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Wang Z, Ren B. Role of H3K4 monomethylation in gene regulation. Curr Opin Genet Dev 2024; 84:102153. [PMID: 38278054 PMCID: PMC11065453 DOI: 10.1016/j.gde.2024.102153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/28/2024]
Abstract
Methylation of histone H3 on the lysine-4 residue (H3K4me) is found throughout the eukaryotic domain, and its initial discovery as a conserved epigenetic mark of active transcription from yeast to mammalian cells has contributed to the histone code hypothesis. However, recent studies have raised questions on whether the different forms of H3K4me play a direct role in gene regulation or are simply by-products of the transcription process. Here, we review the often-conflicting experimental evidence, focusing on the monomethylation of lysine 4 on histone H3 that has been linked to the transcriptional state of enhancers in metazoans. We suggest that this epigenetic mark acts in a context-dependent manner to directly facilitate the transcriptional output of the genome and the establishment of cellular identity.
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Affiliation(s)
- Zhaoning Wang
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA. https://twitter.com/@ZhaoningWang
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA; Institute of Genomic Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
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2
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Voon HPJ, Hii L, Garvie A, Udugama M, Krug B, Russo C, Chüeh AC, Daly RJ, Morey A, Bell TDM, Turner SJ, Rosenbluh J, Daniel P, Firestein R, Mann JR, Collas P, Jabado N, Wong LH. Pediatric glioma histone H3.3 K27M/G34R mutations drive abnormalities in PML nuclear bodies. Genome Biol 2023; 24:284. [PMID: 38066546 PMCID: PMC10704828 DOI: 10.1186/s13059-023-03122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Point mutations in histone variant H3.3 (H3.3K27M, H3.3G34R) and the H3.3-specific ATRX/DAXX chaperone complex are frequent events in pediatric gliomas. These H3.3 point mutations affect many chromatin modifications but the exact oncogenic mechanisms are currently unclear. Histone H3.3 is known to localize to nuclear compartments known as promyelocytic leukemia (PML) nuclear bodies, which are frequently mutated and confirmed as oncogenic drivers in acute promyelocytic leukemia. RESULTS We find that the pediatric glioma-associated H3.3 point mutations disrupt the formation of PML nuclear bodies and this prevents differentiation down glial lineages. Similar to leukemias driven by PML mutations, H3.3-mutated glioma cells are sensitive to drugs that target PML bodies. We also find that point mutations in IDH1/2-which are common events in adult gliomas and myeloid leukemias-also disrupt the formation of PML bodies. CONCLUSIONS We identify PML as a contributor to oncogenesis in a subset of gliomas and show that targeting PML bodies is effective in treating these H3.3-mutated pediatric gliomas.
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Affiliation(s)
- Hsiao P J Voon
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Linda Hii
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Andrew Garvie
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Maheshi Udugama
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Brian Krug
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Caterina Russo
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Anderly C Chüeh
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Roger J Daly
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Alison Morey
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Toby D M Bell
- School of Chemistry, Monash University, Clayton, VIC, Australia
| | - Stephen J Turner
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Joseph Rosenbluh
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Paul Daniel
- Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Ron Firestein
- Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Jeffrey R Mann
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424, Oslo, Norway
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Department of Paediatrics, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Lee H Wong
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.
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3
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Voon HPJ, Wong LH. Chromatin mutations in pediatric high grade gliomas. Front Oncol 2023; 12:1104129. [PMID: 36686810 PMCID: PMC9853562 DOI: 10.3389/fonc.2022.1104129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Pediatric high grade gliomas (HGG) are lethal tumors which are currently untreatable. A number of recent studies have provided much needed insights into the mutations and mechanisms which drive oncogenesis in pediatric HGGs. It is now clear that mutations in chromatin proteins, particularly H3.3 and its associated chaperone complex (ATRX), are a hallmark feature of pediatric HGGs. We review the current literature on the normal roles of the ATRX/H3.3 complex and how these functions are disrupted by oncogenic mutations. We discuss the current clinical trials and pre-clinical models that target chromatin and DNA, and how these agents fit into the ATRX/H3.3 mutation model. As chromatin mutations are a relatively new discovery in pediatric HGGs, developing clear mechanistic insights are a key step to improving therapies for these tumors.
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Brady SW, Roberts KG, Gu Z, Shi L, Pounds S, Pei D, Cheng C, Dai Y, Devidas M, Qu C, Hill AN, Payne-Turner D, Ma X, Iacobucci I, Baviskar P, Wei L, Arunachalam S, Hagiwara K, Liu Y, Flasch DA, Liu Y, Parker M, Chen X, Elsayed AH, Pathak O, Li Y, Fan Y, Michael JR, Rusch M, Wilkinson MR, Foy S, Hedges D, Newman S, Zhou X, Wang J, Reilly C, Sioson E, Rice SV, Loyola VP, Wu G, Rampersaud E, Reshmi SC, Gastier-Foster J, Guidry-Auvil JM, Gesuwan P, Smith MA, Winick N, Carroll AJ, Heerema NA, Harvey RC, Willman CL, Larsen E, Raetz EA, Borowitz MJ, Wood BL, Carroll WL, Zweidler-McKay PA, Rabin KR, Mattano LA, Maloney KW, Winter SS, Burke MJ, Salzer W, Dunsmore KP, Angiolillo AL, Crews KR, Downing JR, Jeha S, Pui CH, Evans WE, Yang JJ, Relling MV, Gerhard DS, Loh ML, Hunger SP, Zhang J, Mullighan C. The genomic landscape of pediatric acute lymphoblastic leukemia. Nat Genet 2022; 54:1376-1389. [PMID: 36050548 PMCID: PMC9700506 DOI: 10.1038/s41588-022-01159-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Here, using whole-genome, exome and transcriptome sequencing of 2,754 childhood patients with ALL, we find that, despite a generally low mutation burden, ALL cases harbor a median of four putative somatic driver alterations per sample, with 376 putative driver genes identified varying in prevalence across ALL subtypes. Most samples harbor at least one rare gene alteration, including 70 putative cancer driver genes associated with ubiquitination, SUMOylation, noncoding transcripts and other functions. In hyperdiploid B-ALL, chromosomal gains are acquired early and synchronously before ultraviolet-induced mutation. By contrast, ultraviolet-induced mutations precede chromosomal gains in B-ALL cases with intrachromosomal amplification of chromosome 21. We also demonstrate the prognostic significance of genetic alterations within subtypes. Intriguingly, DUX4- and KMT2A-rearranged subtypes separate into CEBPA/FLT3- or NFATC4-expressing subgroups with potential clinical implications. Together, these results deepen understanding of the ALL genomic landscape and associated outcomes.
