1
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Liu F, Liao Z, Zhang Z. MYC in liver cancer: mechanisms and targeted therapy opportunities. Oncogene 2023; 42:3303-3318. [PMID: 37833558 DOI: 10.1038/s41388-023-02861-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
MYC, a major oncogenic transcription factor, regulates target genes involved in various pathways such as cell proliferation, metabolism and immune evasion, playing a critical role in the tumor initiation and development in multiple types of cancer. In liver cancer, MYC and its signaling pathways undergo significant changes, exerting a profound impact on liver cancer progression, including tumor proliferation, metastasis, dedifferentiation, metabolism, immune microenvironment, and resistance to comprehensive therapies. This makes MYC an appealing target, despite it being previously considered an undruggable protein. In this review, we discuss the role and mechanisms of MYC in liver physiology, chronic liver diseases, hepatocarcinogenesis, and liver cancer progression, providing a theoretical basis for targeting MYC as an ideal therapeutic target for liver cancer. We also summarize and prospect the strategies for targeting MYC, including direct and indirect approaches to abolish the oncogenic function of MYC in liver cancer.
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Affiliation(s)
- Furong Liu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Zhibin Liao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Zhanguo Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, 430030, China.
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China.
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2
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Hurd M, Pino J, Jang K, Allevato MM, Vorontchikhina M, Ichikawa W, Zhao Y, Gates R, Villalpando E, Hamilton MJ, Faiola F, Pan S, Qi Y, Hung YW, Girke T, Ann D, Seewaldt V, Martinez E. MYC acetylated lysine residues drive oncogenic cell transformation and regulate select genetic programs for cell adhesion-independent growth and survival. Genes Dev 2023; 37:865-882. [PMID: 37852796 PMCID: PMC10691474 DOI: 10.1101/gad.350736.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
The MYC oncogenic transcription factor is acetylated by the p300 and GCN5 histone acetyltransferases. The significance of MYC acetylation and the functions of specific acetylated lysine (AcK) residues have remained unclear. Here, we show that the major p300-acetylated K148(149) and K157(158) sites in human (or mouse) MYC and the main GCN5-acetylated K323 residue are reversibly acetylated in various malignant and nonmalignant cells. Oncogenic overexpression of MYC enhances its acetylation and alters the regulation of site-specific acetylation by proteasome and deacetylase inhibitors. Acetylation of MYC at different K residues differentially affects its stability in a cell type-dependent manner. Lysine-to-arginine substitutions indicate that although none of the AcK residues is required for MYC stimulation of adherent cell proliferation, individual AcK sites have gene-specific functions controlling select MYC-regulated processes in cell adhesion, contact inhibition, apoptosis, and/or metabolism and are required for the malignant cell transformation activity of MYC. Each AcK site is required for anchorage-independent growth of MYC-overexpressing cells in vitro, and both the AcK148(149) and AcK157(158) residues are also important for the tumorigenic activity of MYC transformed cells in vivo. The MYC AcK site-specific signaling pathways identified may offer new avenues for selective therapeutic targeting of MYC oncogenic activities.
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Affiliation(s)
- Matthew Hurd
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Jeffrey Pino
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Kay Jang
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Michael M Allevato
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Marina Vorontchikhina
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Wataru Ichikawa
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Yifan Zhao
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Ryan Gates
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Emily Villalpando
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Michael J Hamilton
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Francesco Faiola
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA
| | - Songqin Pan
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, California 92521, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California 92521, USA
| | - Yue Qi
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
| | - Yu-Wen Hung
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
| | - Thomas Girke
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, California 92521, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California 92521, USA
| | - David Ann
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
| | - Victoria Seewaldt
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
- Department of Population Sciences, Beckman Research Institute, Comprehensive Cancer Center, City of Hope, Duarte, California 91010, USA
| | - Ernest Martinez
- Department of Biochemistry, University of California Riverside, Riverside, California 92521, USA;
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, California 92521, USA
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3
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Romhányi D, Szabó K, Kemény L, Groma G. Histone and Histone Acetylation-Related Alterations of Gene Expression in Uninvolved Psoriatic Skin and Their Effects on Cell Proliferation, Differentiation, and Immune Responses. Int J Mol Sci 2023; 24:14551. [PMID: 37833997 PMCID: PMC10572426 DOI: 10.3390/ijms241914551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Psoriasis is a chronic immune-mediated skin disease in which the symptom-free, uninvolved skin carries alterations in gene expression, serving as a basis for lesion formation. Histones and histone acetylation-related processes are key regulators of gene expression, controlling cell proliferation and immune responses. Dysregulation of these processes is likely to play an important role in the pathogenesis of psoriasis. To gain a complete overview of these potential alterations, we performed a meta-analysis of a psoriatic uninvolved skin dataset containing differentially expressed transcripts from nearly 300 individuals and screened for histones and histone acetylation-related molecules. We identified altered expression of the replication-dependent histones HIST2H2AA3 and HIST2H4A and the replication-independent histones H2AFY, H2AFZ, and H3F3A/B. Eight histone chaperones were also identified. Among the histone acetyltransferases, ELP3 and KAT5 and members of the ATAC, NSL, and SAGA acetyltransferase complexes are affected in uninvolved skin. Histone deacetylation-related alterations were found to affect eight HDACs and members of the NCOR/SMRT, NURD, SIN3, and SHIP HDAC complexes. In this article, we discuss how histone and histone acetylation-related expression changes may affect proliferation and differentiation, as well as innate, macrophage-mediated, and T cell-mediated pro- and anti-inflammatory responses, which are known to play a central role in the development of psoriasis.
