1
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Buquicchio FA, Fonseca R, Yan PK, Wang F, Evrard M, Obers A, Gutierrez JC, Raposo CJ, Belk JA, Daniel B, Zareie P, Yost KE, Qi Y, Yin Y, Nico KF, Tierney FM, Howitt MR, Lareau CA, Satpathy AT, Mackay LK. Distinct epigenomic landscapes underlie tissue-specific memory T cell differentiation. Immunity 2024; 57:2202-2215.e6. [PMID: 39043184 DOI: 10.1016/j.immuni.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/07/2024] [Accepted: 06/27/2024] [Indexed: 07/25/2024]
Abstract
The memory CD8+ T cell pool contains phenotypically and transcriptionally heterogeneous subsets with specialized functions and recirculation patterns. Here, we examined the epigenetic landscape of CD8+ T cells isolated from seven non-lymphoid organs across four distinct infection models, alongside their circulating T cell counterparts. Using single-cell transposase-accessible chromatin sequencing (scATAC-seq), we found that tissue-resident memory T (TRM) cells and circulating memory T (TCIRC) cells develop along distinct epigenetic trajectories. We identified organ-specific transcriptional regulators of TRM cell development, including FOSB, FOS, FOSL1, and BACH2, and defined an epigenetic signature common to TRM cells across organs. Finally, we found that although terminal TEX cells share accessible regulatory elements with TRM cells, they are defined by TEX-specific epigenetic features absent from TRM cells. Together, this comprehensive data resource shows that TRM cell development is accompanied by dynamic transcriptome alterations and chromatin accessibility changes that direct tissue-adapted and functionally distinct T cell states.
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Affiliation(s)
- Frank A Buquicchio
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Raissa Fonseca
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Patrick K Yan
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Fangyi Wang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Maximilien Evrard
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Andreas Obers
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jacob C Gutierrez
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Colin J Raposo
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Julia A Belk
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Pirooz Zareie
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Kathryn E Yost
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Yajie Yin
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Katherine F Nico
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Flora M Tierney
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Michael R Howitt
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA
| | - Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA; Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA 94129, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Program in Immunology, Stanford University, Stanford, CA 94304, USA; Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA 94129, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.
| | - Laura K Mackay
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
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2
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Xu Y, Liu W, Jiang X, Li J, Liu Q, Su F, Ruan S, Zhang Z, Tao F. Regulation of hPCL3 isoforms' ubiquitination by TRIM21 in non-small cell lung cancer progression. Life Sci Alliance 2023; 6:e202302060. [PMID: 37507137 PMCID: PMC10387491 DOI: 10.26508/lsa.202302060] [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: 03/26/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is the main subtype of lung cancer. The role of hPCL3 isoforms, hPCL3S and hPCL3L, remains ambiguous. This study examines the functional implications of these isoforms in NSCLC, using lung cancer cell lines A549 and NCI-H226c for in vivo and in vitro analyses. The results indicate that elevated expression of both hPCL3S and hPCL3L correlates with diminished overall survival, although only hPCL3S levels are augmented in clinical NSCLC specimens. Inhibition of either isoform leads to reduced cell proliferation, invasion, and migration, with hPCL3S knockdown displaying superior effectiveness. Moreover, the findings reveal that TRIM21 interacts with both isoforms and mediates hPCL3S degradation through K48-linked ubiquitination in NSCLC cells. Conversely, TRIM21 does not facilitate hPCL3L degradation, despite forming K63-linked polyubiquitin chains. These observations highlight the divergent roles of hPCL3 isoforms in NSCLC and underscore the potential therapeutic value of targeting hPCL3S.
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Affiliation(s)
- Ye Xu
- Department of Immunology and Microbiology, School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Wenhong Liu
- Department of Immunology and Microbiology, School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiawei Jiang
- Department of Immunology and Microbiology, School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Junfeng Li
- Department of Immunology and Microbiology, School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qingling Liu
- Department of Immunology and Microbiology, School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Fang Su
- Department of Medical Oncology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Shanming Ruan
- Department of Medical Oncology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhiqian Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Fangfang Tao
- Department of Immunology and Microbiology, School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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3
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Misetic H, Keddar MR, Jeannon JP, Ciccarelli FD. Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment. Genome Med 2023; 15:40. [PMID: 37277866 DOI: 10.1186/s13073-023-01197-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/25/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND The crosstalk between cancer and the tumour immune microenvironment (TIME) has attracted significant interest in the latest years because of its impact on cancer evolution and response to treatment. Despite this, cancer-specific tumour-TIME interactions and their mechanistic insights are still poorly understood. METHODS Here, we compute the significant interactions occurring between cancer-specific genetic drivers and five anti- and pro-tumour TIME features in 32 cancer types using Lasso regularised ordinal regression. Focusing on head and neck squamous cancer (HNSC), we rebuild the functional networks linking specific TIME driver alterations to the TIME state they associate with. RESULTS The 477 TIME drivers that we identify are multifunctional genes whose alterations are selected early in cancer evolution and recur across and within cancer types. Tumour suppressors and oncogenes have an opposite effect on the TIME and the overall anti-tumour TIME driver burden is predictive of response to immunotherapy. TIME driver alterations predict the immune profiles of HNSC molecular subtypes, and perturbations in keratinization, apoptosis and interferon signalling underpin specific driver-TIME interactions. CONCLUSIONS Overall, our study delivers a comprehensive resource of TIME drivers, gives mechanistic insights into their immune-regulatory role, and provides an additional framework for patient prioritisation to immunotherapy. The full list of TIME drivers and associated properties are available at http://www.network-cancer-genes.org .
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Affiliation(s)
- Hrvoje Misetic
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Mohamed Reda Keddar
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK
| | - Jean-Pierre Jeannon
- Department of Head & Neck Surgery, Great Maze Pond, Guy's Hospital, London, SE1 9RT, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE11UL, UK.
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4
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Ibarra IL, Ratnu VS, Gordillo L, Hwang I, Mariani L, Weinand K, Hammarén HM, Heck J, Bulyk ML, Savitski MM, Zaugg JB, Noh K. Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements. Mol Syst Biol 2022; 18:e10473. [PMID: 35996956 PMCID: PMC9396287 DOI: 10.15252/msb.202110473] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 12/30/2022] Open
Abstract
Neuronal stimulation induced by the brain-derived neurotrophic factor (BDNF) triggers gene expression, which is crucial for neuronal survival, differentiation, synaptic plasticity, memory formation, and neurocognitive health. However, its role in chromatin regulation is unclear. Here, using temporal profiling of chromatin accessibility and transcription in mouse primary cortical neurons upon either BDNF stimulation or depolarization (KCl), we identify features that define BDNF-specific chromatin-to-gene expression programs. Enhancer activation is an early event in the regulatory control of BDNF-treated neurons, where the bZIP motif-binding Fos protein pioneered chromatin opening and cooperated with co-regulatory transcription factors (Homeobox, EGRs, and CTCF) to induce transcription. Deleting cis-regulatory sequences affect BDNF-mediated Arc expression, a regulator of synaptic plasticity. BDNF-induced accessible regions are linked to preferential exon usage by neurodevelopmental disorder-related genes and the heritability of neuronal complex traits, which were validated in human iPSC-derived neurons. Thus, we provide a comprehensive view of BDNF-mediated genome regulatory features using comparative genomic approaches to dissect mammalian neuronal stimulation.
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Affiliation(s)
- Ignacio L Ibarra
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Faculty of BiosciencesCollaboration for Joint PhD Degree between EMBL and Heidelberg UniversityHeidelbergGermany
- Institute of Computational BiologyHelmholtz Center MunichOberschleißheimGermany
| | - Vikram S Ratnu
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Lucia Gordillo
- Faculty of BiosciencesCollaboration for Joint PhD Degree between EMBL and Heidelberg UniversityHeidelbergGermany
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - In‐Young Hwang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Luca Mariani
- Division of Genetics, Department of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMAUSA
| | - Kathryn Weinand
- Division of Genetics, Department of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMAUSA
| | - Henrik M Hammarén
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Jennifer Heck
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Martha L Bulyk
- Division of Genetics, Department of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMAUSA
- Department of PathologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMAUSA
| | - Mikhail M Savitski
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Kyung‐Min Noh
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
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5
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Abstract
Lamins interact with a host of nuclear membrane proteins, transcription factors, chromatin regulators, signaling molecules, splicing factors, and even chromatin itself to form a nuclear subcompartment, the nuclear lamina, that is involved in a variety of cellular processes such as the governance of nuclear integrity, nuclear positioning, mitosis, DNA repair, DNA replication, splicing, signaling, mechanotransduction and -sensation, transcriptional regulation, and genome organization. Lamins are the primary scaffold for this nuclear subcompartment, but interactions with lamin-associated peptides in the inner nuclear membrane are self-reinforcing and mutually required. Lamins also interact, directly and indirectly, with peripheral heterochromatin domains called lamina-associated domains (LADs) and help to regulate dynamic 3D genome organization and expression of developmentally regulated genes.
