, Yuseong-gu, Daejeon, 305-806, South Korea.,Department of Functional Genomics, University of Science and Technology (UST), Yuseong-gu, Daejeon, 305-350, South Korea
| | - Sunwha Cho
- Development and Differentiation Research Center, KRIBB, Yuseong-gu, Daejeon, 305-806, South Korea
| | - Jung Sun Park
- Development and Differentiation Research Center, KRIBB, Yuseong-gu, Daejeon, 305-806, South Korea.,Aging Research Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, South Korea
| | - Jisun Kim
- Department of Molecular and Life Sciences, Hanyang University, Sangnok-gu, Ansan, Gyeonggi-do, 15588, South Korea
| | - Jeha Jeon
- Department of Molecular and Life Sciences, Hanyang University, Sangnok-gu, Ansan, Gyeonggi-do, 15588, South Korea
| | - Jinhoi Song
- Aging Research Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, South Korea
| | - Seokho Kim
- Aging Research Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, South Korea
| | - Sangkyun Jeong
- Mibyeong Research Center, Korea Institute of Oriental Medicine (KIOM), Yuseong-gu, Daejeon, 305-811, South Korea
| | - Hyemyung Seo
- Department of Molecular and Life Sciences, Hanyang University, Sangnok-gu, Ansan, Gyeonggi-do, 15588, South Korea
| | - Yong-Kook Kang
- Development and Differentiation Research Center, KRIBB, Yuseong-gu, Daejeon, 305-806, South Korea.,Aging Research Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, South Korea.,Department of Functional Genomics, University of Science and Technology (UST), Yuseong-gu, Daejeon, 305-350, South Korea
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13
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Connelly KE, Dykhuizen EC. Compositional and functional diversity of canonical PRC1 complexes in mammals. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:233-245. [PMID: 28007606 DOI: 10.1016/j.bbagrm.2016.12.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/12/2016] [Accepted: 12/15/2016] [Indexed: 12/17/2022]
Abstract
The compositional complexity of Polycomb Repressive Complex 1 (PRC1) increased dramatically during vertebrate evolution. What is considered the "canonical" PRC1 complex consists of four subunits originally identified as regulators of body segmentation in Drosophila. In mammals, each of these four canonical subunits consists of two to six paralogs that associate in a combinatorial manner to produce over a hundred possible distinct PRC1 complexes with unknown function. Genetic studies have begun to define the phenotypic roles for different PRC1 paralogs; however, relating these phenotypes to unique biochemical and transcriptional function for the different paralogs has been challenging. In this review, we attempt to address how the compositional diversity of canonical PRC1 complexes relates to unique roles for individual PRC1 paralogs in transcriptional regulation. This review focuses primarily on PRC1 complex composition, genome targeting, and biochemical function.
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Affiliation(s)
- Katelyn E Connelly
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907, USA.
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14
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Lui JC, Garrison P, Nguyen Q, Ad M, Keembiyehetty C, Chen W, Jee YH, Landman E, Nilsson O, Barnes KM, Baron J. EZH1 and EZH2 promote skeletal growth by repressing inhibitors of chondrocyte proliferation and hypertrophy. Nat Commun 2016; 7:13685. [PMID: 27897169 PMCID: PMC5477487 DOI: 10.1038/ncomms13685] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 10/25/2016] [Indexed: 12/16/2022] Open
Abstract
Histone methyltransferases EZH1 and EZH2 catalyse the trimethylation of histone H3 at lysine 27 (H3K27), which serves as an epigenetic signal for chromatin condensation and transcriptional repression. Genome-wide associated studies have implicated EZH2 in the control of height and mutations in EZH2 cause Weaver syndrome, which includes skeletal overgrowth. Here we show that the combined loss of Ezh1 and Ezh2 in chondrocytes severely impairs skeletal growth in mice. Both of the principal processes underlying growth plate chondrogenesis, chondrocyte proliferation and hypertrophy, are compromised. The decrease in chondrocyte proliferation is due in part to derepression of cyclin-dependent kinase inhibitors Ink4a/b, while ineffective chondrocyte hypertrophy is due to the suppression of IGF signalling by the increased expression of IGF-binding proteins. Collectively, our findings reveal a critical role for H3K27 methylation in the regulation of chondrocyte proliferation and hypertrophy in the growth plate, which are the central determinants of skeletal growth.
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Affiliation(s)
- Julian C Lui
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive, MSC-1103, Bethesda, Maryland 20892, USA
| | - Presley Garrison
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive, MSC-1103, Bethesda, Maryland 20892, USA
| | - Quang Nguyen
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive, MSC-1103, Bethesda, Maryland 20892, USA
| | - Michal Ad
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive, MSC-1103, Bethesda, Maryland 20892, USA
| | - Chithra Keembiyehetty
- Genomic Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg8, Room 1A11, 8 Center Drive, Bethesda, Maryland 20892, USA
| | - Weiping Chen
- Genomic Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg8, Room 1A11, 8 Center Drive, Bethesda, Maryland 20892, USA
| | - Youn Hee Jee
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive, MSC-1103, Bethesda, Maryland 20892, USA
| | - Ellie Landman
- Division of Pediatric Endocrinology. Q2:08, Department of Women's and Children's Health, Karolinska Institutet and University Hospital, 171 76 Stockholm, Sweden
| | - Ola Nilsson
- Division of Pediatric Endocrinology. Q2:08, Department of Women's and Children's Health, Karolinska Institutet and University Hospital, 171 76 Stockholm, Sweden.,Department of Medical Sciences, Rm C1213, Örebro University and University Hospital, 701 85 Örebro, Sweden
| | - Kevin M Barnes
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive, MSC-1103, Bethesda, Maryland 20892, USA
| | - Jeffrey Baron
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive, MSC-1103, Bethesda, Maryland 20892, USA
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15
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Sha MQ, Zhao XL, Li L, Li LH, Li Y, Dong TG, Niu WX, Jia LJ, Shao RG, Zhen YS, Wang Z. EZH2 mediates lidamycin-induced cellular senescence through regulating p21 expression in human colon cancer cells. Cell Death Dis 2016; 7:e2486. [PMID: 27882937 PMCID: PMC5260875 DOI: 10.1038/cddis.2016.383] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 10/03/2016] [Accepted: 10/17/2016] [Indexed: 02/07/2023]
Abstract
Lidamycin (LDM) is a novel member of the enediyne antibiotics identified in China with potent antitumor activity. However, it remains unclear whether LDM has potential molecular targets that may affect its antitumor activity. Enhancer of zeste homolog 2 (EZH2) functions as a histone lysine methyltransferase and mediates trimethylation on histone 3 lysine 27 (H3K27me3). High EZH2 level is found to be positively correlated with the aggressiveness, metastasis and poor prognosis of cancer. Here, we aim to study the role of EZH2 in LDM-induced senescence, as well as in the cytotoxicity of LDM in human colon cancer cells. LDM is found to be relatively more potent in inhibiting the colon cancer cells harboring high EZH2 level and induces irreversible cellular senescence at IC50 dose range, as evidenced by senescence-associated β-galactosidase staining, cell cycle arrest and molecular changes of senescence regulators including p21 in HCT116 and SW620 cells. More importantly, LDM is found to markedly inhibit EZH2 expression at both protein and mRNA levels upon the induction of p21 and cellular senescence. LDM also selectively inhibits EZH2 expression as compared with other histone lysine methyltransferases. Knockdown of p21 with siRNAs abolishes LDM-induced senescence, whereas EZH2 knockdown markedly increases p21 expression and causes senescent phenotype. Enrichment of both EZH2 and H3K27me3 levels in the p21 promoter region is reduced by LDM. Moreover, EZH2 overexpression reduces cellular senescence, p21 expression and DNA damage response upon LDM exposure. LDM also demonstrates potent antitumor efficacy in xenografted animal models. Collectively, our work provides first demonstration that EZH2 may mediate, at least partially, the senescence-inducing effects of LDM by regulating p21 expression and DNA damage effect. Thus, EZH2 may serve as a potential target and biomarker to indicate the clinical efficacy of the potent enediyne antitumor drug.