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Affiliation(s)
- Dóra Romhányi
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary; (D.R.); (K.S.); (L.K.)
| | - Kornélia Szabó
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary; (D.R.); (K.S.); (L.K.)
- Hungarian Centre of Excellence for Molecular Medicine-University of Szeged Skin Research Group (HCEMM-USZ Skin Research Group), H-6720 Szeged, Hungary
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
| | - Lajos Kemény
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary; (D.R.); (K.S.); (L.K.)
- Hungarian Centre of Excellence for Molecular Medicine-University of Szeged Skin Research Group (HCEMM-USZ Skin Research Group), H-6720 Szeged, Hungary
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
| | - Gergely Groma
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary; (D.R.); (K.S.); (L.K.)
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
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4
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Guo Z, Chu C, Lu Y, Zhang X, Xiao Y, Wu M, Gao S, Wong CCL, Zhan X, Wang C. Structure of a SIN3-HDAC complex from budding yeast. Nat Struct Mol Biol 2023:10.1038/s41594-023-00975-z. [PMID: 37081318 DOI: 10.1038/s41594-023-00975-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/23/2023] [Indexed: 04/22/2023]
Abstract
SIN3-HDAC (histone deacetylases) complexes have important roles in facilitating local histone deacetylation to regulate chromatin accessibility and gene expression. Here, we present the cryo-EM structure of the budding yeast SIN3-HDAC complex Rpd3L at an average resolution of 2.6 Å. The structure reveals that two distinct arms (ARM1 and ARM2) hang on a T-shaped scaffold formed by two coiled-coil domains. In each arm, Sin3 interacts with different subunits to create a different environment for the histone deacetylase Rpd3. ARM1 is in the inhibited state with the active site of Rpd3 blocked, whereas ARM2 is in an open conformation with the active site of Rpd3 exposed to the exterior space. The observed asymmetric architecture of Rpd3L is different from those of available structures of other class I HDAC complexes. Our study reveals the organization mechanism of the SIN3-HDAC complex and provides insights into the interaction pattern by which it targets histone deacetylase to chromatin.
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Affiliation(s)
- Zhouyan Guo
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Chen Chu
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yichen Lu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xiaofeng Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yihang Xiao
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
| | - Mingxuan Wu
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
| | - Shuaixin Gao
- Human Nutrition Program & James Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - Catherine C L Wong
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xiechao Zhan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
| | - Chengcheng Wang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
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5
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Wang C, Guo Z, Chu C, Lu Y, Zhang X, Zhan X. Two assembly modes for SIN3 histone deacetylase complexes. Cell Discov 2023; 9:42. [PMID: 37076472 PMCID: PMC10115800 DOI: 10.1038/s41421-023-00539-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/10/2023] [Indexed: 04/21/2023] Open
Abstract
The switch-independent 3 (SIN3)/histone deacetylase (HDAC) complexes play essential roles in regulating chromatin accessibility and gene expression. There are two major types of SIN3/HDAC complexes (named SIN3L and SIN3S) targeting different chromatin regions. Here we present the cryo-electron microscopy structures of the SIN3L and SIN3S complexes from Schizosaccharomyces pombe (S. pombe), revealing two distinct assembly modes. In the structure of SIN3L, each Sin3 isoform (Pst1 and Pst3) interacts with one histone deacetylase Clr6, and one WD40-containing protein Prw1, forming two lobes. These two lobes are bridged by two vertical coiled-coil domains from Sds3/Dep1 and Rxt2/Png2, respectively. In the structure of SIN3S, there is only one lobe organized by another Sin3 isoform Pst2; each of the Cph1 and Cph2 binds to an Eaf3 molecule, providing two modules for histone recognition and binding. Notably, the Pst1 Lobe in SIN3L and the Pst2 Lobe in SIN3S adopt similar conformation with their deacetylase active sites exposed to the space; however, the Pst3 Lobe in SIN3L is in a compact state with its active center buried inside and blocked. Our work reveals two classical organization mechanisms for the SIN3/HDAC complexes to achieve specific targeting and provides a framework for studying the histone deacetylase complexes.