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Affiliation(s)
- Samuel W. Brady
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Kathryn G. Roberts
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Zhaohui Gu
- Department of Computational and Quantitative Medicine & Systems Biology, Beckman Research Institute of City of Hope, Duarte CA, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Yunfeng Dai
- Department of Biostatistics, University of Florida, Gainesville FL, USA
| | - Meenakshi Devidas
- Department of Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Chunxu Qu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Ashley N. Hill
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Pradyuamna Baviskar
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Lei Wei
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Sasi Arunachalam
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Diane A. Flasch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Yu Liu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Matthew Parker
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Abdelrahman H. Elsayed
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA,Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Omkar Pathak
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - J. Robert Michael
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Mark R. Wilkinson
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Scott Foy
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Dale Hedges
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Jian Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Colleen Reilly
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Edgar Sioson
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Stephen V. Rice
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Victor Pastor Loyola
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Shalini C. Reshmi
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus OH, USA
| | | | - Jaime M. Guidry-Auvil
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda MD, USA
| | - Patee Gesuwan
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda MD, USA
| | - Malcolm A. Smith
- Cancer Therapeutics Evaluation Program, National Cancer Institute, National Institutes of Health, Bethesda MD, USA
| | - Naomi Winick
- Department of Pediatric Hematology Oncology and Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, USA
| | - Andrew J. Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham AL, USA
| | | | - Richard C. Harvey
- Department of Pathology, University of New Mexico Cancer Center, Albuquerque NM, USA
| | | | - Eric Larsen
- Department of Pediatrics, Maine Children’s Cancer Program, Scarborough ME, USA
| | - Elizabeth A. Raetz
- Department of Pediatrics and Perlmutter Cancer Center, New York University Langone Medical Center, New York NY, USA
| | - Michael J. Borowitz
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore MD, USA
| | - Brent L. Wood
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, University of Southern California, CA, USA
| | - William L. Carroll
- Department of Pediatrics and Perlmutter Cancer Center, New York University Langone Medical Center, New York NY, USA
| | | | - Karen R. Rabin
- Department of Pediatrics, Baylor College of Medicine, Houston TX, USA
| | | | - Kelly W. Maloney
- Department of Pediatrics and Children’s Hospital Colorado, University of Colorado, Aurora CO, USA
| | - Stuart S. Winter
- Children’s Minnesota Research Institute and Cancer and Blood Disorders Program, Minneapolis MN, USA
| | - Michael J. Burke
- Division of Pediatric Hematology-Oncology, Medical College of Wisconsin, Milwaukee WI, USA
| | - Wanda Salzer
- Uniformed Services University, School of Medicine, Bethesda, MD, USA
| | | | | | - Kristine R. Crews
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - James R. Downing
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Sima Jeha
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - William E. Evans
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Jun J. Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Mary V. Relling
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Daniela S. Gerhard
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda MD, USA
| | - Mignon L. Loh
- Department of Pediatrics, Benioff Children’s Hospital and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco CA, USA
| | - Stephen P. Hunger
- Department of Pediatrics and the Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia PA, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Charles Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
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5
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Knockdown of Lamin B1 and the Corresponding Lamin B Receptor Leads to Changes in Heterochromatin State and Senescence Induction in Malignant Melanoma. Cells 2022; 11:cells11142154. [PMID: 35883595 PMCID: PMC9321645 DOI: 10.3390/cells11142154] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
Modifications in nuclear structures of cells are implicated in several diseases including cancer. They result in changes in nuclear activity, structural dynamics and cell signalling. However, the role of the nuclear lamina and related proteins in malignant melanoma is still unknown. Its molecular characterisation might lead to a deeper understanding and the development of new therapy approaches. In this study, we analysed the functional effects of dysregulated nuclear lamin B1 (LMNB1) and its nuclear receptor (LBR). According to their cellular localisation and function, we revealed that these genes are crucially involved in nuclear processes like chromatin organisation. RNA sequencing and differential gene expression analysis after knockdown of LMNB1 and LBR revealed their implication in important cellular processes driving ER stress leading to senescence and changes in chromatin state, which were also experimentally validated. We determined that melanoma cells need both molecules independently to prevent senescence. Hence, downregulation of both molecules in a BRAFV600E melanocytic senescence model as well as in etoposide-treated melanoma cells indicates both as potential senescence markers in melanoma. Our findings suggest that LMNB1 and LBR influence senescence and affect nuclear processes like chromatin condensation and thus are functionally relevant for melanoma progression.
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Bryant L, Li D, Cox SG, Marchione D, Joiner EF, Wilson K, Janssen K, Lee P, March ME, Nair D, Sherr E, Fregeau B, Wierenga KJ, Wadley A, Mancini GMS, Powell-Hamilton N, van de Kamp J, Grebe T, Dean J, Ross A, Crawford HP, Powis Z, Cho MT, Willing MC, Manwaring L, Schot R, Nava C, Afenjar A, Lessel D, Wagner M, Klopstock T, Winkelmann J, Catarino CB, Retterer K, Schuette JL, Innis JW, Pizzino A, Lüttgen S, Denecke J, Strom TM, Monaghan KG, Yuan ZF, Dubbs H, Bend R, Lee JA, Lyons MJ, Hoefele J, Günthner R, Reutter H, Keren B, Radtke K, Sherbini O, Mrokse C, Helbig KL, Odent S, Cogne B, Mercier S, Bezieau S, Besnard T, Kury S, Redon R, Reinson K, Wojcik MH, Õunap K, Ilves P, Innes AM, Kernohan KD, Costain G, Meyn MS, Chitayat D, Zackai E, Lehman A, Kitson H, Martin MG, Martinez-Agosto JA, Nelson SF, Palmer CGS, Papp JC, Parker NH, Sinsheimer JS, Vilain E, Wan J, Yoon AJ, Zheng A, Brimble E, Ferrero GB, Radio FC, Carli D, Barresi S, Brusco A, Tartaglia M, Thomas JM, Umana L, Weiss MM, Gotway G, Stuurman KE, Thompson ML, McWalter K, Stumpel CTRM, Stevens SJC, Stegmann APA, Tveten K, Vøllo A, Prescott T, Fagerberg C, Laulund LW, Larsen MJ, Byler M, Lebel RR, Hurst AC, Dean J, Schrier Vergano SA, Norman J, Mercimek-Andrews S, Neira J, Van Allen MI, Longo N, Sellars E, Louie RJ, Cathey SS, Brokamp E, Heron D, Snyder M, Vanderver A, Simon C, de la Cruz X, Padilla N, Crump JG, Chung W, Garcia B, Hakonarson HH, Bhoj EJ. Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients. SCIENCE ADVANCES 2020; 6:eabc9207. [PMID: 33268356 PMCID: PMC7821880 DOI: 10.1126/sciadv.abc9207] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/19/2020] [Indexed: 05/07/2023]
Abstract
Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A (H3F3A) or H3F3B with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation.