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Affiliation(s)
- Ming-Quan Sha
- Department of Biochemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao-Li Zhao
- Department of Biochemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liang Li
- Department of Biochemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li-Hui Li
- Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Li
- Department of Biochemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tian-Geng Dong
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wei-Xin Niu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li-Jun Jia
- Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Rong-Guang Shao
- Department of Biochemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong-Su Zhen
- Department of Biochemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhen Wang
- Department of Biochemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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16
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Akizu N, Martínez-Balbás MA. EZH2 orchestrates apicobasal polarity and neuroepithelial cell renewal. NEUROGENESIS 2016; 3:e1250034. [PMID: 28090544 DOI: 10.1080/23262133.2016.1250034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 01/20/2023]
Abstract
During early stages of neural development, neuroepithelial cells translocate their nuclei along the apicobasal axis in a harmonized manner with the cell cycle. How cell cycle progression and neuroepithelium polarity are coordinated remains unclear. It has been proposed that developmental cues, epigenetic mechanisms and cell cycle regulators must be linked in order to orchestrate these processes. We have recently discovered that a master epigenetic factor, EZH2 is essential to coordinate these events. EZH2 directly represses the cell cycle regulator p21WAF1/CIP in the chicken spinal cord. By doing so, EZH2 controls neural progenitor cell renewal and fine-tunes Rho signaling pathway, which is essential to maintain neuroepithelial structure. Our findings point to a new role of EZH2 during development that could have potential implication in other areas as cancer.
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Affiliation(s)
- Naiara Akizu
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC) , Barcelona, Spain
| | - Marian A Martínez-Balbás
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC) , Barcelona, Spain
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17
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Zhang J, Han B, Li X, Bies J, Jiang P, Koller RP, Wolff L. Distal regulation of c-myb expression during IL-6-induced differentiation in murine myeloid progenitor M1 cells. Cell Death Dis 2016; 7:e2364. [PMID: 27607579 PMCID: PMC5059869 DOI: 10.1038/cddis.2016.267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/25/2016] [Accepted: 07/29/2016] [Indexed: 12/31/2022]
Abstract
The c-Myb transcription factor is a major regulator that controls differentiation and proliferation of hematopoietic progenitor cells, which is frequently deregulated in hematological diseases, such as lymphoma and leukemia. Understanding of the mechanisms regulating the transcription of c-myb gene is challenging as it lacks a typical promoter and multiple factors are involved. Our previous studies identified some distal regulatory elements in the upstream regions of c-myb gene in murine myeloid progenitor M1 cells, but the detailed mechanisms still remain unclear. In the present study, we found that a cell differentiation-related DNase1 hypersensitive site is located at a -28k region upstream of c-myb gene and that transcription factors Hoxa9, Meis1 and PU.1 bind to the -28k region. Circular chromosome conformation capture (4C) assay confirmed the interaction between the -28k region and the c-myb promoter, which is supported by the enrichment of CTCF and Cohesin. Our analysis also points to a critical role for Hoxa9 and PU.1 in distal regulation of c-myb expression in murine myeloid cells and cell differentiation. Overexpression of Hoxa9 disrupted the IL-6-induced differentiation of M1 cells and upregulated c-myb expression through binding of the -28k region. Taken together, our results provide an evidence for critical role of the -28k region in distal regulatory mechanism for c-myb gene expression during differentiation of myeloid progenitor M1 cells.
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Affiliation(s)
- Junfang Zhang
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, No.999 Huchenghuan Road, Pudong New District, Shanghai 201306, China
| | - Bingshe Han
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, No.999 Huchenghuan Road, Pudong New District, Shanghai 201306, China
| | - Xiaoxia Li
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, No.999 Huchenghuan Road, Pudong New District, Shanghai 201306, China
| | - Juraj Bies
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Penglei Jiang
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, No.999 Huchenghuan Road, Pudong New District, Shanghai 201306, China
| | - Richard P Koller
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Linda Wolff
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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18
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Han Li C, Chen Y. Targeting EZH2 for cancer therapy: progress and perspective. Curr Protein Pept Sci 2016; 16:559-70. [PMID: 25854924 PMCID: PMC4997953 DOI: 10.2174/1389203716666150409100233] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 04/02/2015] [Indexed: 01/22/2023]
Abstract
Enhancer of Zeste Homolog 2 (EZH2) is the core component of the polycomb repressive complex 2 (PRC2), possessing the enzymatic activity in generating di/tri-methylated lysine 27 in histone H3. EZH2 has important roles during early development, and its dysregulation is heavily linked to oncogenesis in various tissue types. Accumulating evidences suggest a remarkable therapeutic potential by targeting EZH2 in cancer cells. The first part reviews current strategies to target EZH2 in cancers, and evaluates the available compounds and agents used to disrupt EZH2 functions. Then we provide insight to the future direction of the research on targeting EZH2 in different cancer types. We comprehensively discuss the current understandings of the 1) structure and biological activity of EZH2, 2) its role during the assembling of PRC2 and recruitment of other protein components, 3) the molecular events directing EZH2 to target genomic regions, and 4) post-translational modification at EZH2 protein. The discussion provides the basis to inspire the development of novel strategies to abolish EZH2-related effects in cancer cells.
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Affiliation(s)
| | - Yangchao Chen
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, NT, Hong Kong.