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Affiliation(s)
- Xianrong Wong
- Laboratory of Developmental and Regenerative Biology, Skin Research Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore 138648
| | - Ashley J Melendez-Perez
- Department of Biological Chemistry and Center for Epigenetics, Johns Hopkins University of Medicine, Baltimore, Maryland 21205, USA
| | - Karen L Reddy
- Department of Biological Chemistry and Center for Epigenetics, Johns Hopkins University of Medicine, Baltimore, Maryland 21205, USA
- Sidney Kimmel Cancer Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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6
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Park SH, Fong KW, Mong E, Martin MC, Schiltz GE, Yu J. Going beyond Polycomb: EZH2 functions in prostate cancer. Oncogene 2021; 40:5788-5798. [PMID: 34349243 PMCID: PMC8487936 DOI: 10.1038/s41388-021-01982-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023]
Abstract
The Polycomb group (PcG) protein Enhancer of Zeste Homolog 2 (EZH2) is one of the three core subunits of the Polycomb Repressive Complex 2 (PRC2). It harbors histone methyltransferase activity (MTase) that specifically catalyze histone 3 lysine 27 (H3K27) methylation on target gene promoters. As such, PRC2 are epigenetic silencers that play important roles in cellular identity and embryonic stem cell maintenance. In the past two decades, mounting evidence supports EZH2 mutations and/or over-expression in a wide array of hematological cancers and solid tumors, including prostate cancer. Further, EZH2 is among the most upregulated genes in neuroendocrine prostate cancers, which become abundant due to the clinical use of high-affinity androgen receptor pathway inhibitors. While numerous studies have reported epigenetic functions of EZH2 that inhibit tumor suppressor genes and promote tumorigenesis, discordance between EZH2 and H3K27 methylation has been reported. Further, enzymatic EZH2 inhibitors have shown limited efficacy in prostate cancer, warranting a more comprehensive understanding of EZH2 functions. Here we first review how canonical functions of EZH2 as a histone MTase are regulated and describe the various mechanisms of PRC2 recruitment to the chromatin. We further outline non-histone substrates of EZH2 and discuss post-translational modifications to EZH2 itself that may affect substrate preference. Lastly, we summarize non-canonical functions of EZH2, beyond its MTase activity and/or PRC2, as a transcriptional cofactor and discuss prospects of its therapeutic targeting in prostate cancer.
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Affiliation(s)
- Su H Park
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ka-Wing Fong
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Ezinne Mong
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - M Cynthia Martin
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Gary E Schiltz
- Department of Chemistry, Northwestern University, Evanston, IL, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Jindan Yu
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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7
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Assumpção ALFV, Fu G, Singh DK, Lu Z, Kuehnl AM, Welch R, Ong IM, Wen R, Pan X. A lineage-specific requirement for YY1 Polycomb Group protein function in early T cell development. Development 2021; 148:dev.197319. [PMID: 33766932 DOI: 10.1242/dev.197319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/12/2021] [Indexed: 01/22/2023]
Abstract
Yin Yang 1 (YY1) is a ubiquitous transcription factor and mammalian Polycomb Group protein (PcG) with important functions for regulating lymphocyte development and stem cell self-renewal. YY1 mediates stable PcG-dependent transcriptional repression via recruitment of PcG proteins that result in histone modifications. Many questions remain unanswered regarding how cell- and tissue-specificity is achieved by PcG proteins. Here, we demonstrate that a conditional knockout of Yy1 in the hematopoietic system results in an early T cell developmental blockage at the double negative (DN) 1 stage with reduced Notch1 signaling. There is a lineage-specific requirement for YY1 PcG function. YY1 PcG domain is required for T and B cell development but not necessary for myeloid cells. YY1 functions in early T cell development are multicomponent and involve both PcG-dependent and -independent regulations. Although YY1 promotes early T cell survival through its PcG function, its function to promote the DN1-to-DN2 transition and Notch1 expression and signaling is independent of its PcG function. Our results reveal how a ubiquitously expressed PcG protein mediates lineage-specific and context-specific functions to control early T cell development.
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Affiliation(s)
- Anna L F V Assumpção
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
| | - Guoping Fu
- Versiti, Blood Research Institute, 8701 Watertown Plank Road, Milwaukee, WI 53223, USA
| | - Deependra K Singh
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
| | - Zhanping Lu
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
| | - Ashley M Kuehnl
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
| | - Rene Welch
- Department of Obstetrics and Gynecology, University of Wisconsin School of Medicine and Public Health, 750 Highland Ave, Madison, WI 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, 610 Walnut St, Madison, WI 53726, USA
| | - Irene M Ong
- Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA.,Department of Obstetrics and Gynecology, University of Wisconsin School of Medicine and Public Health, 750 Highland Ave, Madison, WI 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, 610 Walnut St, Madison, WI 53726, USA
| | - Renren Wen
- Versiti, Blood Research Institute, 8701 Watertown Plank Road, Milwaukee, WI 53223, USA
| | - Xuan Pan
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
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8
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Abdul-Aziz D, Hathiramani N, Phung L, Sykopetrites V, Edge ASB. HIC1 Represses Atoh1 Transcription and Hair Cell Differentiation in the Cochlea. Stem Cell Reports 2021; 16:797-809. [PMID: 33770497 PMCID: PMC8072069 DOI: 10.1016/j.stemcr.2021.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 11/23/2022] Open
Abstract
Across species, expression of the basic helix-loop-helix transcription factor ATOH1 promotes differentiation of cochlear supporting cells to sensory hair cells required for hearing. In mammals, this process is limited to development, whereas nonmammalian vertebrates can also regenerate hair cells after injury. The mechanistic basis for this difference is not fully understood. Hypermethylated in cancer 1 (HIC1) is a transcriptional repressor known to inhibit Atoh1 in the cerebellum. We therefore investigated its potential role in cochlear hair cell differentiation. We find that Hic1 is expressed throughout the postnatal murine cochlear sensory epithelium. In cochlear organoids, Hic1 knockdown induces Atoh1 expression and promotes hair cell differentiation, while Hic1 overexpression hinders differentiation. Wild-type HIC1, but not the DNA-binding mutant C521S, suppresses activity of the Atoh1 autoregulatory enhancer and blocks its responsiveness to β-catenin activation. Our findings reveal the importance of HIC1 repression of Atoh1 in the cochlea, which may be targeted to promote hair cell regeneration.
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Affiliation(s)
- Dunia Abdul-Aziz
- Department of Otolaryngology, Harvard Medical School, Boston, MA, USA; Eaton Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA, USA
| | | | - Lauren Phung
- Eaton Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA, USA
| | - Vittoria Sykopetrites
- Eaton Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA, USA; Università degli Studi di Milano, Milan, Italy
| | - Albert S B Edge
- Department of Otolaryngology, Harvard Medical School, Boston, MA, USA; Eaton Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA.
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9
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Ray H, Chang C. The transcription factor Hypermethylated in Cancer 1 (Hic1) regulates neural crest migration via interaction with Wnt signaling. Dev Biol 2020; 463:169-181. [PMID: 32502469 DOI: 10.1016/j.ydbio.2020.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 01/20/2023]
Abstract
The transcription factor Hypermethylated in Cancer 1 (HIC1) is associated with both tumorigenesis and the complex human developmental disorder Miller-Dieker Syndrome. While many studies have characterized HIC1 as a tumor suppressor, HIC1 function in development is less understood. Loss-of-function mouse alleles show embryonic lethality accompanied with developmental defects, including craniofacial abnormalities that are reminiscent of human Miller-Dieker Syndrome patients. However, the tissue origin of the defects has not been reported. In this study, we use the power of the Xenopus laevis model system to explore Hic1 function in early development. We show that hic1 mRNA is expressed throughout early Xenopus development and has a spatial distribution within the neural plate border and in migrating neural crest cells in branchial arches. Targeted manipulation of hic1 levels in the dorsal ectoderm that gives rise to neural and neural crest tissues reveals that both overexpression and knockdown of hic1 result in craniofacial defects with malformations of the craniofacial cartilages. Neural crest specification is not affected by altered hic1 levels, but migration of the cranial neural crest is impaired both in vivo and in tissue explants. Mechanistically, we find that Hic1 regulates cadherin expression profiles and canonical Wnt signaling. Taken together, these results identify Hic1 as a novel regulator of the canonical Wnt pathway during neural crest migration.