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Affiliation(s)
- Chengcheng Wang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China.
| | - Zhouyan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China
| | - Chen Chu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China
| | - Yichen Lu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China
| | - Xiaofeng Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China
| | - Xiechao Zhan
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China.
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6
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Affiliation(s)
- Mark Roschewski
- From the Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Louis M Staudt
- From the Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Wyndham H Wilson
- From the Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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7
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Transcriptome Analysis of Schwann Cells at Various Stages of Myelination Implicates Chromatin Regulator Sin3A in Control of Myelination Identity. Neurosci Bull 2022; 38:720-740. [DOI: 10.1007/s12264-022-00850-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/13/2021] [Indexed: 10/18/2022] Open
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8
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Cen HH, Hussein B, Botezelli JD, Wang S, Zhang JA, Noursadeghi N, Jessen N, Rodrigues B, Timmons JA, Johnson JD. Human and mouse muscle transcriptomic analyses identify insulin receptor mRNA downregulation in hyperinsulinemia-associated insulin resistance. FASEB J 2022; 36:e22088. [PMID: 34921686 PMCID: PMC9255858 DOI: 10.1096/fj.202100497rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 01/03/2023]
Abstract
Hyperinsulinemia is commonly viewed as a compensatory response to insulin resistance, yet studies have demonstrated that chronically elevated insulin may also drive insulin resistance. The molecular mechanisms underpinning this potentially cyclic process remain poorly defined, especially on a transcriptome-wide level. Transcriptomic meta-analysis in >450 human samples demonstrated that fasting insulin reliably and negatively correlated with INSR mRNA in skeletal muscle. To establish causality and study the direct effects of prolonged exposure to excess insulin in muscle cells, we incubated C2C12 myotubes with elevated insulin for 16 h, followed by 6 h of serum starvation, and established that acute AKT and ERK signaling were attenuated in this model of in vitro hyperinsulinemia. Global RNA-sequencing of cells both before and after nutrient withdrawal highlighted genes in the insulin receptor (INSR) signaling, FOXO signaling, and glucose metabolism pathways indicative of 'hyperinsulinemia' and 'starvation' programs. Consistently, we observed that hyperinsulinemia led to a substantial reduction in Insr gene expression, and subsequently a reduced surface INSR and total INSR protein, both in vitro and in vivo. Bioinformatic modeling combined with RNAi identified SIN3A as a negative regulator of Insr mRNA (and JUND, MAX, and MXI as positive regulators of Irs2 mRNA). Together, our analysis identifies mechanisms which may explain the cyclic processes underlying hyperinsulinemia-induced insulin resistance in muscle, a process directly relevant to the etiology and disease progression of type 2 diabetes.
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Affiliation(s)
- Haoning Howard Cen
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bahira Hussein
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - José Diego Botezelli
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Su Wang
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jiashuo Aaron Zhang
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nilou Noursadeghi
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Niels Jessen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Brian Rodrigues
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - James A Timmons
- Augur Precision Medicine LTD, Stirling University Innovation Park, Stirling, Scotland.,William Harvey Research Institute, Queen Mary University of London, London, UK
| | - James D Johnson
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
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9
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RN7SK small nuclear RNA controls bidirectional transcription of highly expressed gene pairs in skin. Nat Commun 2021; 12:5864. [PMID: 34620876 PMCID: PMC8497571 DOI: 10.1038/s41467-021-26083-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/10/2021] [Indexed: 11/16/2022] Open
Abstract
Pausing of RNA polymerase II (Pol II) close to promoters is a common regulatory step in RNA synthesis, and is coordinated by a ribonucleoprotein complex scaffolded by the noncoding RNA RN7SK. The function of RN7SK-regulated gene transcription in adult tissue homoeostasis is currently unknown. Here, we deplete RN7SK during mouse and human epidermal stem cell differentiation. Unexpectedly, loss of this small nuclear RNA specifically reduces transcription of numerous cell cycle regulators leading to cell cycle exit and differentiation. Mechanistically, we show that RN7SK is required for efficient transcription of highly expressed gene pairs with bidirectional promoters, which in the epidermis co-regulated cell cycle and chromosome organization. The reduction in transcription involves impaired splicing and RNA decay, but occurs in the absence of chromatin remodelling at promoters and putative enhancers. Thus, RN7SK is directly required for efficient Pol II transcription of highly transcribed bidirectional gene pairs, and thereby exerts tissue-specific functions, such as maintaining a cycling cell population in the epidermis. The noncoding RNA RN7SK regulates RNA polymerase II pausing and splicing. Here the authors deplete RN7SK in mouse and human during epidermal stem cell differentiation and reveal a novel role in orchestrating bidirectional transcription of highly expressed gene pairs.