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19
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ANRIL: a pivotal tumor suppressor long non-coding RNA in human cancers. Tumour Biol 2016; 37:5657-61. [PMID: 26753962 DOI: 10.1007/s13277-016-4808-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/06/2016] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a family of non-protein-coding RNAs with length more than 200 nucleotides. LncRNAs played important roles in many biological processes such as cell development, proliferation, invasion and migration. Deregulation of LncRNAs was found in multiple tumors where they can act as a tumor suppressor gene or oncogene. LncRNA ANRIL was identified as an oncogene involved in a number of tumors such as gastric cancer, lung cancer, hepatocellular carcinoma, and esophageal squamous cell carcinoma. Inhibition of ANRIL suppressed the cancer cell proliferation, migration and invasion. Increasing data has showed that ANRIL may act as a diagnostic and prognostic biomarker for some tumors. In our review, we summarize an overview of current knowledge concerning the expression and role of ANRIL in various cancers.
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20
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NF-kB2 induces senescence bypass in melanoma via a direct transcriptional activation of EZH2. Oncogene 2015; 35:2735-45. [DOI: 10.1038/onc.2015.331] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 07/02/2015] [Accepted: 07/17/2015] [Indexed: 12/23/2022]
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21
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Abstract
Post-translational modifications of histones (so-called epigenetic modifications) play a major role in transcriptional control and normal development, and are tightly regulated. Disruption of their control is a frequent event in disease. In particular, the methylation of lysine 27 on histone H3 (H3K27), induced by the methylase EZH2, emerges as a key control of gene expression and a major regulator of cell physiology. The identification of driver mutations in EZH2 has already led to new prognostic and therapeutic advances, and new classes of potent and specific inhibitors for EZH2 show promising results in preclinical trials. This review examines the roles of histone lysine methylases and demethylases in cells and focuses on the recent knowledge and developments about EZH2.
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22
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MK3 modulation affects BMI1-dependent and independent cell cycle check-points. PLoS One 2015; 10:e0118840. [PMID: 25853770 PMCID: PMC4390245 DOI: 10.1371/journal.pone.0118840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/14/2015] [Indexed: 01/04/2023] Open
Abstract
Although the MK3 gene was originally found deleted in some cancers, it is highly expressed in others. The relevance of MK3 for oncogenesis is currently not clear. We recently reported that MK3 controls ERK activity via a negative feedback mechanism. This prompted us to investigate a potential role for MK3 in cell proliferation. We here show that overexpression of MK3 induces a proliferative arrest in normal diploid human fibroblasts, characterized by enhanced expression of replication stress- and senescence-associated markers. Surprisingly, MK3 depletion evokes similar senescence characteristics in the fibroblast model. We previously identified MK3 as a binding partner of Polycomb Repressive Complex 1 (PRC1) proteins. In the current study we show that MK3 overexpression results in reduced cellular EZH2 levels and concomitant loss of epigenetic H3K27me3-marking and PRC1/chromatin-occupation at the CDKN2A/INK4A locus. In agreement with this, the PRC1 oncoprotein BMI1, but not the PCR2 protein EZH2, bypasses MK3-induced senescence in fibroblasts and suppresses P16INK4A expression. In contrast, BMI1 does not rescue the MK3 loss-of-function phenotype, suggesting the involvement of multiple different checkpoints in gain and loss of MK3 function. Notably, MK3 ablation enhances proliferation in two different cancer cells. Finally, the fibroblast model was used to evaluate the effect of potential tumorigenic MK3 driver-mutations on cell proliferation and M/SAPK signaling imbalance. Taken together, our findings support a role for MK3 in control of proliferation and replicative life-span, in part through concerted action with BMI1, and suggest that the effect of MK3 modulation or mutation on M/SAPK signaling and, ultimately, proliferation, is cell context-dependent.
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Chromatin-Driven Behavior of Topologically Associating Domains. J Mol Biol 2015; 427:608-25. [DOI: 10.1016/j.jmb.2014.09.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 12/19/2022]
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The EBNA3 Family: Two Oncoproteins and a Tumour Suppressor that Are Central to the Biology of EBV in B Cells. Curr Top Microbiol Immunol 2015; 391:61-117. [PMID: 26428372 DOI: 10.1007/978-3-319-22834-1_3] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Epstein-Barr virus nuclear antigens EBNA3A , EBNA3B and EBNA3C are a family of three large latency-associated proteins expressed in B cells induced to proliferate by the virus. Together with the other nuclear antigens (EBNA-LP, EBNA2 and EBNA1), they are expressed from a polycistronic transcription unit that is probably unique to B cells. However, compared with the other EBNAs, hitherto the EBNA3 proteins were relatively neglected and their roles in EBV biology rather poorly understood. In recent years, powerful new technologies have been used to show that these proteins are central to the latency of EBV in B cells, playing major roles in reprogramming the expression of host genes affecting cell proliferation, survival, differentiation and immune surveillance. This indicates that the EBNA3s are critical in EBV persistence in the B cell system and in modulating B cell lymphomagenesis. EBNA3A and EBNA3C are necessary for the efficient proliferation of EBV-infected B cells because they target important tumour suppressor pathways--so operationally they are considered oncoproteins. In contrast, it is emerging that EBNA3B restrains the oncogenic capacity of EBV, so it can be considered a tumour suppressor--to our knowledge the first to be described in a tumour virus. Here, we provide a general overview of the EBNA3 genes and proteins. In particular, we describe recent research that has highlighted the complexity of their functional interactions with each other, with specific sites on the human genome and with the molecular machinery that controls transcription and epigenetic states of diverse host genes.
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Epstein-Barr virus nuclear antigen 3A partially coincides with EBNA3C genome-wide and is tethered to DNA through BATF complexes. Proc Natl Acad Sci U S A 2014; 112:554-9. [PMID: 25540416 DOI: 10.1073/pnas.1422580112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Epstein-Barr Virus (EBV) conversion of B-lymphocytes to Lymphoblastoid Cell Lines (LCLs) requires four EBV nuclear antigen (EBNA) oncoproteins: EBNA2, EBNALP, EBNA3A, and EBNA3C. EBNA2 and EBNALP associate with EBV and cell enhancers, up-regulate the EBNA promoter, MYC, and EBV Latent infection Membrane Proteins (LMPs), which up-regulate BCL2 to protect EBV-infected B-cells from MYC proliferation-induced cell death. LCL proliferation induces p16(INK4A) and p14(ARF)-mediated cell senescence. EBNA3A and EBNA3C jointly suppress p16(INK4A) and p14(ARF), enabling continuous cell proliferation. Analyses of the EBNA3A human genome-wide ChIP-seq landscape revealed 37% of 10,000 EBNA3A sites to be at strong enhancers; 28% to be at weak enhancers; 4.4% to be at active promoters; and 6.9% to be at weak and poised promoters. EBNA3A colocalized with BATF-IRF4, ETS-IRF4, RUNX3, and other B-cell Transcription Factors (TFs). EBNA3A sites clustered into seven unique groups, with differing B-cell TFs and epigenetic marks. EBNA3A coincidence with BATF-IRF4 or RUNX3 was associated with stronger EBNA3A ChIP-Seq signals. EBNA3A was at MYC, CDKN2A/B, CCND2, CXCL9/10, and BCL2, together with RUNX3, BATF, IRF4, and SPI1. ChIP-re-ChIP revealed complexes of EBNA3A on DNA with BATF. These data strongly support a model in which EBNA3A is tethered to DNA through a BATF-containing protein complexes to enable continuous cell proliferation.