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Affiliation(s)
- Heather Ray
- Dept. of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, MCLM 338, 1918 University Dr. Birmingham, AL, 35294, USA.
| | - Chenbei Chang
- Dept. of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, MCLM 338, 1918 University Dr. Birmingham, AL, 35294, USA
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10
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Wong X, Stewart CL. The Laminopathies and the Insights They Provide into the Structural and Functional Organization of the Nucleus. Annu Rev Genomics Hum Genet 2020; 21:263-288. [PMID: 32428417 DOI: 10.1146/annurev-genom-121219-083616] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In recent years, our perspective on the cell nucleus has evolved from the view that it is a passive but permeable storage organelle housing the cell's genetic material to an understanding that it is in fact a highly organized, integrative, and dynamic regulatory hub. In particular, the subcompartment at the nuclear periphery, comprising the nuclear envelope and the underlying lamina, is now known to be a critical nexus in the regulation of chromatin organization, transcriptional output, biochemical and mechanosignaling pathways, and, more recently, cytoskeletal organization. We review the various functional roles of the nuclear periphery and their deregulation in diseases of the nuclear envelope, specifically the laminopathies, which, despite their rarity, provide insights into contemporary health-care issues.
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Affiliation(s)
- Xianrong Wong
- Regenerative and Developmental Biology Group, Institute of Medical Biology, Singapore 138648; ,
| | - Colin L Stewart
- Regenerative and Developmental Biology Group, Institute of Medical Biology, Singapore 138648; ,
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11
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Abdelfettah S, Boulay G, Dubuissez M, Spruyt N, Garcia SP, Rengarajan S, Loison I, Leroy X, Rivera MN, Leprince D. hPCL3S promotes proliferation and migration of androgen-independent prostate cancer cells. Oncotarget 2020; 11:1051-1074. [PMID: 32256978 PMCID: PMC7105160 DOI: 10.18632/oncotarget.27511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) allows the deposition of H3K27me3. PRC2 facultative subunits modulate its activity and recruitment such as hPCL3/PHF19, a human ortholog of Drosophila Polycomb-like protein (PCL). These proteins contain a TUDOR domain binding H3K36me3, two PHD domains and a “Winged-helix” domain involved in GC-rich DNA binding. The human PCL3 locus encodes the full-length hPCL3L protein and a shorter isoform, hPCL3S containing the TUDOR and PHD1 domains only. In this study, we demonstrated by RT-qPCR analyses of 25 prostate tumors that hPCL3S is frequently up-regulated. In addition, hPCL3S is overexpressed in the androgen-independent DU145 and PC3 cells, but not in the androgen-dependent LNCaP cells. hPCL3S knockdown decreased the proliferation and migration of DU145 and PC3 whereas its forced expression into LNCaP increased these properties. A mutant hPCL3S unable to bind H3K36me3 (TUDOR-W50A) increased proliferation and migration of LNCaP similarly to wt hPCL3S whereas inactivation of its PHD1 domain decreased proliferation. These effects partially relied on the up-regulation of genes known to be important for the proliferation and/or migration of prostate cancer cells such as S100A16, PlexinA2, and Spondin1. Collectively, our results suggest hPCL3S as a new potential therapeutic target in castration resistant prostate cancers.
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Affiliation(s)
- Souhila Abdelfettah
- University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Gaylor Boulay
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Marion Dubuissez
- Present Address: Maisonneuve-Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 3W5, Canada
| | - Nathalie Spruyt
- University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Sara P Garcia
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Shruthi Rengarajan
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Ingrid Loison
- University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Xavier Leroy
- Department of Pathology, University de Lille, CHU de Lille, F-59000 Lille, France
| | - Miguel N Rivera
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Dominique Leprince
- University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
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12
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Jain P, Ballare C, Blanco E, Vizan P, Di Croce L. PHF19 mediated regulation of proliferation and invasiveness in prostate cancer cells. eLife 2020; 9:51373. [PMID: 32155117 PMCID: PMC7064337 DOI: 10.7554/elife.51373] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
The Polycomb-like protein PHF19/PCL3 associates with PRC2 and mediates its recruitment to chromatin in embryonic stem cells. PHF19 is also overexpressed in many cancers. However, neither PHF19 targets nor misregulated pathways involving PHF19 are known. Here, we investigate the role of PHF19 in prostate cancer cells. We find that PHF19 interacts with PRC2 and binds to PRC2 targets on chromatin. PHF19 target genes are involved in proliferation, differentiation, angiogenesis, and extracellular matrix organization. Depletion of PHF19 triggers an increase in MTF2/PCL2 chromatin recruitment, with a genome-wide gain in PRC2 occupancy and H3K27me3 deposition. Transcriptome analysis shows that PHF19 loss promotes deregulation of key genes involved in growth, metastasis, invasion, and of factors that stimulate blood vessels formation. Consistent with this, PHF19 silencing reduces cell proliferation, while promotes invasive growth and angiogenesis. Our findings reveal a role for PHF19 in controlling the balance between cell proliferation and invasiveness in prostate cancer.
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Affiliation(s)
- Payal Jain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Cecilia Ballare
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Pedro Vizan
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
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13
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Yang MH, Zhao L, Wang L, Ou-Yang W, Hu SS, Li WL, Ai ML, Wang YQ, Han Y, Li TT, Ding YQ, Wang S. Nuclear lncRNA HOXD-AS1 suppresses colorectal carcinoma growth and metastasis via inhibiting HOXD3-induced integrin β3 transcriptional activating and MAPK/AKT signalling. Mol Cancer 2019; 18:31. [PMID: 30823921 PMCID: PMC6397497 DOI: 10.1186/s12943-019-0955-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/06/2019] [Indexed: 02/06/2023] Open
Abstract
Background Long noncoding RNAs (lncRNAs) have been indicated to play critical roles in cancer development and progression. LncRNA HOXD cluster antisense RNA1 (HOXD-AS1) has recently been found to be dysregulated in several cancers. However, the expression levels, cellular localization, precise function and mechanism of HOXD-AS1 in colorectal carcinoma (CRC) are largely unknown. Methods Real-time PCR and in situ hybridization were used to detect the expression of HOXD-AS1 in CRC tissue samples and cell lines. Gain- and loss-of-function experiments were performed to investigate the biological roles of HOXD-AS1 in CRC cell line. RNA pull down, RNA immunoprecipitation and chromatin immunoprecipitation assays were conducted to investigate the mechanisms underlying the functions of HOXD-AS1 in CRC. Results We observed that HOXD-AS1 was located in the nucleus of CRC cells and that nuclear HOXD-AS1 was downregulated in most CRC specimens and cell lines. Lower levels of nuclear HOXD-AS1 expression were associated with poor outcomes of CRC patients. HOXD-AS1 downregulation enhanced proliferation and migration of CRC cells in vitro and facilitated CRC tumourigenesis and metastasis in vivo. Mechanistic investigations revealed that HOXD-AS1 could suppress HOXD3 transcription by recruiting PRC2 to induce the accumulation of the repressive marker H3K27me3 at the HOXD3 promoter. Subsequently, HOXD3, as a transcriptional activator, promoted Integrin β3 transcription, thereby activating the MAPK/AKT signalling pathways. Conclusion Our results reveal a previously unrecognized HOXD-AS1-HOXD3-Integrin β3 regulatory axis involving in epigenetic and transcriptional regulation constitutes to CRC carcinogenesis and progression. Electronic supplementary material The online version of this article (10.1186/s12943-019-0955-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min-Hui Yang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Li Zhao
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, Ghuangzhou, 510150, China
| | - Lan Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Wen Ou-Yang
- The Second Clinical Medical College, Zhujang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Sha-Sha Hu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Wen-Lu Li
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Mei-Ling Ai
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yi-Qing Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yue Han
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ting-Ting Li
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yan-Qing Ding
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Shuang Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. .,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
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14
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Decourcelle A, Leprince D, Dehennaut V. Regulation of Polycomb Repression by O-GlcNAcylation: Linking Nutrition to Epigenetic Reprogramming in Embryonic Development and Cancer. Front Endocrinol (Lausanne) 2019; 10:117. [PMID: 30873122 PMCID: PMC6400832 DOI: 10.3389/fendo.2019.00117] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/08/2019] [Indexed: 11/25/2022] Open
Abstract
Epigenetic modifications are major actors of early embryogenesis and carcinogenesis and are sensitive to nutritional environment. In recent years, the nutritional sensor O-GlcNAcylation has been recognized as a key regulator of chromatin remodeling. In this review, we summarize and discuss recent clues that OGT and O-GlcNAcylation intimately regulate the functions of the Polycomb group proteins at different levels especially during Drosophila melanogaster embryonic development and in human cancer cell lines. These observations define an additional connection between nutrition and epigenetic reprogramming associated to embryonic development and cancer.