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10
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Perna S, Pinoli P, Ceri S, Wong L. NAUTICA: classifying transcription factor interactions by positional and protein-protein interaction information. Biol Direct 2020; 15:13. [PMID: 32938476 PMCID: PMC7493360 DOI: 10.1186/s13062-020-00268-1] [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: 02/19/2019] [Accepted: 08/25/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Inferring the mechanisms that drive transcriptional regulation is of great interest to biologists. Generally, methods that predict physical interactions between transcription factors (TFs) based on positional information of their binding sites (e.g. chromatin immunoprecipitation followed by sequencing (ChIP-Seq) experiments) cannot distinguish between different kinds of interaction at the same binding spots, such as co-operation and competition. RESULTS In this work, we present the Network-Augmented Transcriptional Interaction and Coregulation Analyser (NAUTICA), which employs information from protein-protein interaction (PPI) networks to assign TF-TF interaction candidates to one of three classes: competition, co-operation and non-interactions. NAUTICA filters available PPI network edges and fits a prediction model based on the number of shared partners in the PPI network between two candidate interactors. CONCLUSIONS NAUTICA improves on existing positional information-based TF-TF interaction prediction results, demonstrating how PPI information can improve the quality of TF interaction prediction. NAUTICA predictions - both co-operations and competitions - are supported by literature investigation, providing evidence on its capability of providing novel interactions of both kinds. REVIEWERS This article was reviewed by Zoltán Hegedüs and Endre Barta.
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Affiliation(s)
- Stefano Perna
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Via Giuseppe Ponzio 34/5, 20133, Milan, Italy.
| | - Pietro Pinoli
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Via Giuseppe Ponzio 34/5, 20133, Milan, Italy
| | - Stefano Ceri
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Via Giuseppe Ponzio 34/5, 20133, Milan, Italy
| | - Limsoon Wong
- National University of Singapore, Singapore, Singapore
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11
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Yang X, Graff SM, Heiser CN, Ho KH, Chen B, Simmons AJ, Southard-Smith AN, David G, Jacobson DA, Kaverina I, Wright CVE, Lau KS, Gu G. Coregulator Sin3a Promotes Postnatal Murine β-Cell Fitness by Regulating Genes in Ca 2+ Homeostasis, Cell Survival, Vesicle Biosynthesis, Glucose Metabolism, and Stress Response. Diabetes 2020; 69:1219-1231. [PMID: 32245798 PMCID: PMC7243292 DOI: 10.2337/db19-0721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 03/26/2020] [Indexed: 02/06/2023]
Abstract
Swi-independent 3a and 3b (Sin3a and Sin3b) are paralogous transcriptional coregulators that direct cellular differentiation, survival, and function. Here, we report that mouse Sin3a and Sin3b are coproduced in most pancreatic cells during embryogenesis but become much more enriched in endocrine cells in adults, implying continued essential roles in mature endocrine cell function. Mice with loss of Sin3a in endocrine progenitors were normal during early postnatal stages but gradually developed diabetes before weaning. These physiological defects were preceded by the compromised survival, insulin-vesicle packaging, insulin secretion, and nutrient-induced Ca2+ influx of Sin3a-deficient β-cells. RNA sequencing coupled with candidate chromatin immunoprecipitation assays revealed several genes that could be directly regulated by Sin3a in β-cells, which modulate Ca2+/ion transport, cell survival, vesicle/membrane trafficking, glucose metabolism, and stress responses. Finally, mice with loss of both Sin3a and Sin3b in multipotent embryonic pancreatic progenitors had significantly reduced islet cell mass at birth, caused by decreased endocrine progenitor production and increased β-cell death. These findings highlight the stage-specific requirements for the presumed "general" coregulators Sin3a and Sin3b in islet β-cells, with Sin3a being dispensable for differentiation but required for postnatal function and survival.