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Li Z, Wang Y, Qiu J, Li Q, Yuan C, Zhang W, Wang D, Ye J, Jiang H, Yang J, Cheng J. The polycomb group protein EZH2 is a novel therapeutic target in tongue cancer. Oncotarget 2014; 4:2532-49. [PMID: 24345883 PMCID: PMC3926847 DOI: 10.18632/oncotarget.1503] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
EZH2, a core member of the Polycomb Repressor Complex 2 (PRC2), mediates transcriptional silencing by catalyzing the trimethylation of histone 3 lysine 27 (H3K27), which plays key roles in cancer initiation and progression. Here, we investigated the expression pattern and biological roles of EZH2 in tongue tumorigenesis by loss-of-function assays using small interference RNA and EZH2 inhibitor DZNep. Also we determined the therapeutic efficiency of DZNep against tongue cancer in vivo. We found that aberrantly overexpressed EZH2 was associated with pathological grade, cervical nodes metastasis and Ki-67 expression in tongue cancers. Elevated EZH2 correlated with shorter overall survival and showed significant and independent prognostic importance in patients with tongue cancer. Both genetic and pharmacological depletion of EZH2 inhibited cell proliferation, migration, invasion and colony formation and decreased CD44+ subpopulation probably in part through modulating p16, p21 and E-caherin. Moreover, DZNep enhanced the anticancer effects of 5-Fluorouracil. Furthermore, intratumoral EZH2 inhibition induced by DZNep intraperitoneal administration significantly attenuated tumor growth in a tongue cancer xenograft model. Taken together, our results indicate that EZH2 serves as a key driver with multiple oncogenic functions during tongue tumorigenesis and a new biomarker for tongue cancer diagnosis and prognostic prediction. These findings open up possibilities for therapeutic intervention against EZH2 in tongue cancer.
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Affiliation(s)
- Zhongwu Li
- Head Neck Cancer Center, Institute of Stomatology, Affiliated Stomatological Hospital, Nanjing Medical University, Jiangsu, China PRC
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Wolff L, Humeniuk R. Concise review: erythroid versus myeloid lineage commitment: regulating the master regulators. Stem Cells 2014; 31:1237-44. [PMID: 23559316 DOI: 10.1002/stem.1379] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 02/18/2013] [Indexed: 12/26/2022]
Abstract
Developmental processes, like blood formation, are orchestrated by transcriptional networks. Those transcriptional networks are highly responsive to various environmental stimuli and affect common precursors resulting in increased production of cells of the erythroid lineage or myeloid lineage (granulocytes, neutrophils, and macrophages). A significant body of knowledge has accumulated describing transcription factors that drive differentiation of these two major cellular pathways, in particular the antagonistic master regulators such as GATA-1 and PU.1. However, little is known about factors that work upstream of master regulators to enhance differentiation toward one lineage. These functions become especially important under various stress conditions like sudden loss of red blood cells or pathogen infection. This review describes recent studies that begin to provide evidence for such factors. An increased understanding of factors regulating cellular commitment will advance our understanding of the etiology of diseases like anemia, cancer, and possibly other blood related disorders.
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Affiliation(s)
- Linda Wolff
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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Bai J, Ma M, Cai M, Xu F, Chen J, Wang G, Shuai X, Tao K. Inhibition enhancer of zeste homologue 2 promotes senescence and apoptosis induced by doxorubicin in p53 mutant gastric cancer cells. Cell Prolif 2014; 47:211-8. [PMID: 24738879 DOI: 10.1111/cpr.12103] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 01/17/2014] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVES Enhancer of zeste homologue 2 (EZH2) is crucially involved in epigenetic silencing by acting as a histone methyltransferase. Although EZH2 is overexpressed in many cancers and is involved in malignant cell proliferation and invasion, the role of EZH2 in senescence induced by DNA damage has up to now remained largely unknown. In this study, we sought to explore the outcome of EZH2 depletion along with exposure of doxorubicin (DOX), and related mechanisms, in gastric cancer cells. MATERIALS AND METHODS Here, senescence induced by DNA damage was achieved in gastric cancer cells by DOX treatment. EZH2 was downregulated by transfection with siRNA or treated with (-)-epigallocatechin-3-gallate, a targeted inhibitor. Senescence-associated β galactosidase (SA-β-gal) and formation of senescence-associated heterochromatin foci were used to identify cell senescence. To investigate effects of EZH2 depletion on the cell cycle, apoptosis and proliferation, flow cytometry and MTT analysis were employed. Changes in p53-p21 axis activation were detected by Western blotting. RESULTS We found that cell proliferative arrest caused by DOX could be promoted by EZH2 depletion. Mechanistically, EZH2 depletion not only worked in coordination with DNA damage during the progression of cell senescence but also promoted apoptosis in p53 mutant cells. However, it had no cooperative relationship with DOX in p53 wild-type cells. CONCLUSIONS These data help unravel a crucial role for EZH2 in senescence and apoptosis in gastric cancer cells and that p53 genomic status was associated with different cell responses to EZH2 silencing.