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15
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Luo Y, He J, Xu X, Sun MA, Wu X, Lu X, Xie H. Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells. PLoS Comput Biol 2018; 14:e1006034. [PMID: 29561833 PMCID: PMC5862410 DOI: 10.1371/journal.pcbi.1006034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 02/09/2018] [Indexed: 12/29/2022] Open
Abstract
Embryonic stem cells (ESCs) consist of a population of self-renewing cells displaying extensive phenotypic and functional heterogeneity. Research towards the understanding of the epigenetic mechanisms underlying the heterogeneity among ESCs is still in its initial stage. Key issues, such as how to identify cell-subset specifically methylated loci and how to interpret the biological meanings of methylation variations remain largely unexplored. To fill in the research gap, we implemented a computational pipeline to analyze single-cell methylome and to perform an integrative analysis with single-cell transcriptome data. According to the origins of variation in DNA methylation, we determined the genomic loci associated with allelic-specific methylation or asymmetric DNA methylation, and explored a beta mixture model to infer the genomic loci exhibiting cell-subset specific methylation (CSM). We observed that the putative CSM loci in ESCs are significantly enriched in CpG island (CGI) shelves and regions with histone marks for promoter and enhancer, and the genes hosting putative CSM loci show wide-ranging expression among ESCs. More interestingly, the putative CSM loci may be clustered into co-methylated modules enriching the binding motifs of distinct sets of transcription factors. Taken together, our study provided a novel tool to explore single-cell methylome and transcriptome to reveal the underlying transcriptional regulatory networks associated with epigenetic heterogeneity of ESCs. DNA methylation is an epigenetic mark with covalent modification that occurs directly on genetic material. In vertebrates, the most common form of DNA methylation is 5-methylcytosine (5-mC) at which a methyl group (CH3) is attached to the cytosine nucleotide, especially in the context of CpG dinucleotide. DNA methylation has important regulatory roles in a broad range of biological processes and diseases, such as embryonic stem cells (ESCs) differentiation and development. ESC populations can be strikingly heterogeneous in DNA methylation. Emerging single-cell methods for capturing DNA methylation are being developed with the exciting potential to investigate the DNA methylation feature within complex and heterogeneous tissues. In this study, we implemented a computational pipeline to infer cell-subset specific methylation of ESCs from single-cell methylome. Through integrative analyses with transcription factor binding and single-cell transcriptome, we explored the underlying regulatory mechanisms associated with methylation heterogeneity in ESCs to interpret the biological functional relevance of methylation variations.
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Affiliation(s)
- Yanting Luo
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jianlin He
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Epigenomics and Computational Biology Lab, Biocomplexity Institute of Virginia Tech, Blacksburg, United States of America
| | - Xiguang Xu
- Epigenomics and Computational Biology Lab, Biocomplexity Institute of Virginia Tech, Blacksburg, United States of America
- Department of Biological Sciences, Virginia Tech, Blacksburg, United States of America
| | - Ming-an Sun
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaowei Wu
- Department of Statistics, Virginia Tech, Blacksburg, United States of America
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (XL); (HX)
| | - Hehuang Xie
- Epigenomics and Computational Biology Lab, Biocomplexity Institute of Virginia Tech, Blacksburg, United States of America
- Department of Biological Sciences, Virginia Tech, Blacksburg, United States of America
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, United States of America
- * E-mail: (XL); (HX)
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16
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Ling Z, You Z, Hu L, Zhang L, Wang Y, Zhang M, Zhang G, Chen S, Xu B, Chen M. Effects of four single nucleotide polymorphisms of EZH2 on cancer risk: a systematic review and meta-analysis. Onco Targets Ther 2018; 11:851-865. [PMID: 29497317 PMCID: PMC5820467 DOI: 10.2147/ott.s158173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background Although the relationship between several single nucleotide polymorphisms (SNPs) of the oncogene EZH2 and cancer risk has been assessed by some case–control studies, results of subsequent studies are controversial. Sample sizes from single-center studies are also limited, thereby providing unreliable findings. Hence, we conducted a comprehensive search and meta-analysis to evaluate the associations between EZH2 SNPs and cancer risk. Materials and methods A comprehensive literature search for studies focusing on EZH2 SNPs and cancer risk was conducted on PubMed, Web of Science, Embase, and China National Knowledge Infrastructure online databases. Genotype data were extracted and examined through a meta-analysis, and pooled odds ratios (ORs) with 95% CIs were used to assess the corresponding associations. Sensitivity analysis, publication bias assessment, and heterogeneity test were performed using STATA 12.0. Results Twelve eligible studies were included in this meta-analysis. The association of 4 SNPs, namely, rs887569, rs2302427, rs3757441, and rs41277434, in the EZH2 locus with cancer risk was evaluated. Five studies (1,794 cases and 1,878 controls) indicated that rs887569 was related to a decreased cancer risk (CTTT/CC: OR =0.849, 95% CI: [0.740 to 0.973], P=0.019; TT/CCCT: OR =0.793, 95% CI: [0.654 to 0.962], P=0.019). Seven studies (2,408 cases and 2,910 controls) showed that rs2302427 was linked to a decreased cancer risk (GG/CC: OR =0.562, 95% CI: [0.400 to 0.792], P=0.001; CGGG/CC: OR =0.856, 95% CI: [0.748 to 0.980], P=0.024; GG/CCCG: OR =0.733, 95% CI: [0.571 to 0.940], P=0.015). No relationships were observed between rs3757441 or rs41277434 and cancer risk. Conclusion rs887569 and rs2302427 in EZH2 may be correlated with a decreased cancer risk. Although rs3757441 and rs41277434 are independent risk factors of cancer, further large-scale and functional studies are warranted to validate our findings.
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Affiliation(s)
- Zhixin Ling
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China
| | - Zonghao You
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China
| | - Ling Hu
- Department of Nephrology, People's Hospital of Wuxi City, Wuxi, China
| | - Lei Zhang
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China
| | - Yiduo Wang
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China
| | - Minhao Zhang
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China
| | - Guangyuan Zhang
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China
| | - Shuqiu Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China
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17
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Burrows K, Antignano F, Bramhall M, Chenery A, Scheer S, Korinek V, Underhill TM, Zaph C. The transcriptional repressor HIC1 regulates intestinal immune homeostasis. Mucosal Immunol 2017; 10:1518-1528. [PMID: 28327618 DOI: 10.1038/mi.2017.17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/09/2017] [Indexed: 02/04/2023]
Abstract
The intestine is a unique immune environment that must respond to infectious organisms but remain tolerant to commensal microbes and food antigens. However, the molecular mechanisms that regulate immune cell function in the intestine remain unclear. Here we identify the POK/ZBTB family transcription factor hypermethylated in cancer 1 (HIC1, ZBTB29) as a central component of immunity and inflammation in the intestine. HIC1 is specifically expressed in immune cells in the intestinal lamina propria (LP) in the steady state and mice with a T-cell-specific deletion of HIC1 have reduced numbers of T cells in the LP. HIC1 expression is regulated by the Vitamin A metabolite retinoic acid, as mice raised on a Vitamin A-deficient diet lack HIC1-positive cells in the intestine. HIC1-deficient T cells overproduce IL-17A in vitro and in vivo, and fail to induce intestinal inflammation, identifying a critical role for HIC1 in the regulation of T-cell function in the intestinal microenvironment under both homeostatic and inflammatory conditions.