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Affiliation(s)
- Laura Bryant
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Samuel G Cox
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, CA 90033, USA
| | - Dylan Marchione
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Evan F Joiner
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Khadija Wilson
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin Janssen
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pearl Lee
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Divya Nair
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elliott Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brieana Fregeau
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Alexandrea Wadley
- Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, Netherlands
| | - Nina Powell-Hamilton
- Department of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19810, USA
| | | | - Theresa Grebe
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - John Dean
- Department of Medical Genetics, Aberdeen Royal Infirmary, Aberdeen, Scotland, UK
| | - Alison Ross
- Department of Medical Genetics, Aberdeen Royal Infirmary, Aberdeen, Scotland, UK
| | - Heather P Crawford
- Clinical and Metabolic Genetics, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Zoe Powis
- Department of Emerging Genetic Medicine, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Megan T Cho
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Marcia C Willing
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Linda Manwaring
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Rachel Schot
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, Netherlands
| | - Caroline Nava
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, Paris, France
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013 Paris, France
| | - Alexandra Afenjar
- Service de génétique, CRMR des malformations et maladies congénitales du cervelet et CRMR déficience intellectuelle, hôpital Trousseau, AP-HP, France
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Undiagnosed Disease Program at the University Medical Center Hamburg-Eppendorf (UDP-UKE), Martinistrasse 52, 20246 Hamburg, Germany
| | - Matias Wagner
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Technische Universität München, Munich, Germany
| | - Thomas Klopstock
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians University, Ziemssenstr. 1a, 80336 Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Juliane Winkelmann
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
- Klinik und Poliklinik für Neurologie, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Claudia B Catarino
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians University, Ziemssenstr. 1a, 80336 Munich, Germany
| | - Kyle Retterer
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Jane L Schuette
- Division of Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey W Innis
- Division of Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amy Pizzino
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Sabine Lüttgen
- Department of Pediatrics, University Medical Center Eppendorf, 20246 Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, 20246 Hamburg, Germany
| | - Tim M Strom
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany
- Institut für Humangenetik, Technische Universität München, Munich, Germany
| | | | - Zuo-Fei Yuan
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Holly Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Renee Bend
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | | | - Julia Hoefele
- Institut für Humangenetik, Technische Universität München, Munich, Germany
| | - Roman Günthner
- Department of Nephrology, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Heiko Reutter
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University Hospital Bonn & Institute of Human Genetics, University Hospital Bonn, Bonn, Germany
| | - Boris Keren
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013 Paris, France
| | - Kelly Radtke
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Omar Sherbini
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Cameron Mrokse
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Katherine L Helbig
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sylvie Odent
- CHU Rennes, Service de Génétique Clinique, CNRS UMR6290, University Rennes1, Rennes, France
| | - Benjamin Cogne
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Stephane Bezieau
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Thomas Besnard
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Sebastien Kury
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, France
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Richard Redon
- INSERM, CNRS, UNIV Nantes, CHU Nantes, l'institut du thorax, 44007 Nantes, France
| | - Karit Reinson
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H Wojcik
- Division of Genetics and Genomics and Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute, Cambridge, MA 02142, USA
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Pilvi Ilves
- Radiology Department of Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - A Micheil Innes
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H8L1, Canada
- Newborn Screening Ontario (NSO), Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - M Stephen Meyn
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Center for Human Genomics and Precision Medicine, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, Wisconsin 53705, USA
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Hilary Kitson
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
| | - Martin G Martin
- Division of Gastroenterology and Nutrition, Department of Pediatrics, Mattel Children's Hospital, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research and the David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Stan F Nelson
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Christina G S Palmer
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Institute for Society and Genetics, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jeanette C Papp
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Neil H Parker
- David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Janet S Sinsheimer
- Institute for Society and Genetics, Departments of Human Genetics, Biomathematics, and Biostatistics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Jijun Wan
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Amanda J Yoon
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Allison Zheng
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Elise Brimble
- Department of Neurology and Neurological Sciences, Stanford Medicine, Stanford, CA 94305, USA
| | | | | | - Diana Carli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Jennifer Muncy Thomas
- Pediatrics and Neurology and Neurotherapeutics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luis Umana
- Genetics and Metabolism, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marjan M Weiss
- Department of Clinical Genetics, VU Medical Center, Amsterdam, Netherlands
| | - Garrett Gotway
- Genetics and Metabolism, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - K E Stuurman
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, Netherlands
| | | | | | - Constance T R M Stumpel
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Arve Vøllo
- Department of Pediatrics, Hospital of Østfold, 1714 Grålum, Norway
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Melissa Byler
- SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | | | - Anna C Hurst
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joy Dean
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk VA 23507, USA
| | | | - Saadet Mercimek-Andrews
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Juanita Neira
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Margot I Van Allen
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Medical Genetics Programs, Provincial Health Shared Services BC and Vancouver Island Health Shared Services BC, Canada
| | - Nicola Longo
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA
| | - Elizabeth Sellars
- University of Arkansas for Medical Sciences, Little Rock, AR 72701, USA
| | | | | | | | - Delphine Heron
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013 Paris, France
| | - Molly Snyder
- Child Neurology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Celeste Simon
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Xavier de la Cruz
- Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Natália Padilla
- Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, CA 90033, USA
| | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Garcia
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, CA 90033, USA
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hakon H Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elizabeth J Bhoj
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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7
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Abstract
Canonical histones (H2A, H2B, H3, and H4) are present in all eukaryotes where they package genomic DNA and participate in numerous cellular processes, such as transcription regulation and DNA repair. In addition to the canonical histones, there are many histone variants, which have different amino acid sequences, possess tissue-specific expression profiles, and function distinctly from the canonical counterparts. A number of histone variants, including both core histones (H2A/H2B/H3/H4) and linker histones (H1/H5), have been identified to date. Htz1 (H2A.Z) and CENP-A (CenH3) are present from yeasts to mammals, and H3.3 is present from Tetrahymena to humans. In addition to the prevalent variants, others like H3.4 (H3t), H2A.Bbd, and TH2B, as well as several H1 variants, are found to be specific to mammals. Among them, H2BFWT, H3.5, H3.X, H3.Y, and H4G are unique to primates (or Hominidae). In this review, we focus on localization and function of primate- or hominidae-specific histone variants.