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Affiliation(s)
- J Bai
- Department of Gastrointestinal Surgery II, Wuhan Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, 430022, China
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Epstein-Barr virus nuclear antigen 3C binds to BATF/IRF4 or SPI1/IRF4 composite sites and recruits Sin3A to repress CDKN2A. Proc Natl Acad Sci U S A 2013; 111:421-6. [PMID: 24344258 DOI: 10.1073/pnas.1321704111] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Epstein-Barr virus nuclear antigen 3C (EBNA3C) repression of CDKN2A p14(ARF) and p16(INK4A) is essential for immortal human B-lymphoblastoid cell line (LCL) growth. EBNA3C ChIP-sequencing identified >13,000 EBNA3C sites in LCL DNA. Most EBNA3C sites were associated with active transcription; 64% were strong H3K4me1- and H3K27ac-marked enhancers and 16% were active promoters marked by H3K4me3 and H3K9ac. Using ENCODE LCL transcription factor ChIP-sequencing data, EBNA3C sites coincided (±250 bp) with RUNX3 (64%), BATF (55%), ATF2 (51%), IRF4 (41%), MEF2A (35%), PAX5 (34%), SPI1 (29%), BCL11a (28%), SP1 (26%), TCF12 (23%), NF-κB (23%), POU2F2 (23%), and RBPJ (16%). EBNA3C sites separated into five distinct clusters: (i) Sin3A, (ii) EBNA2/RBPJ, (iii) SPI1, and (iv) strong or (v) weak BATF/IRF4. EBNA3C signals were positively affected by RUNX3, BATF/IRF4 (AICE) and SPI1/IRF4 (EICE) cooccupancy. Gene set enrichment analyses correlated EBNA3C/Sin3A promoter sites with transcription down-regulation (P < 1.6 × 10(-4)). EBNA3C signals were strongest at BATF/IRF4 and SPI1/IRF4 composite sites. EBNA3C bound strongly to the p14(ARF) promoter through SPI1/IRF4/BATF/RUNX3, establishing RBPJ-, Sin3A-, and REST-mediated repression. EBNA3C immune precipitated with Sin3A and conditional EBNA3C inactivation significantly decreased Sin3A binding at the p14(ARF) promoter (P < 0.05). These data support a model in which EBNA3C binds strongly to BATF/IRF4/SPI1/RUNX3 sites to enhance transcription and recruits RBPJ/Sin3A- and REST/NRSF-repressive complexes to repress p14(ARF) and p16(INK4A) expression.
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Razin SV, Gavrilov AA, Ioudinkova ES, Iarovaia OV. Communication of genome regulatory elements in a folded chromosome. FEBS Lett 2013; 587:1840-7. [PMID: 23651551 DOI: 10.1016/j.febslet.2013.04.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 10/26/2022]
Abstract
The most popular model of gene activation by remote enhancers postulates that the enhancers interact directly with target promoters via the looping of intervening DNA fragments. This interaction is thought to be necessary for the stabilization of the Pol II pre-initiation complex and/or for the transfer of transcription factors and Pol II, which are initially accumulated at the enhancer, to the promoter. The direct interaction of enhancer(s) and promoter(s) is only possible when these elements are located in close proximity within the nuclear space. Here, we discuss the molecular mechanisms for maintaining the close proximity of the remote regulatory elements of the eukaryotic genome. The models of an active chromatin hub (ACH) and an active nuclear compartment are considered, focusing on the role of chromatin folding in juxtaposing remote DNA sequences. The interconnection between the functionally dependent architecture of the interphase chromosome and nuclear compartmentalization is also discussed.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia.
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Lo Sardo F, Lanzuolo C, Comoglio F, De Bardi M, Paro R, Orlando V. PcG-mediated higher-order chromatin structures modulate replication programs at the Drosophila BX-C. PLoS Genet 2013; 9:e1003283. [PMID: 23437006 PMCID: PMC3578750 DOI: 10.1371/journal.pgen.1003283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 12/14/2012] [Indexed: 12/03/2022] Open
Abstract
Polycomb group proteins (PcG) exert conserved epigenetic functions that convey maintenance of repressed transcriptional states, via post-translational histone modifications and high order structure formation. During S-phase, in order to preserve cell identity, in addition to DNA information, PcG-chromatin-mediated epigenetic signatures need to be duplicated requiring a tight coordination between PcG proteins and replication programs. However, the interconnection between replication timing control and PcG functions remains unknown. Using Drosophila embryonic cell lines, we find that, while presence of specific PcG complexes and underlying transcription state are not the sole determinants of cellular replication timing, PcG-mediated higher-order structures appear to dictate the timing of replication and maintenance of the silenced state. Using published datasets we show that PRC1, PRC2, and PhoRC complexes differently correlate with replication timing of their targets. In the fully repressed BX-C, loss of function experiments revealed a synergistic role for PcG proteins in the maintenance of replication programs through the mediation of higher-order structures. Accordingly, replication timing analysis performed on two Drosophila cell lines differing for BX-C gene expression states, PcG distribution, and chromatin domain conformation revealed a cell-type-specific replication program that mirrors lineage-specific BX-C higher-order structures. Our work suggests that PcG complexes, by regulating higher-order chromatin structure at their target sites, contribute to the definition and the maintenance of genomic structural domains where genes showing the same epigenetic state replicate at the same time. DNA replication is a tightly orchestrated process that precisely duplicates the entire genome during cell division to ensure that daughter cells inherit the same genetic information. The genome is replicated following a specific temporal program, where different segments replicate in distinct moments of the S phase correlating with active (early) and repressed (late) transcriptional state of resident genes. Moreover, replicating chromosomal domains are organized in the nuclear space, perhaps to guarantee the conservation of the same topological order in daughter cells. Epigenetic mechanisms, acting via chromatin organization, determine transcriptional states and must be maintained through cell division. Here, we analyzed in detail the link between Polycomb Group (PcG) proteins, higher-order chromatin structure, and replication timing in Drosophila. By using bioinformatic analyses combined with functional experiments, we show that Polycomb Repressive Complex 1 (PRC1), PRC2, and PhoRC differently correlate with replication timing of their targets and that transcription per se does not determine replication timing. Strikingly, by analyzing the PcG-regulated Bithorax Complex, where PRC1, PRC2, and PhoRC complexes are bound to repressed targets, we provide evidence for a synergistic role of PcG proteins in the modulation and maintenance of replication timing through the definition of specific, topologically distinct genomic domains.
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Affiliation(s)
- Federica Lo Sardo
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Chiara Lanzuolo
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
- CNR Institute of Cellular Biology and Neurobiology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Federico Comoglio
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zürich, Basel, Switzerland
| | - Marco De Bardi
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Renato Paro
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zürich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Valerio Orlando
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
- * E-mail:
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Pourfarzad F, von Lindern M, Azarkeivan A, Hou J, Kia SK, Esteghamat F, van Ijcken W, Philipsen S, Najmabadi H, Grosveld F. Hydroxyurea responsiveness in β-thalassemic patients is determined by the stress response adaptation of erythroid progenitors and their differentiation propensity. Haematologica 2012; 98:696-704. [PMID: 23100274 DOI: 10.3324/haematol.2012.074492] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
β-thalassemia is caused by mutations in the β-globin locus resulting in loss of, or reduced, hemoglobin A (adult hemoglobin, HbA, α2β2) production. Hydroxyurea treatment increases fetal γ-globin (fetal hemoglobin, HbF, α2γ2) expression in postnatal life substituting for the missing adult β-globin and is, therefore, an attractive therapeutic approach. Patients treated with hydroxyurea fall into three categories: i) 'responders' who increase hemoglobin to therapeutic levels; (ii) 'moderate-responders' who increase hemoglobin levels but still need transfusions at longer intervals; and (iii) 'non-responders' who do not reach adequate hemoglobin levels and remain transfusion-dependent. The mechanisms underlying these differential responses remain largely unclear. We generated RNA expression profiles from erythroblast progenitors of 8 responder and 8 non-responder β-thalassemia patients. These profiles revealed that hydroxyurea treatment induced differential expression of many genes in cells from non-responders while it had little impact on cells from responders. Part of the gene program up-regulated by hydroxyurea in non-responders was already highly expressed in responders before hydroxyurea treatment. Baseline HbF expression was low in non-responders, and hydroxyurea treatment induced significant cell death. We conclude that cells from responders have adapted well to constitutive stress conditions and display a propensity to proceed to the erythroid differentiation program.