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Affiliation(s)
- K Burrows
- The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - F Antignano
- The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - M Bramhall
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia.,Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - A Chenery
- The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - S Scheer
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia.,Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - V Korinek
- Department of Cell and Developmental Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - T M Underhill
- The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Cellular &Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - C Zaph
- The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia.,Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
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18
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Paget S, Dubuissez M, Dehennaut V, Nassour J, Harmon BT, Spruyt N, Loison I, Abbadie C, Rood BR, Leprince D. HIC1 (hypermethylated in cancer 1) SUMOylation is dispensable for DNA repair but is essential for the apoptotic DNA damage response (DDR) to irreparable DNA double-strand breaks (DSBs). Oncotarget 2017; 8:2916-2935. [PMID: 27935866 PMCID: PMC5356852 DOI: 10.18632/oncotarget.13807] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/23/2016] [Indexed: 11/25/2022] Open
Abstract
The tumor suppressor gene HIC1 (Hypermethylated In Cancer 1) encodes a transcriptional repressor mediating the p53-dependent apoptotic response to irreparable DNA double-strand breaks (DSBs) through direct transcriptional repression of SIRT1. HIC1 is also essential for DSB repair as silencing of endogenous HIC1 in BJ-hTERT fibroblasts significantly delays DNA repair in functional Comet assays. HIC1 SUMOylation favours its interaction with MTA1, a component of NuRD complexes. In contrast with irreparable DSBs induced by 16-hours of etoposide treatment, we show that repairable DSBs induced by 1 h etoposide treatment do not increase HIC1 SUMOylation or its interaction with MTA1. Furthermore, HIC1 SUMOylation is dispensable for DNA repair since the non-SUMOylatable E316A mutant is as efficient as wt HIC1 in Comet assays. Upon induction of irreparable DSBs, the ATM-mediated increase of HIC1 SUMOylation is independent of its effector kinase Chk2. Moreover, irreparable DSBs strongly increase both the interaction of HIC1 with MTA1 and MTA3 and their binding to the SIRT1 promoter. To characterize the molecular mechanisms sustained by this increased repression potential, we established global expression profiles of BJ-hTERT fibroblasts transfected with HIC1-siRNA or control siRNA and treated or not with etoposide. We identified 475 genes potentially repressed by HIC1 with cell death and cell cycle as the main cellular functions identified by pathway analysis. Among them, CXCL12, EPHA4, TGFβR3 and TRIB2, also known as MTA1 target-genes, were validated by qRT-PCR analyses. Thus, our data demonstrate that HIC1 SUMOylation is important for the transcriptional response to non-repairable DSBs but dispensable for DNA repair.
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Affiliation(s)
- Sonia Paget
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Marion Dubuissez
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
- Present Address: Maisonneuve-Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital, Boulevard l'Assomption Montreal, Canada
| | - Vanessa Dehennaut
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Joe Nassour
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
- Present Address: The Salk Institute for Biological Studies, Molecular and Cell Biology Department, La Jolla, California, USA
| | - Brennan T. Harmon
- Genomics Core, Children's National Medical Center, Washington DC, USA
| | - Nathalie Spruyt
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Ingrid Loison
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Corinne Abbadie
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Brian R. Rood
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington DC, USA
| | - Dominique Leprince
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
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19
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Zeng S, Yang Y, Cheng X, Zhou B, Li P, Zhao Y, Kong X, Xu Y. HIC1 epigenetically represses CIITA transcription in B lymphocytes. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:1481-1489. [PMID: 27720955 DOI: 10.1016/j.bbagrm.2016.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/05/2016] [Accepted: 10/05/2016] [Indexed: 02/06/2023]
Abstract
Differentiation of B lymphocytes into isotope-specific plasma cells represents a hallmark event in adaptive immunity. During B cell maturation, expression of the class II transactivator (CIITA) gene is down-regulated although the underlying epigenetic mechanism is not completely defined. Here we report that hypermethylated in cancer 1 (HIC1) was up-regulated in differentiating B lymphocytes paralleling CIITA repression. Over-expression of HIC1 directly repressed endogenous CIITA transcription in B cells. Reporter assay and chromatin immunoprecipitation (ChIP) assay confirmed that HIC1 bound to the proximal CIITA type III promoter (-545/-113); mutation of a conserved HIC1 site within this region abrogated CIITA trans-repression. More important, depletion of HIC1 with small interfering RNA (siRNA) restored CIITA expression in differentiating B cells. Mechanistically, HIC1 preferentially interacted with and recruited DNMT1 and DNMT3b to the CIITA promoter to synergistically repress CIITA transcription. On the contrary, silencing of DNMT1/DNMT3b or inhibition of DNMT activity with 5-aza-dC attenuated CIITA trans-repression. Therefore, our data identify HIC1 as a novel factor involved in B cell differentiation acting as an epigenetic repressor of CIITA transcription.
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Affiliation(s)
- Sheng Zeng
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Yuyu Yang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Xian Cheng
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China; Jiangsu Institute of Nuclear Medicine, Wuxi, China
| | - Bisheng Zhou
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Ping Li
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Second Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yuhao Zhao
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Xiaocen Kong
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China; Department of Endocrinology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.
| | - Yong Xu
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
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20
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Dubuissez M, Loison I, Paget S, Vorng H, Ait-Yahia S, Rohr O, Tsicopoulos A, Leprince D. Protein Kinase C-Mediated Phosphorylation of BCL11B at Serine 2 Negatively Regulates Its Interaction with NuRD Complexes during CD4+ T-Cell Activation. Mol Cell Biol 2016; 36:1881-98. [PMID: 27161321 PMCID: PMC4911745 DOI: 10.1128/mcb.00062-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 02/16/2016] [Accepted: 05/03/2016] [Indexed: 12/17/2022] Open
Abstract
The transcription factor BCL11B/CTIP2 is a major regulatory protein implicated in various aspects of development, function and survival of T cells. Mitogen-activated protein kinase (MAPK)-mediated phosphorylation and SUMOylation modulate BCL11B transcriptional activity, switching it from a repressor in naive murine thymocytes to a transcriptional activator in activated thymocytes. Here, we show that BCL11B interacts via its conserved N-terminal MSRRKQ motif with endogenous MTA1 and MTA3 proteins to recruit various NuRD complexes. Furthermore, we demonstrate that protein kinase C (PKC)-mediated phosphorylation of BCL11B Ser2 does not significantly impact BCL11B SUMOylation but negatively regulates NuRD recruitment by dampening the interaction with MTA1 or MTA3 (MTA1/3) and RbAp46 proteins. We detected increased phosphorylation of BCL11B Ser2 upon in vivo activation of transformed and primary human CD4(+) T cells. We show that following activation of CD4(+) T cells, BCL11B still binds to IL-2 and Id2 promoters but activates their transcription by recruiting P300 instead of MTA1. Prolonged stimulation results in the direct transcriptional repression of BCL11B by KLF4. Our results unveil Ser2 phosphorylation as a new BCL11B posttranslational modification linking PKC signaling pathway to T-cell receptor (TCR) activation and define a simple model for the functional switch of BCL11B from a transcriptional repressor to an activator during TCR activation of human CD4(+) T cells.
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Affiliation(s)
- Marion Dubuissez
- Université Lille, CNRS, Institut Pasteur de Lille, UMR 8161, Mechanisms of Tumorigenesis and Targeted Therapies (M3T), Lille, France
| | - Ingrid Loison
- Université Lille, CNRS, Institut Pasteur de Lille, UMR 8161, Mechanisms of Tumorigenesis and Targeted Therapies (M3T), Lille, France
| | - Sonia Paget
- Université Lille, CNRS, Institut Pasteur de Lille, UMR 8161, Mechanisms of Tumorigenesis and Targeted Therapies (M3T), Lille, France
| | - Han Vorng
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019, UMR8204, Center for Infection and Immunity of Lille (CIIL), Lille, France
| | - Saliha Ait-Yahia
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019, UMR8204, Center for Infection and Immunity of Lille (CIIL), Lille, France
| | - Olivier Rohr
- University of Strasbourg, IUT Louis Pasteur, EA7292, Dynamic of Host Pathogen Interactions, Institute of Parasitology and Tropical Pathology, Strasbourg, France Institut Universitaire de France, Paris, France
| | - Anne Tsicopoulos
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019, UMR8204, Center for Infection and Immunity of Lille (CIIL), Lille, France
| | - Dominique Leprince
- Université Lille, CNRS, Institut Pasteur de Lille, UMR 8161, Mechanisms of Tumorigenesis and Targeted Therapies (M3T), Lille, France
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21
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The roles of Polycomb group proteins in hematopoietic stem cells and hematological malignancies. Int J Hematol 2016; 103:634-42. [PMID: 27086351 DOI: 10.1007/s12185-016-2011-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/07/2016] [Accepted: 04/07/2016] [Indexed: 12/19/2022]
Abstract
Polycomb group (PcG) proteins are epigenetic regulatory factors that maintain the repression of target gene expression through histone modification. PcG proteins control the repression of genes that regulate differentiation and the cell cycle in the maintenance of hematopoietic stem cells (HSC). Moreover, abnormalities in expression level and mutations in PcG genes have been reported in various types of cancer, including hematological malignancies. In this review, we present an overview of the roles of PcG proteins in HSC and various types of hematological malignancies.
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22
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Abstract
The Polycomb group of proteins (PcGs) are transcriptional repressor complexes that regulate important biological processes and play critical roles in cancer. Mutating or deleting EZH2 can have both oncogenic and tumor suppressive functions by increasing or decreasing H3K27me3. In contrast, mutations of SUZ12 and EED are reported to have tumor suppressive functions. EZH2 is overexpressed in many cancers, including prostate cancer, which can lead to silencing of tumor suppressors, genes regulating epithelial to mesenchymal transition (EMT), and interferon signaling. In some cases, EZH2 overexpression also leads to its use of non-histone substrates. Lastly, PRC2 associated factors can influence the progression of cancer through progressive mutations or by specific binding to certain target genes. Here, we discuss which mutations and deletions of the PRC2 complex have been detected in different cancers, with a specific focus on the overexpression of EZH2 in prostate cancer.