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Affiliation(s)
- Xiaodun Yang
- Vanderbilt Program in Developmental Biology, Vanderbilt Center for Stem Cell Biology, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Sarah M Graff
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Cody N Heiser
- Vanderbilt Program in Developmental Biology, Vanderbilt Center for Stem Cell Biology, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN
- Epithelial Biology Center, Vanderbilt Medical Center, Nashville, TN
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Kung-Hsien Ho
- Vanderbilt Program in Developmental Biology, Vanderbilt Center for Stem Cell Biology, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Bob Chen
- Vanderbilt Program in Developmental Biology, Vanderbilt Center for Stem Cell Biology, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN
- Epithelial Biology Center, Vanderbilt Medical Center, Nashville, TN
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Alan J Simmons
- Vanderbilt Program in Developmental Biology, Vanderbilt Center for Stem Cell Biology, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN
- Epithelial Biology Center, Vanderbilt Medical Center, Nashville, TN
| | - Austin N Southard-Smith
- Vanderbilt Program in Developmental Biology, Vanderbilt Center for Stem Cell Biology, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN
- Epithelial Biology Center, Vanderbilt Medical Center, Nashville, TN
| | - Gregory David
- Department of Biochemistry and Molecular Pharmacology, New York University, New York, NY
| | - David A Jacobson
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Irina Kaverina
- Vanderbilt Program in Developmental Biology, Vanderbilt Center for Stem Cell Biology, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Christopher V E Wright
- Vanderbilt Program in Developmental Biology, Vanderbilt Center for Stem Cell Biology, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Ken S Lau
- Vanderbilt Program in Developmental Biology, Vanderbilt Center for Stem Cell Biology, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN
- Epithelial Biology Center, Vanderbilt Medical Center, Nashville, TN
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Guoqiang Gu
- Vanderbilt Program in Developmental Biology, Vanderbilt Center for Stem Cell Biology, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN
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12
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Szigety KM, Liu F, Yuan CY, Moran DJ, Horrell J, Gochnauer HR, Cohen RN, Katz JP, Kaestner KH, Seykora JT, Tobias JW, Lazar MA, Xu M, Millar SE. HDAC3 ensures stepwise epidermal stratification via NCoR/SMRT-reliant mechanisms independent of its histone deacetylase activity. Genes Dev 2020; 34:973-988. [PMID: 32467224 PMCID: PMC7328513 DOI: 10.1101/gad.333674.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/23/2020] [Indexed: 12/12/2022]
Abstract
Here, Szigety et al. investigated the function of histone deacetylases in epidermal development, and they found that HDAC3 operates in conjunction with KLF4 to repress inappropriate expression of Tgm1, Krt16, and Aqp3, and suppresses expression of inflammatory cytokines through a Rela-dependent mechanism. Their data identify HDAC3 as a hub coordinating multiple aspects of epidermal barrier acquisition. Chromatin modifiers play critical roles in epidermal development, but the functions of histone deacetylases in this context are poorly understood. The class I HDAC, HDAC3, is of particular interest because it plays divergent roles in different tissues by partnering with tissue-specific transcription factors. We found that HDAC3 is expressed broadly in embryonic epidermis and is required for its orderly stepwise stratification. HDAC3 protein stability in vivo relies on NCoR and SMRT, which function redundantly in epidermal development. However, point mutations in the NCoR and SMRT deacetylase-activating domains, which are required for HDAC3's enzymatic function, permit normal stratification, indicating that HDAC3's roles in this context are largely independent of its histone deacetylase activity. HDAC3-bound sites are significantly enriched for predicted binding motifs for critical epidermal transcription factors including AP1, GRHL, and KLF family members. Our results suggest that among these, HDAC3 operates in conjunction with KLF4 to repress inappropriate expression of Tgm1, Krt16, and Aqp3. In parallel, HDAC3 suppresses expression of inflammatory cytokines through a Rela-dependent mechanism. These data identify HDAC3 as a hub coordinating multiple aspects of epidermal barrier acquisition.
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Affiliation(s)
- Katherine M Szigety
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Fang Liu
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Chase Y Yuan
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Deborah J Moran
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jeremy Horrell
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Heather R Gochnauer
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ronald N Cohen
- Section of Endocrinology, Diabetes, and Metabolism, University of Chicago, Chicago, Illinois 60637, USA
| | - Jonathan P Katz
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Klaus H Kaestner
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - John T Seykora
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - John W Tobias
- Penn Genomic Analysis Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, Division of Endocrinology, Diabetes, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mingang Xu
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Sarah E Millar
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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13
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AL-Eitan LN, Alghamdi MA, Tarkhan AH, Al-Qarqaz FA. Genome-Wide Tiling Array Analysis of HPV-Induced Warts Reveals Aberrant Methylation of Protein-Coding and Non-Coding Regions. Genes (Basel) 2019; 11:E34. [PMID: 31892232 PMCID: PMC7017144 DOI: 10.3390/genes11010034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/18/2019] [Accepted: 12/22/2019] [Indexed: 12/18/2022] Open
Abstract
The human papillomaviruses (HPV) are a group of double-stranded DNA viruses that exhibit an exclusive tropism for squamous epithelia. HPV can either be low- or high-risk depending on its ability to cause benign lesions or cancer, respectively. Unsurprisingly, the majority of epigenetic research has focused on the high-risk HPV types, neglecting the low-risk types in the process. Therefore, the main objective of this study is to better understand the epigenetics of wart formation by investigating the differences in methylation between HPV-induced cutaneous warts and normal skin. A number of clear and very significant differences in methylation patterns were found between cutaneous warts and normal skin. Around 55% of the top-ranking 100 differentially methylated genes in warts were protein coding, including the EXOC4, KCNU, RTN1, LGI1, IRF2, and NRG1 genes. Additionally, non-coding RNA genes, such as the AZIN1-AS1, LINC02008, and MGC27382 genes, constituted 11% of the top-ranking 100 differentially methylated genes. Warts exhibited a unique pattern of methylation that is a possible explanation for their transient nature. Since the genetics of cutaneous wart formation are not completely known, the findings of the present study could contribute to a better understanding of how HPV infection modulates host methylation to give rise to warts in the skin.