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Abstract
The first genes composing the Polycomb group (PcG) were identified 50 years ago in Drosophila melanogaster as essential developmental functions that regulate the correct segmental expression of homeotic selector genes. In the past two decades, what was initially described as a large family of chromatin-associated proteins involved in the maintenance of transcriptional repression to maintain cellular memory of homeotic genes turned out to be a highly conserved and sophisticated network of epigenetic regulators that play key roles in multiple aspects of cell physiology and identity, including regulation of all developmental genes, cell differentiation, stem and somatic cell reprogramming and response to environmental stimuli. These myriad phenotypes further spread interest for the contribution that PcG proteins revealed in the pathogenesis and progression of cancer and other complex diseases. Recent novel insights have increasingly clarified the molecular regulatory mechanisms at the basis of PcG-mediated epigenetic silencing and opened new visions about PcG functions in cells. In this review, we focus on the multiple modes of action of the PcG complexes and describe their biological roles.
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Affiliation(s)
- Chiara Lanzuolo
- Dulbecco Telethon Institute, Epigenetics and Genome Reprogramming, IRCCS Santa Lucia Foundation, 00143 Rome, Italy
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O'Sullivan RJ, Karlseder J. The great unravelling: chromatin as a modulator of the aging process. Trends Biochem Sci 2012; 37:466-76. [PMID: 22959736 DOI: 10.1016/j.tibs.2012.08.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 08/01/2012] [Accepted: 08/07/2012] [Indexed: 02/01/2023]
Abstract
During embryogenesis, the establishment of chromatin states permits the implementation of genetic programs that allow the faithful development of the organism. However, these states are not fixed and there is much evidence that stochastic or chronic deterioration of chromatin organization, as correlated by transcriptional alterations and the accumulation of DNA damage in cells, occurs during the lifespan of the individual. Whether causal or simply a byproduct of macromolecular decay, these changes in chromatin states have emerged as potentially central conduits of mammalian aging. This review explores the current state of our understanding of the links between chromatin organization and aging.
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Affiliation(s)
- Roderick J O'Sullivan
- The Salk Institute for Biological Studies, Molecular and Cellular Biology Department, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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Lanzuolo C. Epigenetic alterations in muscular disorders. Comp Funct Genomics 2012; 2012:256892. [PMID: 22761545 PMCID: PMC3385594 DOI: 10.1155/2012/256892] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 04/11/2012] [Accepted: 04/19/2012] [Indexed: 11/18/2022] Open
Abstract
Epigenetic mechanisms, acting via chromatin organization, fix in time and space different transcriptional programs and contribute to the quality, stability, and heritability of cell-specific transcription programs. In the last years, great advances have been made in our understanding of mechanisms by which this occurs in normal subjects. However, only a small part of the complete picture has been revealed. Abnormal gene expression patterns are often implicated in the development of different diseases, and thus epigenetic studies from patients promise to fill an important lack of knowledge, deciphering aberrant molecular mechanisms at the basis of pathogenesis and diseases progression. The identification of epigenetic modifications that could be used as targets for therapeutic interventions could be particularly timely in the light of pharmacologically reversion of pathological perturbations, avoiding changes in DNA sequences. Here I discuss the available information on epigenetic mechanisms that, altered in neuromuscular disorders, could contribute to the progression of the disease.
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Affiliation(s)
- Chiara Lanzuolo
- CNR Institute of Cellular Biology and Neurobiology, IRCCS Santa Lucia Foundation, Via Del Fosso di Fiorano 64, 00143 Rome, Italy
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French BA, Oliva J, Bardag-Gorce F, Li J, Zhong J, Buslon V, French SW. Mallory-Denk bodies form when EZH2/H3K27me3 fails to methylate DNA in the nuclei of human and mice liver cells. Exp Mol Pathol 2012; 92:318-26. [PMID: 22465358 DOI: 10.1016/j.yexmp.2012.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 11/28/2022]
Abstract
EZH2/H3K27me3 and polycomb group complex (PcG) play a major role in regulating global gene expression including tumor suppressor genes. EZH2 is linked to cell cycle regulated EZH2 phosphorylation by CDK1, a mitotic kinase which increases in arrested mitosis compared to S phase. CDK1 phosphorylation of EZH2 accelerates the degradation of pEZH2. Phospho-EZH2 is subjected to ubiquitination. The half-like of pEZH2 is shorter when compared to total EZH2. In the present study, pEZH2 was found concentrated together with ubiquitin in the Mallory-Denk bodies (MDB) that were formed in hepatocytes in the livers of drug primed mice refed DDC and humans with alcoholic hepatitis or hepatocellular carcinoma. The cells that formed MDBs in the mice livers studied were associated with a growth advantage and a high proliferative index. However, the livers from patients with alcoholic hepatitis showed evidence of cell cycle arrest where PCNA, cyclin D1 and p27 positive nuclei were numerous but Ki-67 positive nuclei were scarce. It is concluded that MDB formation is linked to the cell cycle and global gene expression (i.e. loss of gene silencing) through its association with the regulation of the polycomb group PRC2/EZH2/H3K27me3 complex.
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Affiliation(s)
- B A French
- Department of Pathology, Harbor-UCLA Medical Center, Torrance, CA 90509, USA.
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Kolovos P, Knoch TA, Grosveld FG, Cook PR, Papantonis A. Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin 2012; 5:1. [PMID: 22230046 PMCID: PMC3281776 DOI: 10.1186/1756-8935-5-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 01/09/2012] [Indexed: 12/27/2022] Open
Abstract
Regulatory DNA elements such as enhancers, silencers and insulators are embedded in metazoan genomes, and they control gene expression during development. Although they fulfil different roles, they share specific properties. Herein we discuss some examples and a parsimonious model for their function is proposed. All are transcription units that tether their target promoters close to, or distant from, transcriptional hot spots (or 'factories').