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Affiliation(s)
- Payal Jain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avancats, Barcelona, Spain
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23
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Lim JH. Zinc finger and BTB domain-containing protein 3 is essential for the growth of cancer cells. BMB Rep 2015; 47:405-10. [PMID: 24856827 PMCID: PMC4163853 DOI: 10.5483/bmbrep.2014.47.7.075] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Indexed: 11/23/2022] Open
Abstract
ZBTB3 belongs to the Zinc finger and BTB/POZ domain containing transcription factor family; however, its biological role has rarely been studied. We demonstrate for the first time, to our knowledge, that ZBTB3 is an essential factor for cancer cell growth via the regulation of the ROS detoxification pathway. Suppression of ZBTB3 using two different short hairpin RNAs in human melanoma, lung carcinoma, and breast carcinoma results in diminished cell growth. In addition, we found that suppression of ZBTB3 activates a caspase cascade, including caspase-9, -3, and PARP leading to cellular apoptosis, resulting from failed ROS detoxification. We identified that ZBTB3 plays an important role in the gene expression of ROS detoxification enzymes. Our results reveal that ZBTB3 may play a critical role in cancer cell growth via the ROS detoxification system. Therefore, therapeutic strategies that target ZBTB3 could be used in selective cancer treatments. [BMB Reports 2014; 47(7): 405-410]
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Affiliation(s)
- Ji-Hong Lim
- Department of Biomedical Chemistry, College of Biomedical and Health Science, Konkuk University, Chungju 380-701, Korea
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24
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Harr JC, Luperchio TR, Wong X, Cohen E, Wheelan SJ, Reddy KL. Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins. ACTA ACUST UNITED AC 2015; 208:33-52. [PMID: 25559185 PMCID: PMC4284222 DOI: 10.1083/jcb.201405110] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nuclear organization has been implicated in regulating gene activity. Recently, large developmentally regulated regions of the genome dynamically associated with the nuclear lamina have been identified. However, little is known about how these lamina-associated domains (LADs) are directed to the nuclear lamina. We use our tagged chromosomal insertion site system to identify small sequences from borders of fibroblast-specific variable LADs that are sufficient to target these ectopic sites to the nuclear periphery. We identify YY1 (Ying-Yang1) binding sites as enriched in relocating sequences. Knockdown of YY1 or lamin A/C, but not lamin A, led to a loss of lamina association. In addition, targeted recruitment of YY1 proteins facilitated ectopic LAD formation dependent on histone H3 lysine 27 trimethylation and histone H3 lysine di- and trimethylation. Our results also reveal that endogenous loci appear to be dependent on lamin A/C, YY1, H3K27me3, and H3K9me2/3 for maintenance of lamina-proximal positioning.
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Affiliation(s)
- Jennifer C Harr
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Teresa Romeo Luperchio
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Xianrong Wong
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Erez Cohen
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Sarah J Wheelan
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Karen L Reddy
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
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25
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Ertaylan G, Okawa S, Schwamborn JC, Del Sol A. Gene regulatory network analysis reveals differences in site-specific cell fate determination in mammalian brain. Front Cell Neurosci 2014; 8:437. [PMID: 25565969 PMCID: PMC4270183 DOI: 10.3389/fncel.2014.00437] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/02/2014] [Indexed: 01/17/2023] Open
Abstract
Neurogenesis-the generation of new neurons-is an ongoing process that persists in the adult mammalian brain of several species, including humans. In this work we analyze two discrete brain regions: the subventricular zone (SVZ) lining the walls of the lateral ventricles; and the subgranular zone (SGZ) of the dentate gyrus (DG) of the hippocampus in mice and shed light on the SVZ and SGZ specific neurogenesis. We propose a computational model that relies on the construction and analysis of region specific gene regulatory networks (GRNs) from the publicly available data on these two regions. Using this model a number of putative factors involved in neuronal stem cell (NSC) identity and maintenance were identified. We also demonstrate potential gender and niche-derived differences based on cell surface and nuclear receptors via Ar, Hif1a, and Nr3c1. We have also conducted cell fate determinant analysis for SVZ NSC populations to Olfactory Bulb interneurons and SGZ NSC populations to the granule cells of the Granular Cell Layer. We report 31 candidate cell fate determinant gene pairs, ready to be validated. We focus on Ar-Pax6 in SVZ and Sox2-Ncor1 in SGZ. Both pairs are expressed and localized in the suggested anatomical structures as shown by in situ hybridization and found to physically interact. Finally, we conclude that there are fundamental differences between SGZ and SVZ neurogenesis. We argue that these regulatory mechanisms are linked to the observed differential neurogenic potential of these regions. The presence of nuclear and cell surface receptors in the region specific regulatory circuits indicate the significance of niche derived extracellular factors, hormones and region specific factors such as the oxygen sensitivity, dictating SGZ and SVZ specific neurogenesis.
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Affiliation(s)
- Gökhan Ertaylan
- Computational Biology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg Belval, Luxembourg
| | - Satoshi Okawa
- Computational Biology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg Belval, Luxembourg
| | - Jens C Schwamborn
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg Belval, Luxembourg
| | - Antonio Del Sol
- Computational Biology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg Belval, Luxembourg
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26
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Martin N, Beach D, Gil J. Ageing as developmental decay: insights from p16INK4a. Trends Mol Med 2014; 20:667-74. [DOI: 10.1016/j.molmed.2014.09.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/07/2014] [Accepted: 09/09/2014] [Indexed: 01/03/2023]
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27
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Vizán P, Beringer M, Ballaré C, Di Croce L. Role of PRC2-associated factors in stem cells and disease. FEBS J 2014; 282:1723-35. [PMID: 25271128 DOI: 10.1111/febs.13083] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/19/2014] [Accepted: 09/26/2014] [Indexed: 01/01/2023]
Abstract
The Polycomb group (PcG) of proteins form chromatin-binding complexes with histone-modifying activity. The two main PcG repressive complexes studied (PRC1 and PRC2) are generally associated with chromatin in its repressed state. PRC2 is responsible for methylation of histone H3 at lysine 27 (H3K27me3), an epigenetic mark that is linked with numerous biological processes, including development, adult homeostasis and cancer. The core canonical complex PRC2, which contains the EZH1/2, SUZ12 and EED proteins, may be extended and functionally manipulated through interactions with several other proteins. In this review, we focus on these PRC2-associated proteins. As PRC2 functions are diverse, the variability conferred by these sub-stoichiometrically associated members may help to understand specific changes in PRC2 activity, chromatin recruitment and distribution required for gene repression.
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Affiliation(s)
- Pedro Vizán
- Centre for Genomic Regulation, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain
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28
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Yamaguchi H, Hung MC. Regulation and Role of EZH2 in Cancer. Cancer Res Treat 2014; 46:209-22. [PMID: 25038756 PMCID: PMC4132442 DOI: 10.4143/crt.2014.46.3.209] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 06/05/2014] [Indexed: 12/11/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) is the epigenetic regulator that induces histone H3 lysine 27 methylation (H3K27me3) and silences specific gene transcription. Enhancer of zeste homolog 2 (EZH2) is an enzymatic subunit of PRC2, and evidence shows that EZH2 plays an essential role in cancer initiation, development, progression, metastasis, and drug resistance. EZH2 expression is indeed regulated by various oncogenic transcription factors, tumor suppressor miRNAs, and cancer-associated non-coding RNA. EZH2 activity is also controlled by post-translational modifications, which are deregulated in cancer. The canonical role of EZH2 is gene silencing through H3K27me3, but accumulating evidence shows that EZH2 methlyates substrates other than histone and has methylase-independent functions. These non-canonical functions of EZH2 are shown to play a role in cancer progression. In this review, we summarize current information on the regulation and roles of EZH2 in cancer. We also discuss various therapeutic approaches to targeting EZH2.