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Affiliation(s)
- Dongbo Ding
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong SAR, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong SAR, China
| | - Thi Thuy Nguyen
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong SAR, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong SAR, China
| | - Matthew Y H Pang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong SAR, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong SAR, China
| | - Toyotaka Ishibashi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong SAR, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong SAR, China
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8
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Ruiz-Estevez M, Staats J, Paatela E, Munson D, Katoku-Kikyo N, Yuan C, Asakura Y, Hostager R, Kobayashi H, Asakura A, Kikyo N. Promotion of Myoblast Differentiation by Fkbp5 via Cdk4 Isomerization. Cell Rep 2019; 25:2537-2551.e8. [PMID: 30485818 PMCID: PMC6350781 DOI: 10.1016/j.celrep.2018.11.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/29/2018] [Accepted: 10/31/2018] [Indexed: 01/10/2023] Open
Abstract
Fkbp5 is a widely expressed peptidyl prolyl isomerase that serves as a molecular chaperone through conformational changes of binding partners. Although it regulates diverse protein functions, little is known about its roles in myogenesis. We found here that Fkbp5 plays critical roles in myoblast differentiation through two mechanisms. First, it sequesters Cdk4 within the Hsp90 storage complex and prevents the formation of the cyclin D1-Cdk4 complex, which is a major inhibitor of differentiation. Second, Fkbp5 promotes cis-trans isomerization of the Thr172-Pro173 peptide bond in Cdk4 and inhibits phosphorylation of Thr172, an essential step for Cdk4 activation. Consistent with these in vitro findings, muscle regeneration is delayed in Fkbp5−/− mice. The related protein Fkbp4 also sequesters Cdk4 within the Hsp90 complex but does not isomerize Cdk4 or induce Thr173 phosphorylation despite its highly similar sequence. This study demonstrates protein isomerization as a critical regulatory mechanism of myogenesis by targeting Cdk4.
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Affiliation(s)
- Mercedes Ruiz-Estevez
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - James Staats
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ellen Paatela
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dane Munson
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nobuko Katoku-Kikyo
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ce Yuan
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yoko Asakura
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reilly Hostager
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hiroshi Kobayashi
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Atsushi Asakura
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Nobuaki Kikyo
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
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9
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Mendiratta S, Gatto A, Almouzni G. Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle. J Cell Biol 2018; 218:39-54. [PMID: 30257851 PMCID: PMC6314538 DOI: 10.1083/jcb.201807179] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mendiratta et al. review the interplay between the different regulatory layers that affect the transcription and dynamics of distinct histone H3 variants along the cell cycle. As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulation, we highlight situations where perturbations in histone balance may lead to cellular dysfunction and pathologies.
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Affiliation(s)
- Shweta Mendiratta
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Alberto Gatto
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Genevieve Almouzni
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France .,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
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10
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Yu Y, Schleich K, Yue B, Ji S, Lohneis P, Kemper K, Silvis MR, Qutob N, van Rooijen E, Werner-Klein M, Li L, Dhawan D, Meierjohann S, Reimann M, Elkahloun A, Treitschke S, Dörken B, Speck C, Mallette FA, Zon LI, Holmen SL, Peeper DS, Samuels Y, Schmitt CA, Lee S. Targeting the Senescence-Overriding Cooperative Activity of Structurally Unrelated H3K9 Demethylases in Melanoma. Cancer Cell 2018; 33:322-336.e8. [PMID: 29438700 PMCID: PMC5977991 DOI: 10.1016/j.ccell.2018.01.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 10/16/2017] [Accepted: 01/04/2018] [Indexed: 12/23/2022]
Abstract
Oncogene-induced senescence, e.g., in melanocytic nevi, terminates the expansion of pre-malignant cells via transcriptional silencing of proliferation-related genes due to decoration of their promoters with repressive trimethylated histone H3 lysine 9 (H3K9) marks. We show here that structurally distinct H3K9-active demethylases-the lysine-specific demethylase-1 (LSD1) and several Jumonji C domain-containing moieties (such as JMJD2C)-disable senescence and permit Ras/Braf-evoked transformation. In mouse and zebrafish models, enforced LSD1 or JMJD2C expression promoted Braf-V600E-driven melanomagenesis. A large subset of established melanoma cell lines and primary human melanoma samples presented with a collective upregulation of related and unrelated H3K9 demethylase activities, whose targeted inhibition restored senescence, even in Braf inhibitor-resistant melanomas, evoked secondary immune effects and controlled tumor growth in vivo.
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Affiliation(s)
- Yong Yu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Kolja Schleich
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany
| | - Bin Yue
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany
| | - Sujuan Ji
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany
| | - Philipp Lohneis
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, 10117 Berlin, Germany
| | - Kristel Kemper
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Mark R Silvis
- Department of Surgery, University of Utah Health Sciences Center & Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Nouar Qutob
- Weizmann Institute of Science, Department of Molecular Cell Biology, Rehovot 7610001, Israel
| | - Ellen van Rooijen
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Melanie Werner-Klein
- Regensburg Center for Interventional Immunology (RCI) and University Medical Center of Regensburg, 93053 Regensburg, Germany; Experimental Medicine and Therapy Research, University of Regensburg, 93053 Regensburg, Germany
| | - Lianjie Li
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany
| | - Dhriti Dhawan
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany
| | - Svenja Meierjohann
- University of Würzburg, Physiological Chemistry, Biocenter, 97074 Würzburg, Germany
| | - Maurice Reimann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany
| | - Abdel Elkahloun
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Steffi Treitschke
- Fraunhofer-Institute for Toxicology and Experimental Medicine, 93053 Regensburg, Germany
| | - Bernd Dörken
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany; Deutsches Konsortium für Translationale Krebsforschung (German Cancer Consortium), Partner Site Berlin, Germany
| | - Christian Speck
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, and MRC London Institute of Medical Sciences (LMS), London W12 0NN, UK
| | - Frédérick A Mallette
- Department of Medicine, Université de Montréal, Maisonneuve-Rosemont Hospital Research Centre, Montréal, QC H1T 2M4, Canada
| | - Leonard I Zon
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sheri L Holmen
- Department of Surgery, University of Utah Health Sciences Center & Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Yardena Samuels
- Weizmann Institute of Science, Department of Molecular Cell Biology, Rehovot 7610001, Israel
| | - Clemens A Schmitt
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany; Deutsches Konsortium für Translationale Krebsforschung (German Cancer Consortium), Partner Site Berlin, Germany.