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Affiliation(s)
- Petros Kolovos
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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PcG complexes set the stage for epigenetic inheritance of gene silencing in early S phase before replication. PLoS Genet 2011; 7:e1002370. [PMID: 22072989 PMCID: PMC3207895 DOI: 10.1371/journal.pgen.1002370] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 09/20/2011] [Indexed: 11/19/2022] Open
Abstract
Polycomb group (PcG) proteins are part of a conserved cell memory system that conveys epigenetic inheritance of silenced transcriptional states through cell division. Despite the considerable amount of information about PcG mechanisms controlling gene silencing, how PcG proteins maintain repressive chromatin during epigenome duplication is still unclear. Here we identified a specific time window, the early S phase, in which PcG proteins are recruited at BX-C PRE target sites in concomitance with H3K27me3 repressive mark deposition. Notably, these events precede and are uncoupled from PRE replication timing, which occurs in late S phase when most epigenetic signatures are reduced. These findings shed light on one of the key mechanisms for PcG-mediated epigenetic inheritance during S phase, suggesting a conserved model in which the PcG-dependent H3K27me3 mark is inherited by dilution and not by de novo methylation occurring at the time of replication.
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Cao W, Younis RH, Li J, Chen H, Xia R, Mao L, Chen W, Ren H. EZH2 promotes malignant phenotypes and is a predictor of oral cancer development in patients with oral leukoplakia. Cancer Prev Res (Phila) 2011; 4:1816-24. [PMID: 21697275 PMCID: PMC3677701 DOI: 10.1158/1940-6207.capr-11-0130] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Oral leukoplakia (OL) is the most common premalignancy in the oral cavity. A small proportion of OLs progresses to oral squamous cell carcinoma (OSCC). To assess OSCC risk of OLs, we investigated the role of the transcriptional repressor enhancer of zeste homolog 2 (EZH2) in oral tumorigenesis and its clinical implication as an OSCC risk predictor. Immunohistochemistry was used to measure EZH2 expression in OLs from 76 patients, including 37 who later developed OSCC and 39 who did not. EZH2 expression was associated with clinicopathologic parameters and clinical outcomes. To determine the biological role of EZH2 in OL, EZH2 level was reduced using EZH2 siRNAs in Leuk-1 cells, its impact on cell cycle, anchorage-dependent/independent growth, and invasion was assessed. We observed strong EZH2 expression in 34 (45%), moderate expression in 26 (34%), and weak/no expression in 16 (21%) of the OLs. The higher EZH2 levels were strongly associated with dysplasia (P < 0.001) and OSCC development (P < 0.0001). Multivariate analysis indicated that EZH2 expression was the only independent factor for OSCC development (P < 0.0001). At 5 years after diagnosis, 80% of patients whose OLs expressed strong EZH2 developed OSCC whereas only 24% patients with moderate and none with weak/no EZH2 expression did so (P < 0.0001). In Leuk-1 cells, EZH2 downregulation resulted in G(1) arrest; decreased invasion capability, decreased anchorage-independent growth; downregulation of cyclin D1 and upregulation of p15(INK4B). Our data suggest that EZH2 plays an important role in OL malignant transformation and may be a biomarker in predicting OSCC development in patients with OLs.
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MESH Headings
- Adult
- Aged
- Blotting, Western
- Carcinoma, Squamous Cell/etiology
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Adhesion
- Cell Cycle
- Cell Line, Tumor
- Cell Movement
- Cell Proliferation
- Cohort Studies
- DNA-Binding Proteins/antagonists & inhibitors
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Enhancer of Zeste Homolog 2 Protein
- Female
- Follow-Up Studies
- Gene Expression Regulation, Neoplastic
- Humans
- Immunoenzyme Techniques
- Leukoplakia, Oral/complications
- Leukoplakia, Oral/metabolism
- Leukoplakia, Oral/pathology
- Male
- Middle Aged
- Mouth Neoplasms/etiology
- Mouth Neoplasms/metabolism
- Mouth Neoplasms/pathology
- Neoplasm Invasiveness
- Phenotype
- Polycomb Repressive Complex 2
- Prognosis
- RNA, Small Interfering/genetics
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/metabolism
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Affiliation(s)
- Wei Cao
- Department of Oral and Maxillofacial Surgery, Ninth People’s Hospital, School of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, 639 Zhizaoju Road, Shanghai, 200011, China
- Department of Oncology and Diagnostic Sciences, University of Maryland Dental School, 650 W Baltimore St, Baltimore, MD, 21201, USA
| | - Rania H. Younis
- Department of Oncology and Diagnostic Sciences, University of Maryland Dental School, 650 W Baltimore St, Baltimore, MD, 21201, USA
| | - Jiang Li
- Department of Oral and Maxillofacial Surgery, Ninth People’s Hospital, School of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Haiyan Chen
- Department of Oncology and Diagnostic Sciences, University of Maryland Dental School, 650 W Baltimore St, Baltimore, MD, 21201, USA
| | - Ronghui Xia
- Department of Oral and Maxillofacial Surgery, Ninth People’s Hospital, School of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, 639 Zhizaoju Road, Shanghai, 200011, China
- Department of Oncology and Diagnostic Sciences, University of Maryland Dental School, 650 W Baltimore St, Baltimore, MD, 21201, USA
| | - Li Mao
- Department of Oncology and Diagnostic Sciences, University of Maryland Dental School, 650 W Baltimore St, Baltimore, MD, 21201, USA
| | - Wantao Chen
- Department of Oral and Maxillofacial Surgery, Ninth People’s Hospital, School of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Hening Ren
- Department of Oncology and Diagnostic Sciences, University of Maryland Dental School, 650 W Baltimore St, Baltimore, MD, 21201, USA
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Kang H, Wiedmer A, Yuan Y, Robertson E, Lieberman PM. Coordination of KSHV latent and lytic gene control by CTCF-cohesin mediated chromosome conformation. PLoS Pathog 2011; 7:e1002140. [PMID: 21876668 PMCID: PMC3158054 DOI: 10.1371/journal.ppat.1002140] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 05/10/2011] [Indexed: 12/22/2022] Open
Abstract
Herpesvirus persistence requires a dynamic balance between latent and lytic cycle gene expression, but how this balance is maintained remains enigmatic. We have previously shown that the Kaposi's Sarcoma-Associated Herpesvirus (KSHV) major latency transcripts encoding LANA, vCyclin, vFLIP, v-miRNAs, and Kaposin are regulated, in part, by a chromatin organizing element that binds CTCF and cohesins. Using viral genome-wide chromatin conformation capture (3C) methods, we now show that KSHV latency control region is physically linked to the promoter regulatory region for ORF50, which encodes the KSHV immediate early protein RTA. Other linkages were also observed, including an interaction between the 5' and 3' end of the latency transcription cluster. Mutation of the CTCF-cohesin binding site reduced or eliminated the chromatin conformation linkages, and deregulated viral transcription and genome copy number control. siRNA depletion of CTCF or cohesin subunits also disrupted chromosomal linkages and deregulated viral latent and lytic gene transcription. Furthermore, the linkage between the latent and lytic control region was subject to cell cycle fluctuation and disrupted during lytic cycle reactivation, suggesting that these interactions are dynamic and regulatory. Our findings indicate that KSHV genomes are organized into chromatin loops mediated by CTCF and cohesin interactions, and that these inter-chromosomal linkages coordinate latent and lytic gene control.