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Affiliation(s)
- Hirohito Yamaguchi
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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29
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Lin YM, Wang CM, Jeng JC, Leprince D, Shih HM. HIC1 interacts with and modulates the activity of STAT3. Cell Cycle 2014; 12:2266-76. [PMID: 24067369 DOI: 10.4161/cc.25365] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
HIC1 (hypermethylated in cancer 1) is a tumor suppressor gene, expression of which is frequently suppressed in human cancers. Very little is known about the molecular basis of HIC1 in antagonizing oncogenic pathways. Here, we report that HIC1 forms complexes with the signal transducers and activators of transcription 3 (STAT3) and attenuates STAT3-mediated transcription. STAT3 was identified as a HIC1-interacting protein by affinity capture and followed by mass spectrometry analysis. Overexpression or depletion of HIC1 resulted in decreased or increased levels of interleukin-6 (IL-6)/oncostatin M (OSM)-induced STAT3-mediated reporter activity and expression of target genes such as VEGF and c-Myc, respectively. Furthermore, HIC1 suppressing the VEGF and c-Myc promoter activity and the colony formation of MDA-MB 231 cells were STAT3-dependent. Further studies showed that HIC1 interacts with the DNA binding domain of STAT3 and suppresses the binding of STAT3 to its target gene promoters. Domain mapping study revealed that HIC1 C-terminal domain binds to STAT3. HIC1 mutant defective in STAT3 interaction reduced its repressive effect on STAT3 DNA binding activity, the reporter activity and gene expression of the VEGF and c-Myc genes, and cell growth in MDA-MB 231 cells. Altogether, our findings not only provide a novel role of HIC1 in antagonizing STAT3-mediated activation of VEGF and c-Myc gene expression and cell growth, but also elucidate a molecular basis underlying the inhibitory effect of HIC1 on STAT3 transcriptional potential.
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Affiliation(s)
- Ying-Mei Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
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30
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Genome regulation at the peripheral zone: lamina associated domains in development and disease. Curr Opin Genet Dev 2014; 25:50-61. [PMID: 24556270 DOI: 10.1016/j.gde.2013.11.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/29/2013] [Indexed: 12/18/2022]
Abstract
The nuclear periphery has been implicated in gene regulation and it has been proposed that proximity to the nuclear lamina and inner nuclear membrane (INM) leads to gene repression. More recently, it appears that there is a correlation and interdependence between lamina associated domains (LADs), the epigenome and overall three-dimensional architecture of the genome. However, the mechanisms of such organization at the 'peripheral zone' and the functional significance of these associations are poorly understood. The role these domains play in development and disease is an active and exciting area of research, expanding our knowledge of how the three-dimensional (3D) genome is regulated.
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31
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Dehennaut V, Leprince D, Lefebvre T. O-GlcNAcylation, an Epigenetic Mark. Focus on the Histone Code, TET Family Proteins, and Polycomb Group Proteins. Front Endocrinol (Lausanne) 2014; 5:155. [PMID: 25309514 PMCID: PMC4176146 DOI: 10.3389/fendo.2014.00155] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/14/2014] [Indexed: 01/18/2023] Open
Abstract
There are increasing evidences that dietary components and metabolic disorders affect gene expression through epigenetic mechanisms. These observations support the notion that epigenetic reprograming-linked nutrition is connected to the etiology of metabolic diseases and cancer. During the last 5 years, accumulating data revealed that the nutrient-sensing O-GlcNAc glycosylation (O-GlcNAcylation) may be pivotal in the modulation of chromatin remodeling and in the regulation of gene expression by being part of the "histone code," and by identifying OGT (O-GlcNAc transferase) as an interacting partner of the TET family proteins of DNA hydroxylases and as a member of the polycomb group proteins. Thus, it is suggested that O-GlcNAcylation is a post-translational modification that links nutrition to epigenetic. This review summarizes recent findings about the interplay between O-GlcNAcylation and the epigenome and enlightens the contribution of the glycosylation to epigenetic reprograming.
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Affiliation(s)
- Vanessa Dehennaut
- Structural and Functional Glycobiology Unit, Lille 1 University, Villeneuve d’Ascq, France
- Institut de Biologie de Lille, Pasteur Institute of Lille, Université Lille Nord de France, Lille, France
| | - Dominique Leprince
- Institut de Biologie de Lille, Pasteur Institute of Lille, Université Lille Nord de France, Lille, France
| | - Tony Lefebvre
- Structural and Functional Glycobiology Unit, Lille 1 University, Villeneuve d’Ascq, France
- *Correspondence: Tony Lefebvre, CNRS-UMR 8576, Lille 1 University, cité scientifique, Bat C9, 59655 Vileneuve d’Ascq, France e-mail:
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32
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Kaneko S, Bonasio R, Saldaña-Meyer R, Yoshida T, Son J, Nishino K, Umezawa A, Reinberg D. Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin. Mol Cell 2013; 53:290-300. [PMID: 24374312 DOI: 10.1016/j.molcel.2013.11.012] [Citation(s) in RCA: 292] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 10/02/2013] [Accepted: 11/21/2013] [Indexed: 11/17/2022]
Abstract
JARID2 is an accessory component of Polycomb repressive complex-2 (PRC2) required for the differentiation of embryonic stem cells (ESCs). A role for JARID2 in the recruitment of PRC2 to target genes silenced during differentiation has been put forward, but the molecular details remain unclear. We identified a 30-amino-acid region of JARID2 that mediates interactions with long noncoding RNAs (lncRNAs) and found that the presence of lncRNAs stimulated JARID2-EZH2 interactions in vitro and JARID2-mediated recruitment of PRC2 to chromatin in vivo. Native and crosslinked RNA immunoprecipitations of JARID2 revealed that Meg3 and other lncRNAs from the imprinted Dlk1-Dio3 locus, an important regulator of development, interacted with PRC2 via JARID2. Lack of MEG3 expression in human induced pluripotent cells altered the chromatin distribution of JARID2, PRC2, and H3K27me3. Our findings show that lncRNAs facilitate JARID2-PRC2 interactions on chromatin and suggest a mechanism by which lncRNAs contribute to PRC2 recruitment.
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Affiliation(s)
- Syuzo Kaneko
- Howard Hughes Medical Institute and NYU School of Medicine, Department of Molecular Pharmacology and Biochemistry, New York, NY 10016, USA
| | - Roberto Bonasio
- Howard Hughes Medical Institute and NYU School of Medicine, Department of Molecular Pharmacology and Biochemistry, New York, NY 10016, USA
| | - Ricardo Saldaña-Meyer
- Howard Hughes Medical Institute and NYU School of Medicine, Department of Molecular Pharmacology and Biochemistry, New York, NY 10016, USA
| | - Takahaki Yoshida
- National Research Institute for Child Health and Development, Department of Reproductive Biology, Tokyo 157-8535, Japan
| | - Jinsook Son
- Howard Hughes Medical Institute and NYU School of Medicine, Department of Molecular Pharmacology and Biochemistry, New York, NY 10016, USA
| | - Koichiro Nishino
- University of Miyazaki, Faculty of Agriculture, Laboratory of Veterinary Biochemistry and Molecular Biology, Miyazaki 889-2192, Japan
| | - Akihiro Umezawa
- National Research Institute for Child Health and Development, Department of Reproductive Biology, Tokyo 157-8535, Japan
| | - Danny Reinberg
- Howard Hughes Medical Institute and NYU School of Medicine, Department of Molecular Pharmacology and Biochemistry, New York, NY 10016, USA.
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33
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Dubuissez M, Faiderbe P, Pinte S, Dehennaut V, Rood BR, Leprince D. The Reelin receptors ApoER2 and VLDLR are direct target genes of HIC1 (Hypermethylated In Cancer 1). Biochem Biophys Res Commun 2013; 440:424-30. [PMID: 24076391 DOI: 10.1016/j.bbrc.2013.09.091] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 09/17/2013] [Indexed: 11/16/2022]
Abstract
The tumor suppressor gene HIC1 (Hypermethylated In Cancer 1) is located in 17p13.3 a region frequently hypermethylated or deleted in tumors and in a contiguous-gene syndrome, the Miller-Dieker syndrome which includes classical lissencephaly (smooth brain) and severe developmental defects. HIC1 encodes a transcriptional repressor involved in the regulation of growth control, DNA damage response and cell migration properties. We previously demonstrated that the membrane-associated G-protein-coupled receptors CXCR7, ADRB2 and the tyrosine kinase receptor EphA2 are direct target genes of HIC1. Here we show that ectopic expression of HIC1 in U2OS and MDA-MB-231 cell lines decreases expression of the ApoER2 and VLDLR genes, encoding two canonical tyrosine kinase receptors for Reelin. Conversely, knock-down of endogenous HIC1 in BJ-Tert normal human fibroblasts through RNA interference results in the up-regulation of these two Reelin receptors. Finally, through chromatin immunoprecipitation (ChIP) in BJ-Tert fibroblasts, we demonstrate that HIC1 is a direct transcriptional repressor of ApoER2 and VLDLR. These data provide evidence that HIC1 is a new regulator of the Reelin pathway which is essential for the proper migration of neuronal precursors during the normal development of the cerebral cortex, of Purkinje cells in the cerebellum and of mammary epithelial cells. Deregulation of this pathway through HIC1 inactivation or deletion may contribute to its role in tumor promotion. Moreover, HIC1, through the direct transcriptional repression of ATOH1 and the Reelin receptors ApoER2 and VLDLR, could play an essential role in normal cerebellar development.