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Affiliation(s)
- Laith N. AL-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan;
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Mansour A. Alghamdi
- Department of Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia;
| | - Amneh H. Tarkhan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Firas A. Al-Qarqaz
- Department of Internal Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan;
- Division of Dermatology, Department of Internal Medicine, King Abdullah University Hospital, Jordan University of Science and Technology, Irbid 22110, Jordan
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14
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Yang Y, Huang W, Qiu R, Liu R, Zeng Y, Gao J, Zheng Y, Hou Y, Wang S, Yu W, Leng S, Feng D, Wang Y. LSD1 coordinates with the SIN3A/HDAC complex and maintains sensitivity to chemotherapy in breast cancer. J Mol Cell Biol 2019; 10:285-301. [PMID: 29741645 DOI: 10.1093/jmcb/mjy021] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 01/21/2018] [Indexed: 01/26/2023] Open
Abstract
Lysine-specific demethylase 1 (LSD1) was the first histone demethylase identified as catalysing the removal of mono- and di-methylation marks on histone H3-K4. Despite the potential broad action of LSD1 in transcription regulation, recent studies indicate that LSD1 may coordinate with multiple epigenetic regulatory complexes including CoREST/HDAC complex, NuRD complex, SIRT1, and PRC2, implying complicated mechanistic actions of this seemingly simple enzyme. Here, we report that LSD1 is also an integral component of the SIN3A/HDAC complex. Transcriptional target analysis using ChIP-on-chip technology revealed that the LSD1/SIN3A/HDAC complex targets several cellular signalling pathways that are critically involved in cell proliferation, survival, metastasis, and apoptosis, especially the p53 signalling pathway. We have demonstrated that LSD1 coordinates with the SIN3A/HDAC complex in inhibiting a series of genes such as CASP7, TGFB2, CDKN1A(p21), HIF1A, TERT, and MDM2, some of which are oncogenic. Our experiments also found that LSD1 and SIN3A are required for optimal survival and growth of breast cancer cells while also essential for the maintenance of epithelial homoeostasis and chemosensitivity. Our data indicate that LSD1 is a functional alternative subunit of the SIN3A/HDAC complex, providing a molecular basis for the interplay of histone demethylation and deacetylation in chromatin remodelling, and suggest that the LSD1/SIN3A/HDAC complex could be a target for breast cancer therapeutic strategies.
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Affiliation(s)
- Yang Yang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wei Huang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Rongfang Qiu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ruiqiong Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yi Zeng
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jie Gao
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yu Zheng
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Yongqiang Hou
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Shuang Wang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wenqian Yu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Shuai Leng
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Dandan Feng
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yan Wang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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15
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Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood 2019; 133:1313-1324. [PMID: 30617194 PMCID: PMC6428665 DOI: 10.1182/blood-2018-09-871418] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/22/2018] [Indexed: 12/12/2022] Open
Abstract
Although generally curable with intensive chemotherapy in resource-rich settings, Burkitt lymphoma (BL) remains a deadly disease in older patients and in sub-Saharan Africa. Epstein-Barr virus (EBV) positivity is a feature in more than 90% of cases in malaria-endemic regions, and up to 30% elsewhere. However, the molecular features of BL have not been comprehensively evaluated when taking into account tumor EBV status or geographic origin. Through an integrative analysis of whole-genome and transcriptome data, we show a striking genome-wide increase in aberrant somatic hypermutation in EBV-positive tumors, supporting a link between EBV and activation-induced cytidine deaminase (AICDA) activity. In addition to identifying novel candidate BL genes such as SIN3A, USP7, and CHD8, we demonstrate that EBV-positive tumors had significantly fewer driver mutations, especially among genes with roles in apoptosis. We also found immunoglobulin variable region genes that were disproportionally used to encode clonal B-cell receptors (BCRs) in the tumors. These include IGHV4-34, known to produce autoreactive antibodies, and IGKV3-20, a feature described in other B-cell malignancies but not yet in BL. Our results suggest that tumor EBV status defines a specific BL phenotype irrespective of geographic origin, with particular molecular properties and distinct pathogenic mechanisms. The novel mutation patterns identified here imply rational use of DNA-damaging chemotherapy in some patients with BL and targeted agents such as the CDK4/6 inhibitor palbociclib in others, whereas the importance of BCR signaling in BL strengthens the potential benefit of inhibitors for PI3K, Syk, and Src family kinases among these patients.