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Affiliation(s)
- Hyojeung Kang
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
- The Kyungpook National University, College of Pharmacy, Daegu, Korea
| | - Andreas Wiedmer
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Yan Yuan
- The University of Pennsylvania, School of Dentistry, Philadelphia, Pennsylvania, United States of America
| | - Erle Robertson
- The University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Paul M. Lieberman
- The Wistar Institute, Philadelphia, Pennsylvania, United States of America
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41
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Chou RH, Yu YL, Hung MC. The roles of EZH2 in cell lineage commitment. Am J Transl Res 2011; 3:243-250. [PMID: 21654879 PMCID: PMC3102568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Accepted: 04/15/2011] [Indexed: 05/30/2023]
Abstract
Enhancer of zeste homolog 2 (EZH2), a catalytic component of polycomb repressive complex 2 (PRC2), epigenetically regulates chromatin structure and gene expressions through tri-methylation at histone H3K27 and recruitment of DNA methyltransferases for gene silencing. Despite extensive studies of the role of EZH2 in cancer progression and malignancy, increasing evidence also suggest that EZH2 plays a critical role in stem cells renewal, maintenance, and differentiation into specific cell lineages. Here, we review the updated information regarding how EZH2 contributes to stem cell maintenance, cell lineage determination, including myogenesis, adipogenesis, osteogenesis, neurogenesis, hematopoiesis, lymphopoiesis, epidermal differentiation and hepatogenesis, and how EZH2 is regulated by phosphorylation and microRNAs in these processes.
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Affiliation(s)
- Ruey-Hwang Chou
- Center for Molecular Medicine, China Medical University HospitalTaichung 404, Taiwan
- Department of Biotechnology, Asia UniversityTaichung 413, Taiwan
| | - Yung-Luen Yu
- Center for Molecular Medicine, China Medical University HospitalTaichung 404, Taiwan
- Department of Biotechnology, Asia UniversityTaichung 413, Taiwan
- Graduate Institute of Cancer Biology, China Medical UniversityTaichung 404, Taiwan
| | - Mien-Chie Hung
- Center for Molecular Medicine, China Medical University HospitalTaichung 404, Taiwan
- Graduate Institute of Cancer Biology, China Medical UniversityTaichung 404, Taiwan
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
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Zeng Y, Kotake Y, Pei XH, Smith MD, Xiong Y. p53 binds to and is required for the repression of Arf tumor suppressor by HDAC and polycomb. Cancer Res 2011; 71:2781-92. [PMID: 21447739 DOI: 10.1158/0008-5472.can-10-3483] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The expression of tumor suppressor Arf is tightly repressed during normal cell growth at a young age and is activated by oncogenic insults, and during aging, results in p53 activation and cell-cycle arrest to prevent hyperproliferation. The mechanisms of both transcriptional repression and activation of Arf are not understood. We show that p53 binds to and represses Arf expression and that this repression requires the function of both histone deacetylases (HDAC) and polycomb group (PcG) proteins. Inactivation of p53 leads to increased Arf transcription in both mouse embryonic fibroblasts (MEF) cultured in vitro and in tissues and organs of p53 null mice. Activation of endogenous p53 enhances Arf repression, and reintroduction of p53 back into p53 null MEFs restores Arf repression. Both DNA binding and transactivation activities of p53 are required for Arf repression. We show that p53 is required for both HDAC and PcG to repress Arf expression. Bindings of both HDAC and PcG to Arf are disrupted by inactivation of p53 and can be restored in p53 null MEFs by the reintroduction of wild-type, but not mutant, p53. These results indicate that p53 recruits both HDAC and PcG to Arf locus to repress its expression, and this repression constitutes a second feedback loop in p53 regulation.
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Affiliation(s)
- Yaxue Zeng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Chromatin higher-order structures and gene regulation. Curr Opin Genet Dev 2011; 21:175-86. [PMID: 21342762 DOI: 10.1016/j.gde.2011.01.022] [Citation(s) in RCA: 293] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 01/18/2011] [Indexed: 12/16/2022]
Abstract
Genomic DNA in the eukaryotic nucleus is hierarchically packaged by histones into chromatin to fit inside the nucleus. The dynamics of higher-order chromatin compaction play a crucial role in transcription and other biological processes inherent to DNA. Many factors, including histone variants, histone modifications, DNA methylation, and the binding of non-histone architectural proteins regulate the structure of chromatin. Although the structure of nucleosomes, the fundamental repeating unit of chromatin, is clear, there is still much discussion on the higher-order levels of chromatin structure. In this review, we focus on the recent progress in elucidating the structure of the 30-nm chromatin fiber. We also discuss the structural plasticity/dynamics and epigenetic inheritance of higher-order chromatin and the roles of chromatin higher-order organization in eukaryotic gene regulation.
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44
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Polycomb group proteins: multi-faceted regulators of somatic stem cells and cancer. Cell Stem Cell 2010; 7:299-313. [PMID: 20804967 DOI: 10.1016/j.stem.2010.08.002] [Citation(s) in RCA: 526] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 07/30/2010] [Accepted: 08/06/2010] [Indexed: 02/06/2023]
Abstract
Polycomb Group (PcG) proteins are transcriptional repressors that epigenetically modify chromatin and participate in the establishment and maintenance of cell fates. These proteins play important roles in both stem cell self-renewal and in cancer development. Our understanding of their mechanism of action has greatly advanced over the past 10 years, but many unanswered questions remain. In this review, we present the currently available experimental data that connect PcG protein function with some of the key processes which govern somatic stem cell activity. We also highlight recent studies suggesting that a delicate balance in PcG gene dosage is crucial for proper stem cell homeostasis and prevention of cancer stem cell development.
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Hakim O, Sung MH, Hager GL. 3D shortcuts to gene regulation. Curr Opin Cell Biol 2010; 22:305-13. [PMID: 20466532 DOI: 10.1016/j.ceb.2010.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 04/13/2010] [Accepted: 04/14/2010] [Indexed: 11/25/2022]
Abstract
Recent technologies have allowed high-resolution genome-wide binding profiles of numerous transcription factors and other proteins. A widespread observation has emerged from studies in diverse mammalian systems: most binding events are located at great distances from gene promoters. It is becoming apparent that the traditional one-dimensional view of gene regulation via the proximal cis regulatory elements is over-simplified. True proximity and functional relevance can be revealed by studying the three-dimensional structure of the genome packaged inside the nucleus. Thus the spatial architecture of the genome has attracted a lot of interest and has intensified its significance in modern cell biology. Here we discuss current methods, concepts, and controversies in this rapidly evolving field.
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Affiliation(s)
- Ofir Hakim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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