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Affiliation(s)
- Marion Dubuissez
- CNRS-UMR 8161, Institut de Biologie de Lille, Université de Lille Nord de France, Institut Pasteur de Lille, IFR 142, 1 rue Calmette, BP447, 59017 Lille Cedex, France
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Dehennaut V, Loison I, Dubuissez M, Nassour J, Abbadie C, Leprince D. DNA double-strand breaks lead to activation of hypermethylated in cancer 1 (HIC1) by SUMOylation to regulate DNA repair. J Biol Chem 2013; 288:10254-64. [PMID: 23417673 PMCID: PMC3624409 DOI: 10.1074/jbc.m112.421610] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 02/14/2013] [Indexed: 11/06/2022] Open
Abstract
HIC1 (hypermethylated in cancer 1) is a tumor suppressor gene frequently epigenetically silenced in human cancers. HIC1 encodes a transcriptional repressor involved in the regulation of growth control and DNA damage response. We previously demonstrated that HIC1 can be either acetylated or SUMOylated on lysine 314. This deacetylation/SUMOylation switch is governed by an unusual complex made up of SIRT1 and HDAC4 which deacetylates and thereby favors SUMOylation of HIC1 by a mechanism not yet fully deciphered. This switch regulates the interaction of HIC1 with MTA1, a component of the NuRD complex and potentiates the repressor activity of HIC1. Here, we show that HIC1 silencing in human fibroblasts impacts the repair of DNA double-strand breaks whereas ectopic expression of wild-type HIC1, but not of nonsumoylatable mutants, leads to a reduced number of γH2AX foci induced by etoposide treatment. In this way, we demonstrate that DNA damage leads to (i) an enhanced HDAC4/Ubc9 interaction, (ii) the activation of SIRT1 by SUMOylation (Lys-734), and (iii) the SUMO-dependent recruitment of HDAC4 by SIRT1 which permits the deacetylation/SUMOylation switch of HIC1. Finally, we show that this increase of HIC1 SUMOylation favors the HIC1/MTA1 interaction, thus demonstrating that HIC1 regulates DNA repair in a SUMO-dependent way. Therefore, epigenetic HIC1 inactivation, which is an early step in tumorigenesis, could contribute to the accumulation of DNA mutations through impaired DNA repair and thus favor tumorigenesis.
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Affiliation(s)
- Vanessa Dehennaut
- From the CNRS-UMR 8161, Institut de Biologie de Lille, Université de Lille Nord de France, Institut Pasteur de Lille, IFR 142, 1 rue Calmette, BP447, 59017 Lille Cedex, France
| | - Ingrid Loison
- From the CNRS-UMR 8161, Institut de Biologie de Lille, Université de Lille Nord de France, Institut Pasteur de Lille, IFR 142, 1 rue Calmette, BP447, 59017 Lille Cedex, France
| | - Marion Dubuissez
- From the CNRS-UMR 8161, Institut de Biologie de Lille, Université de Lille Nord de France, Institut Pasteur de Lille, IFR 142, 1 rue Calmette, BP447, 59017 Lille Cedex, France
| | - Joe Nassour
- From the CNRS-UMR 8161, Institut de Biologie de Lille, Université de Lille Nord de France, Institut Pasteur de Lille, IFR 142, 1 rue Calmette, BP447, 59017 Lille Cedex, France
| | - Corinne Abbadie
- From the CNRS-UMR 8161, Institut de Biologie de Lille, Université de Lille Nord de France, Institut Pasteur de Lille, IFR 142, 1 rue Calmette, BP447, 59017 Lille Cedex, France
| | - Dominique Leprince
- From the CNRS-UMR 8161, Institut de Biologie de Lille, Université de Lille Nord de France, Institut Pasteur de Lille, IFR 142, 1 rue Calmette, BP447, 59017 Lille Cedex, France
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Rood BR, Leprince D. Deciphering HIC1 control pathways to reveal new avenues in cancer therapeutics. Expert Opin Ther Targets 2013; 17:811-27. [PMID: 23566242 DOI: 10.1517/14728222.2013.788152] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION The tumor suppressor gene HIC1 (Hypermethylated in Cancer 1), which encodes a transcriptional repressor with multiple partners and multiple targets, is epigenetically silenced but not mutated in tumors. HIC1 has broad biological roles during normal development and is implicated in many canonical processes of cancer such as control of cell growth, cell survival upon genotoxic stress, cell migration, and motility. AREAS COVERED The HIC1 literature herein discussed includes its discovery as a candidate tumor suppressor gene hypermethylated or deleted in many human tumors, animal models establishing it as tumor suppressor gene, its role as a sequence-specific transcriptional repressor recruiting several chromatin regulatory complexes, its cognate target genes, and its functional roles in normal tissues. Finally, this review discusses how its loss of function contributes to the early steps in tumorigenesis. EXPERT OPINION Given HIC1's ability to direct repressive complexes to sequence-specific binding sites associated with its target genes, its loss results in specific changes in the transcriptional program of the cell. An understanding of this program through identification of HIC1's target genes and their involvement in feedback loops and cell process regulation will yield the ability to leverage this knowledge for therapeutic translation.
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Affiliation(s)
- Brian R Rood
- Center for Cancer and Blood Disorders, Children's National Medical Center, Division of Oncology, 111 Michigan Ave. NW, Washington, DC 20010, USA
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Dehennaut V, Loison I, Boulay G, Van Rechem C, Leprince D. Identification of p21 (CIP1/WAF1) as a direct target gene of HIC1 (Hypermethylated In Cancer 1). Biochem Biophys Res Commun 2013. [DOI: 10.1016/j.bbrc.2012.11.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Polycomb-group proteins in hematopoietic stem cell regulation and hematopoietic neoplasms. Leukemia 2012; 27:523-33. [PMID: 23257781 DOI: 10.1038/leu.2012.368] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The equilibrium between self-renewal and differentiation of hematopoietic stem cells is regulated by epigenetic mechanisms. In particular, Polycomb-group (PcG) proteins have been shown to be involved in this process by repressing genes involved in cell-cycle regulation and differentiation. PcGs are histone modifiers that reside in two multi-protein complexes: Polycomb Repressive Complex 1 and 2 (PRC1 and PRC2). The existence of multiple orthologs for each Polycomb gene allows the formation of a multitude of distinct PRC1 and PRC2 sub-complexes. Changes in the expression of individual PcG genes are likely to cause perturbations in the composition of the PRC, which affect PRC enzymatic activity and target selectivity. An interesting recent development is that aberrant expression of, and mutations in, PcG genes have been shown to occur in hematopoietic neoplasms, where they display both tumor-suppressor and oncogenic activities. We therefore comprehensively reviewed the latest research on the role of PcG genes in normal and malignant blood cell development. We conclude that future research to elucidate the compositional changes of the PRCs and methods to intervene in PRC assembly will be of great therapeutic relevance to combat hematological malignancies.
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Tani H, Imamachi N, Salam KA, Mizutani R, Ijiri K, Irie T, Yada T, Suzuki Y, Akimitsu N. Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability. RNA Biol 2012; 9:1370-9. [PMID: 23064114 DOI: 10.4161/rna.22360] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
UPF1 eliminates aberrant mRNAs harboring premature termination codons, and regulates the steady-state levels of normal physiological mRNAs. Although genome-wide studies of UPF1 targets performed, previous studies did not distinguish indirect UPF1 targets because they could not determine UPF1-dependent altered RNA stabilities. Here, we measured the decay rates of the whole transcriptome in UPF1-depleted HeLa cells using BRIC-seq, an inhibitor-free method for directly measuring RNA stability. We determined the half-lives and expression levels of 9,229 transcripts. An amount of 785 transcripts were stabilized in UPF1-depleted cells. Among these, the expression levels of 76 transcripts were increased, but those of the other 709 transcripts were not altered. RNA immunoprecipitation showed UPF1 bound to the stabilized transcripts, suggesting that UPF1 directly degrades the 709 transcripts. Many UPF1 targets in this study were newly identified. This study clearly demonstrates that direct determination of RNA stability is a powerful approach for identifying targets of RNA degradation factors.
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Affiliation(s)
- Hidenori Tani
- Radioisotope Center, University of Tokyo, Tokyo, Japan
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