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Affiliation(s)
- Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Aixiang Jiang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Nicholas B Griner
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jeremy S Abramson
- Center for Lymphoma, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Thomas B Alexander
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Leona W Ayers
- Department of Pathology, The Ohio State University, Columbus, OH
| | | | - Kishor Bhatia
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Jay Bowen
- Nationwide Children's Hospital, Columbus, OH
| | - Corey Casper
- Infectious Disease Research Institute, Seattle, WA
| | - John Kim Choi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Luka Culibrk
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Tanja M Davidsen
- Cancer Informatics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Maureen A Dyer
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD
| | - Julie M Gastier-Foster
- Nationwide Children's Hospital, Columbus, OH
- Departments of Pathology and Pediatrics, The Ohio State University, Columbus, OH
| | - Patee Gesuwan
- Cancer Informatics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Timothy C Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Thomas G Gross
- Center for Global Health, National Cancer Institute, National Institutes of Health, Rockville, MD
| | | | - Nancy Lee Harris
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Yiwen He
- Cancer Informatics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - John D Irvin
- Foundation for Burkitt Lymphoma Research, Geneva, Switzerland
| | - Elaine S Jaffe
- Laboratory of Pathology, Clinical Center, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Steven J M Jones
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Patrick Kerchan
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Nicole Knoetze
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Fabio E Leal
- Programa de Oncovirologia, Instituto Nacional de Câncer José de Alencar, Rio de Janeiro, Brazil
| | | | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | | | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | | | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Karen Novik
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Ariela Noy
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | | | | | | | - Steven J Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD; and
| | - Christopher K Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - John T Sandlund
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Roland Schmitz
- Lymphoid Malignancies Branch, Center for Cancer Research and
| | | | | | - George W Wright
- Biometric Research Program, Division of Cancer Diagnosis and Treatment, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Eric Y Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Louis M Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research and
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16
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Zhang M, Lykke-Andersen S, Zhu B, Xiao W, Hoskins JW, Zhang X, Rost LM, Collins I, van de Bunt M, Jia J, Parikh H, Zhang T, Song L, Jermusyk A, Chung CC, Zhu B, Zhou W, Matters GL, Kurtz RC, Yeager M, Jensen TH, Brown KM, Ongen H, Bamlet WR, Murray BA, McCarthy MI, Chanock SJ, Chatterjee N, Wolpin BM, Smith JP, Olson SH, Petersen GM, Shi J, Amundadottir LT. Characterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues. Gut 2018; 67:521-533. [PMID: 28634199 PMCID: PMC5762429 DOI: 10.1136/gutjnl-2016-313146] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To elucidate the genetic architecture of gene expression in pancreatic tissues. DESIGN We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. RESULTS We identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0.1), with the strongest effects seen near transcriptional start sites. Approximately 23% and 42% of genes with significant cis-eQTLs appeared to be specific for tumour-derived and normal-derived tissues, respectively. Significant enrichment of cis-eQTL variants was noted in non-coding regulatory regions, in particular for pancreatic tissues (1.53-fold to 3.12-fold, p≤0.0001), indicating tissue-specific functional relevance. A common pancreatic cancer risk locus on 9q34.2 (rs687289) was associated with ABO expression in histologically normal (p=5.8×10-8) and tumour-derived (p=8.3×10-5) tissues. The high linkage disequilibrium between this variant and the O blood group generating deletion variant in ABO (exon 6) suggested that nonsense-mediated decay (NMD) of the 'O' mRNA might explain this finding. However, knockdown of crucial NMD regulators did not influence decay of the ABO 'O' mRNA, indicating that a gene regulatory element influenced by pancreatic cancer risk alleles may underlie the eQTL. CONCLUSIONS We have identified cis-eQTLs representing potential functional regulatory variants in the pancreas and generated a rich data set for further studies on gene expression and its regulation in pancreatic tissues.