| | - Soyoung Lee
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany; Deutsches Konsortium für Translationale Krebsforschung (German Cancer Consortium), Partner Site Berlin, Germany
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11
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Jorquera R, González C, Clausen P, Petersen B, Holmes DS. Improved ontology for eukaryotic single-exon coding sequences in biological databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:1-6. [PMID: 30239665 PMCID: PMC6146118 DOI: 10.1093/database/bay089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/30/2018] [Indexed: 12/21/2022]
Abstract
Efficient extraction of knowledge from biological data requires the development of structured vocabularies to unambiguously define biological terms. This paper proposes descriptions and definitions to disambiguate the term 'single-exon gene'. Eukaryotic Single-Exon Genes (SEGs) have been defined as genes that do not have introns in their protein coding sequences. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancer and neurological/developmental disorders and many exhibit tissue-specific transcription. Unfortunately, the term 'SEGs' is rife with ambiguity, leading to biological misinterpretations. In the classic definition, no distinction is made between SEGs that harbor introns in their untranslated regions (UTRs) versus those without. This distinction is important to make because the presence of introns in UTRs affects transcriptional regulation and post-transcriptional processing of the mRNA. In addition, recent whole-transcriptome shotgun sequencing has led to the discovery of many examples of single-exon mRNAs that arise from alternative splicing of multi-exon genes, these single-exon isoforms are being confused with SEGs despite their clearly different origin. The increasing expansion of RNA-seq datasets makes it imperative to distinguish the different SEG types before annotation errors become indelibly propagated in biological databases. This paper develops a structured vocabulary for their disambiguation, allowing a major reassessment of their evolutionary trajectories, regulation, RNA processing and transport, and provides the opportunity to improve the detection of gene associations with disorders including cancers, neurological and developmental diseases.
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Affiliation(s)
- Roddy Jorquera
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile.,Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile
| | - Philip Clausen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bent Petersen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile.,Centro de Genómica y Bioinformática Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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12
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Juratli TA, Qin N, Cahill DP, Filbin MG. Molecular pathogenesis and therapeutic implications in pediatric high-grade gliomas. Pharmacol Ther 2017; 182:70-79. [PMID: 28830841 DOI: 10.1016/j.pharmthera.2017.08.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
High-grade gliomas (HGG) are the most common malignant brain tumors in the pediatric population and account for a large subset of all pediatric central nervous system neoplasms. The management of pediatric HGG continues to be challenging, with poor outcome in many cases despite aggressive treatments. Consequently, parallel research efforts have been focused on identifying the underlying genetic and biological basis of pediatric HGG in order to more clearly define prognostic subgroups for treatment stratification as well as identify new treatment targets. These cutting-edge advances have revolutionized pediatric neuro-oncology and have revealed novel oncogenic vulnerabilities that are being therapeutically leveraged. Promising treatments - including pathway-targeting small molecules as well as epigenetic therapy - are being evaluated in clinical trials, and recent genomic discoveries in rare glioma subgroups have led to the identification of additional new potentially-actionable alterations. This review summarizes the current state of knowledge about the molecular characterization of pediatric HGG in correlation to the revised World Health Organization (WHO) classification, as well as provides an overview of some targeted treatment approaches in the modern clinical management of high-grade gliomas.
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Affiliation(s)
- Tareq A Juratli
- Translational Neuro-Oncology Laboratory, Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA; Department of Neurosurgery, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Germany.
| | - Nan Qin
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany; Division of Pediatric Neuro-Oncogenomics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) - partner site Essen/Düsseldorf, Düsseldorf, Germany; Institute of Neuropathology, Medical Faculty, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Daniel P Cahill
- Translational Neuro-Oncology Laboratory, Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Mariella G Filbin
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA.
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13
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Lian R, Ma H, Wu Z, Zhang G, Jiao L, Miao W, Jin Q, Li R, Chen P, Shi H, Yu W. EZH2 promotes cell proliferation by regulating the expression of RUNX3 in laryngeal carcinoma. Mol Cell Biochem 2017; 439:35-43. [PMID: 28795320 DOI: 10.1007/s11010-017-3133-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/26/2017] [Indexed: 01/12/2023]
Abstract
Enhancer of zeste homolog 2 (EZH2) is a highly conserved histone methyltransferase, which is overexpressed in different types of cancers such as breast and prostate cancer. It is reported that EZH2 can directly down-regulate RUNX3 by increasing histone H3 methylation. However, the role of EZH2 in the development and progression of laryngeal carcinoma has not yet been investigated, and the relationship between EZH2 and RUNX3 in laryngeal carcinoma is rarely reported. The current study aims to determine the role of EZH2 in the progression of laryngeal carcinoma, and investigate the interaction between EZH2 and the tumor suppressor RUNX3. Our study found that EZH2 is overexpressed in laryngeal carcinoma patients, and silencing EZH2 by EZH2 siRNA significantly inhibited the proliferation of laryngeal carcinoma cells. Besides, we also found that RUNX3 is repressed in laryngeal carcinoma patients. Moreover, RUNX3 as a downstream target protein of EZH2 is up-regulated by EZH2 siRNA accompanied by a decrease in the trimethylation modification pattern of H3K27. RUNX3 siRNA inhibits the decreased proliferation induced by EZH2 siRNA. Furthermore, β-catenin protein expression is down-regulated by EZH2 siRNA and up-regulated by RUNX3 siRNA, and RUNX3 siRNA inhibits the down-regulation effect of EZH2 siRNA on β-catenin protein expression. Additionally, the Wnt/β-catenin activator BIO reverses the inhibitory effect of EZH2 siRNA on Hep-2 cell proliferation. Taken together, our results suggest that EZH2 regulates cell proliferation potentially by targeting RUNX3 through the Wnt/β-catenin signaling pathway in laryngeal carcinoma.
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Affiliation(s)
- Rong Lian
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical College, No. 88 Healthy Road, Weihui, 453100, Henan, People's Republic of China
| | - Huimin Ma
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical College, No. 88 Healthy Road, Weihui, 453100, Henan, People's Republic of China
| | - Zhiyan Wu
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical College, No. 88 Healthy Road, Weihui, 453100, Henan, People's Republic of China
| | - Guozheng Zhang
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical College, No. 88 Healthy Road, Weihui, 453100, Henan, People's Republic of China
| | - Lei Jiao
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical College, No. 88 Healthy Road, Weihui, 453100, Henan, People's Republic of China
| | - Wenjie Miao
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical College, No. 88 Healthy Road, Weihui, 453100, Henan, People's Republic of China
| | - Qianqian Jin
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical College, No. 88 Healthy Road, Weihui, 453100, Henan, People's Republic of China
| | - Ruixue Li
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical College, No. 88 Healthy Road, Weihui, 453100, Henan, People's Republic of China
| | - Ping Chen
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical College, No. 88 Healthy Road, Weihui, 453100, Henan, People's Republic of China
| | - Haixu Shi
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical College, No. 88 Healthy Road, Weihui, 453100, Henan, People's Republic of China
| | - Wenfa Yu
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical College, No. 88 Healthy Road, Weihui, 453100, Henan, People's Republic of China.
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14
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Taguchi H, Xie Y, Horikoshi N, Maehara K, Harada A, Nogami J, Sato K, Arimura Y, Osakabe A, Kujirai T, Iwasaki T, Semba Y, Tachibana T, Kimura H, Ohkawa Y, Kurumizaka H. Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8. Biochemistry 2017; 56:2184-2196. [DOI: 10.1021/acs.biochem.6b01098] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroyuki Taguchi
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yan Xie
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Naoki Horikoshi
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical
Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical
Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582, Japan
| | - Jumpei Nogami
- Division of Transcriptomics, Medical
Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582, Japan
| | - Koichi Sato
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yasuhiro Arimura
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Akihisa Osakabe
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Tomoya Kujirai
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Takeshi Iwasaki
- Division of Transcriptomics, Medical
Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuichiro Semba
- Division of Transcriptomics, Medical
Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582, Japan
| | - Taro Tachibana
- Department of Bioengineering, Graduate
School of Engineering, Osaka City University, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Hiroshi Kimura
- Cell Biology Unit,
Institute of
Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical
Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi,
Higashi-ku, Fukuoka 812-8582, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural
Biology,
Graduate School of Advanced Science and Engineering, Research Institute
for Science and Engineering, and Institute for Medical-oriented Structural
Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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15
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Canonical and Variant Forms of Histone H3 Are Deposited onto the Human Cytomegalovirus Genome during Lytic and Latent Infections. J Virol 2016; 90:10309-10320. [PMID: 27605676 DOI: 10.1128/jvi.01220-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/30/2016] [Indexed: 01/16/2023] Open
Abstract
Chromatin is the nucleoprotein complex that protects and compacts eukaryotic genomes. It is responsible for a large part of the epigenetic control of transcription. The genomes of DNA viruses such as human cytomegalovirus (HCMV) are devoid of histones within virions but are chromatinized and epigenetically regulated following delivery to the host cell nucleus. How chromatin is initially assembled on viral genomes and which variant forms of the core histone proteins are deposited are incompletely understood. We monitored the deposition of both ectopically expressed and endogenous histones H3.1 and H3.2 (collectively, H3.1/2) and H3.3 during lytic and latent HCMV infections. Here, we show that they are deposited on HCMV genomes during lytic and latent infections, suggesting similar mechanisms of viral chromatin assembly during the different infection types and indicating that both canonical and variant core histones may be important modulators of infecting viral genomes. We further show that association of both H3.1/2 and H3.3 occurs independent of viral DNA synthesis or de novo viral gene expression, implicating cellular factors and/or virion components in the formation of chromatin on virion-delivered genomes during both lytic and latent infections. IMPORTANCE It is well established that infecting herpesvirus genomes are chromatinized upon entry into the host cell nucleus. Why or how this occurs is a mystery. It is important to know why they are chromatinized in order to better understand cellular pathogen recognition (DNA sensing) pathways and viral fate determinations (lytic or latent) and to anticipate how artificially modulating chromatinization may impact viral infections. It is important to know how the genomes are chromatinized in order to potentially modulate the process for therapeutic effect. Our work showing that HCMV genomes are loaded with canonical and variant H3 histones during both lytic and latent infections strengthens the hypothesis that chromatinization pathways are similar between the two infection types, implicates virion or cellular factors in this process, and exposes the possibility that histone variants, in addition to posttranslational modification, may impact viral gene expression. These revelations are important to understanding and intelligently intervening in herpesvirus infections.
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16
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Fesler A, Xu X, Zheng X, Li X, Jiang J, Russo JJ, Ju J. Identification of miR-215 mediated targets/pathways via translational immunoprecipitation expression analysis (TrIP-chip). Oncotarget 2016; 6:24463-73. [PMID: 26287603 PMCID: PMC4695198 DOI: 10.18632/oncotarget.4425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/31/2015] [Indexed: 01/28/2023] Open
Abstract
Steady state mRNA expression profiling can identify the majority of miRNA targets. However, some translationally repressed miRNA targets are missed and thus not considered for functional validation. Therefore, analysis of mRNA translation can enhance miRNA target identification for functional studies. We have applied a unique approach to identify miRNA targets in a small number of cells. Actively translating mRNAs are associated with polyribosomes and newly synthesized peptide chains are associated with molecular chaperones such as HSP70s. Affinity capture beads were used to capture HSP70 chaperones associated with polyribosome complexes. The isolated actively translating mRNAs were used for high throughput expression profiling analysis. miR-215 is an important miRNA in colorectal cancer and loss of miR-215 is significantly associated with prognosis of this disease. miR-215 suppresses the expression of several key targets. We utilized the affinity capture approach to isolate miR-215 mediated mRNA target transcripts. This approach provides a unique way to identify targets regulated by non-coding RNAs and RNA binding proteins from a small number of cells.
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Affiliation(s)
- Andrew Fesler
- Department of Pathology, Stony Brook University, School of Medicine, Stony Brook, NY, USA
| | - Xiao Xu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiao Zheng
- The Third Affiliated Hospital, Soochow University, China
| | - Xiaodong Li
- The Third Affiliated Hospital, Soochow University, China
| | - Jingting Jiang
- The Third Affiliated Hospital, Soochow University, China
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Department of Chemical Engineering, Columbia University, New York, NY, USA
| | - Jingfang Ju
- Department of Pathology, Stony Brook University, School of Medicine, Stony Brook, NY, USA
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17
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Lulla RR, Saratsis AM, Hashizume R. Mutations in chromatin machinery and pediatric high-grade glioma. SCIENCE ADVANCES 2016; 2:e1501354. [PMID: 27034984 PMCID: PMC4803494 DOI: 10.1126/sciadv.1501354] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/04/2016] [Indexed: 05/24/2023]
Abstract
Pediatric central nervous system tumors are the most common solid tumor of childhood. Of these, approximately one-third are gliomas that exhibit diverse biological behaviors in the unique context of the developing nervous system. Although low-grade gliomas predominate and have favorable outcomes, up to 20% of pediatric gliomas are high-grade. These tumors are a major contributor to cancer-related morbidity and mortality in infants, children, and adolescents, with long-term survival rates of only 10 to 15%. The recent discovery of somatic oncogenic mutations affecting chromatin regulation in pediatric high-grade glioma has markedly improved our understanding of disease pathogenesis, and these findings have stimulated the development of novel therapeutic approaches targeting epigenetic regulators for disease treatment. We review the current perspective on pediatric high-grade glioma genetics and epigenetics, and discuss the emerging and experimental therapeutics targeting the unique molecular abnormalities present in these deadly childhood brain tumors.
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Affiliation(s)
- Rishi R. Lulla
- Department of Pediatrics—Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Amanda Muhs Saratsis
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rintaro Hashizume
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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18
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Tissue-specific expression of histone H3 variants diversified after species separation. Epigenetics Chromatin 2015; 8:35. [PMID: 26388943 PMCID: PMC4574566 DOI: 10.1186/s13072-015-0027-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/27/2015] [Indexed: 12/02/2022] Open
Abstract
Background The selective incorporation of appropriate histone variants into chromatin is critical for the regulation of genome function. Although many histone variants have been identified, a complete list has not been compiled. Results We screened mouse, rat and human genomes by in silico hybridization using canonical histone sequences. In the mouse genome, we identified 14 uncharacterized H3 genes, among which 13 are similar to H3.3 and do not have human or rat counterparts, and one is similar to human testis-specific H3 variant, H3T/H3.4, and had a rat paralog. Although some of these genes were previously annotated as pseudogenes, their tissue-specific expression was confirmed by sequencing the 3′-UTR regions of the transcripts. Certain new variants were also detected at the protein level by mass spectrometry. When expressed as GFP-tagged versions in mouse C2C12 cells, some variants were stably incorporated into chromatin and the genome-wide distributions of most variants were similar to that of H3.3. Moreover, forced expression of H3 variants in chromatin resulted in alternate gene expression patterns after cell differentiation. Conclusions We comprehensively identified and characterized novel mouse H3 variant genes that encoded highly conserved amino acid sequences compared to known histone H3. We speculated that the diversity of H3 variants acquired after species separation played a role in regulating tissue-specific gene expression in individual species. Their biological relevance and evolutionary aspect involving pseudogene diversification will be addressed by further functional analysis. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0027-3) contains supplementary material, which is available to authorized users.
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19
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Buczkowicz P, Hawkins C. Pathology, Molecular Genetics, and Epigenetics of Diffuse Intrinsic Pontine Glioma. Front Oncol 2015; 5:147. [PMID: 26175967 PMCID: PMC4485076 DOI: 10.3389/fonc.2015.00147] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/16/2015] [Indexed: 11/13/2022] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is a devastating pediatric brain cancer with no effective therapy. Histological similarity of DIPG to supratentorial high-grade astrocytomas of adults has led to assumptions that these entities possess similar underlying molecular properties and therefore similar therapeutic responses to standard therapies. The failure of all clinical trials in the last 30 years to improve DIPG patient outcome has suggested otherwise. Recent studies employing next-generation sequencing and microarray technologies have provided a breadth of evidence highlighting the unique molecular genetics and epigenetics of this cancer, distinguishing it from both adult and pediatric cerebral high-grade astrocytomas. This review describes the most common molecular genetic and epigenetic signatures of DIPG in the context of molecular subgroups and histopathological diagnosis, including this tumor entity's unique mutational landscape, copy number alterations, and structural variants, as well as epigenetic changes on the global DNA and histone levels. The increased knowledge of DIPG biology and histopathology has opened doors to new diagnostic and therapeutic avenues.
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Affiliation(s)
- Pawel Buczkowicz
- Division of Pathology, The Hospital for Sick Children , Toronto, ON , Canada ; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children , Toronto, ON , Canada
| | - Cynthia Hawkins
- Division of Pathology, The Hospital for Sick Children , Toronto, ON , Canada ; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children , Toronto, ON , Canada ; Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto , Toronto, ON , Canada
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20
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Abstract
Schizophrenia is a major psychiatric disorder that lacks a unifying neuropathology, while currently available pharmacological treatments provide only limited benefits to many patients. This review will discuss how the field of neuroepigenetics could contribute to advancements of the existing knowledge on the neurobiology and treatment of psychosis. Genome-scale mapping of DMA methylation, histone modifications and variants, and chromosomal loopings for promoter-enhancer interactions and other epigenetic determinants of genome organization and function are likely to provide important clues about mechanisms contributing to dysregulated expression of synaptic and metabolic genes in schizophrenia brain, including the potential links to the underlying genetic risk architecture and environmental exposures. In addition, studies in animal models are providing a rapidly increasing list of chromatin-regulatory mechanisms with significant effects on cognition and complex behaviors, thereby pointing to the therapeutic potential of epigenetic drug targets in the nervous system.
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Affiliation(s)
- Schahram Akbarian
- Department of Psychiatry, Friedman Brain Institute Icahn School of Medicine at Mount Sinai, New York, USA
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21
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Zierhut C, Jenness C, Kimura H, Funabiki H. Nucleosomal regulation of chromatin composition and nuclear assembly revealed by histone depletion. Nat Struct Mol Biol 2014; 21:617-25. [PMID: 24952593 PMCID: PMC4082469 DOI: 10.1038/nsmb.2845] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 05/23/2014] [Indexed: 12/13/2022]
Abstract
Nucleosomes are the fundamental unit of chromatin, but analysis of transcription-independent nucleosome functions has been complicated by the gene-expression changes resulting from histone manipulation. Here we solve this dilemma by developing Xenopus laevis egg extracts deficient for nucleosome formation and by analyzing the proteomic landscape and behavior of nucleosomal chromatin and nucleosome-free DNA. We show that although nucleosome-free DNA can recruit nuclear-envelope membranes, nucleosomes are required for spindle assembly and for formation of the lamina and of nuclear pore complexes (NPCs). We show that, in addition to the Ran G-nucleotide exchange factor RCC1, ELYS, the initiator of NPC formation, fails to associate with naked DNA but directly binds histone H2A-H2B dimers and nucleosomes. Tethering ELYS and RCC1 to DNA bypasses the requirement for nucleosomes in NPC formation in a synergistic manner. Thus, the minimal essential function of nucleosomes in NPC formation is to recruit RCC1 and ELYS.
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Affiliation(s)
- Christian Zierhut
- Laboratory of Chromosome and Cell Biology, Rockefeller University, New York, New York, USA
| | - Christopher Jenness
- Laboratory of Chromosome and Cell Biology, Rockefeller University, New York, New York, USA
| | - Hiroshi Kimura
- 1] Graduate School of Frontier Biosciences, Osaka University, Suita, Japan. [2] Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, Suita, Japan
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, Rockefeller University, New York, New York, USA
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22
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Abstract
Comprehensive sequencing of benign and malignant tumors has recently uncovered new driver mutations in childhood tumors. A new report now describes frequent histone H3.3 alterations in chondroblastoma and giant cell tumor of bone, emphasizing the importance of this histone variant in pediatric cancers.
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Affiliation(s)
- Anders M Lindroth
- Division of Epigenomics and Cancer Risk Factors at the German Cancer Research Center (DKFZ), Heidelberg, Germany
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23
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Hasan A, Mitchell A, Schneider A, Halene T, Akbarian S. Epigenetic dysregulation in schizophrenia: molecular and clinical aspects of histone deacetylase inhibitors. Eur Arch Psychiatry Clin Neurosci 2013; 263:273-84. [PMID: 23381549 DOI: 10.1007/s00406-013-0395-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Accepted: 01/18/2013] [Indexed: 12/22/2022]
Abstract
Notwithstanding the considerable advances in the treatment options for schizophrenia, the cognitive symptoms in particular are not receptive to antipsychotic treatment and considered one of the main predictors for poor social and functional outcome of the disease. Recent findings in preclinical model systems indicate that epigenetic modulation might emerge as a promising target for the treatment of cognitive disorders. The aim of this review is to introduce some of the principles of chromatin biology to the reader and to discuss a possible role in the neurobiology and pathophysiology of schizophrenia. We will discuss potential epigenetic targets for drug therapy, including histone deacetylase inhibitors (HDACi). In a second part, conceptual and practical challenges associated with clinical trials of chromatin-modifying drugs in psychiatric patient populations are discussed, including safety profiles, the potential for adverse effects and general issues revolving around pharmacokinetics and pharmacodynamics. Additional investigations are required in order to fully evaluate the potential of HDACi and similar "epigenetic therapies" as novel treatment options for schizophrenia and other psychotic disease.
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Affiliation(s)
- Alkomiet Hasan
- Deparment of Psychiatry and Psychotherapy, Ludwig-Maximilians-University, Nussbaumstr. 7, 80336 Munich, Germany.
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Venneti S, Garimella MT, Sullivan LM, Martinez D, Huse JT, Heguy A, Santi M, Thompson CB, Judkins AR. Evaluation of histone 3 lysine 27 trimethylation (H3K27me3) and enhancer of Zest 2 (EZH2) in pediatric glial and glioneuronal tumors shows decreased H3K27me3 in H3F3A K27M mutant glioblastomas. Brain Pathol 2013; 23:558-64. [PMID: 23414300 DOI: 10.1111/bpa.12042] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 01/29/2013] [Indexed: 12/12/2022] Open
Abstract
H3F3A mutations are seen in ∼30% of pediatric glioblastoma (GBMs) and involve either the lysine residue at position 27 (K27M) or glycine at position 34 (G34R/V). Sixteen genes encode histone H3, each variant differing in only a few amino acids. Therefore, how mutations in a single H3 gene contribute to carcinogenesis is unknown. H3F3A K27M mutations are predicted to alter methylation of H3K27. H3K27me3 is a repressive mark critical to stem cell maintenance and is mediated by EZH2, a member of the polycomb-group (PcG) family. We evaluated H3K27me3 and EZH2 expression using immunohistochemistry in 76 pediatric brain tumors. H3K27me3 was lowered/absent in tumor cells but preserved in endothelial cells and infiltrating lymphocytes in six out of 20 GBMs. H3K27me3 showed strong immunoreactivity in all other tumor subtypes. Sequencing of GBMs showed H3F3A K27M mutations in all six cases with lowered/absent H3K27me3. EZH2 expression was high in GBMs, but absent/focal in other tumors. However, no significant differences in EZH2 expression were observed between H3F3A K27M mutant and wild type GBMs, suggesting that EZH2 mediated trimethylation of H3K27 is inhibited in GBM harboring K27M mutations. Our results indicate that H3F3A K27M mutant GBMs show decreased H3K27me3 that may be of both diagnostic and biological relevance.
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Affiliation(s)
- Sriram Venneti
- Cancer biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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Abstract
Many cellular constituents in the human brain permanently exit from the cell cycle during pre- or early postnatal development, but little is known about epigenetic regulation of neuronal and glial epigenomes during maturation and aging, including changes in mood and psychosis spectrum disorders and other cognitive or emotional disease. Here, we summarize the current knowledge base as it pertains to genome organization in the human brain, including the regulation of DNA cytosine methylation and hydroxymethylation, and a subset of (altogether >100) residue-specific histone modifications associated with gene expression, and silencing and various other functional chromatin states. We propose that high-resolution mapping of epigenetic markings in postmortem brain tissue or neural cultures derived from induced pluripotent cells (iPS), in conjunction with transcriptome profiling and whole-genome sequencing, will increasingly be used to define the molecular pathology of specific cases diagnosed with depression, schizophrenia, autism, or other major psychiatric disease. We predict that these highly integrative explorations of genome organization and function will provide an important alternative to conventional approaches in human brain studies, which mainly are aimed at uncovering group effects by diagnosis but generally face limitations because of cohort size.
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Delbarre E, Ivanauskiene K, Küntziger T, Collas P. DAXX-dependent supply of soluble (H3.3-H4) dimers to PML bodies pending deposition into chromatin. Genome Res 2012; 23:440-51. [PMID: 23222847 PMCID: PMC3589533 DOI: 10.1101/gr.142703.112] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Replication-independent chromatin deposition of histone variant H3.3 is mediated by several chaperones. We report a multistep targeting of newly synthesized epitope-tagged H3.3 to chromatin via PML bodies. H3.3 is recruited to PML bodies in a DAXX-dependent manner, a process facilitated by ASF1A. DAXX is required for enrichment of ATRX, but not ASF1A or HIRA, with PML. Nonetheless, the chaperones colocalize with H3.3 at PML bodies and are found in one or more complexes with PML. Both DAXX and PML are necessary to prevent accumulation of a soluble, nonincorporated pool of H3.3. H3.3 targeting to PML is enhanced with an (H3.3–H4)2 tetramerization mutant of H3.3, suggesting H3.3 recruitment to PML as an (H3.3–H4) dimer rather than as a tetramer. Our data support a model of DAXX-mediated recruitment of (H3.3–H4) dimers to PML bodies, which may function as triage centers for H3.3 deposition into chromatin by distinct chaperones.
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Affiliation(s)
- Erwan Delbarre
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
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