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Affiliation(s)
- Mingfeng Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Soren Lykke-Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Bin Zhu
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Wenming Xiao
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
| | - Jason W. Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Xijun Zhang
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 20892, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Lauren M. Rost
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Irene Collins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Martijn van de Bunt
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford OX3 7LJ, UK
| | - Jinping Jia
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Hemang Parikh
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, USA
| | - Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Lei Song
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Ashley Jermusyk
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Charles C. Chung
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 20892, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 20892, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 20892, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Gail L. Matters
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Robert C. Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 20892, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Kevin M. Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Halit Ongen
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - William R. Bamlet
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Bradley A. Murray
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, Massachusetts 02142, USA
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford OX3 7LJ, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Old Road, Headington, Oxford OX3 7LE, UK
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Nilanjan Chatterjee
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jill P. Smith
- Division of Gastroenterology & Hepatology, Georgetown University Hospital, Washington, DC 20007, USA
| | - Sara H. Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Gloria M. Petersen
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Laufey T. Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
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17
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Moravec CE, Yousef H, Kinney BA, Salerno-Eichenholz R, Monestime CM, Martin BL, Sirotkin HI. Zebrafish sin3b mutants are viable but have size, skeletal, and locomotor defects. Dev Dyn 2017; 246:946-955. [PMID: 28850761 DOI: 10.1002/dvdy.24581] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/12/2017] [Accepted: 08/01/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The transcriptional co-repressor Sin3 is highly conserved from yeast to vertebrates and has multiple roles controlling cell fate, cell cycle progression, and senescence programming. Sin3 proteins recruit histone deacetylases and other chromatin modifying factors to specific loci through interactions with transcription factors including Myc, Rest, p53 and E2F. Most vertebrates have two Sin3 family members (sin3a and sin3b), but zebrafish have a second sin3a paralogue. In mice, sin3a and sin3b are essential for embryonic development. Sin3b knockout mice show defects in growth as well as bone and blood differentiation. RESULTS To study the requirement for Sin3b during development, we disrupted zebrafish sin3b using CRISPR-Cas9, and studied the effects on early development and locomotor behavior. CONCLUSIONS Surprisingly, Sin3b is not essential in zebrafish. sin3b mutants show a decrease in fitness, small size, changes to locomotor behavior, and delayed bone development. We did not detect a role for Sin3b in cell proliferation. Our analysis of the sin3b mutant revealed a more nuanced requirement for zebrafish Sin3b than would be predicted from analysis of mutants in other species. Developmental Dynamics 246:946-955, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Cara E Moravec
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York.,Genetics Gradate Program Stony Brook University, Stony Brook, New York
| | - Hakeem Yousef
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York
| | - Brian A Kinney
- Genetics Gradate Program Stony Brook University, Stony Brook, New York.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York
| | - Ryan Salerno-Eichenholz
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York
| | - Camillia M Monestime
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York
| | - Benjamin L Martin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York
| | - Howard I Sirotkin
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York.,Genetics Gradate Program Stony Brook University, Stony Brook, New York
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18
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Hacker SM, Backus KM, Lazear MR, Forli S, Correia BE, Cravatt BF. Global profiling of lysine reactivity and ligandability in the human proteome. Nat Chem 2017; 9:1181-1190. [PMID: 29168484 DOI: 10.1038/nchem.2826] [Citation(s) in RCA: 281] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/07/2017] [Indexed: 12/28/2022]
Abstract
Nucleophilic amino acids make important contributions to protein function, including performing key roles in catalysis and serving as sites for post-translational modification. Electrophilic groups that target amino-acid nucleophiles have been used to create covalent ligands and drugs, but have, so far, been mainly limited to cysteine and serine. Here, we report a chemical proteomic platform for the global and quantitative analysis of lysine residues in native biological systems. We have quantified, in total, more than 9,000 lysines in human cell proteomes and have identified several hundred residues with heightened reactivity that are enriched at protein functional sites and can frequently be targeted by electrophilic small molecules. We have also discovered lysine-reactive fragment electrophiles that inhibit enzymes by active site and allosteric mechanisms, as well as disrupt protein-protein interactions in transcriptional regulatory complexes, emphasizing the broad potential and diverse functional consequences of liganding lysine residues throughout the human proteome.
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Affiliation(s)
- Stephan M Hacker
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92307, USA
| | - Keriann M Backus
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92307, USA
| | - Michael R Lazear
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92307, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92307, USA
| | - Bruno E Correia
- Laboratory of Protein Design & Immunoengineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Benjamin F Cravatt
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92307, USA
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19
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Simmonds P, Loomis E, Curry E. DNA methylation-based chromatin compartments and ChIP-seq profiles reveal transcriptional drivers of prostate carcinogenesis. Genome Med 2017; 9:54. [PMID: 28592290 PMCID: PMC5463361 DOI: 10.1186/s13073-017-0443-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/23/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Profiles of DNA methylation of many tissues relevant in human disease have been obtained from microarrays and are publicly available. These can be used to generate maps of chromatin compartmentalization, demarcating open and closed chromatin across the genome. Additionally, large sets of genome-wide transcription factor binding profiles have been made available thanks to ChIP-seq technology. METHODS We have identified genomic regions with altered chromatin compartmentalization in prostate adenocarcinoma tissue relative to normal prostate tissue, using DNA methylation microarray data from The Cancer Genome Atlas. DNA binding profiles from the Encyclopedia of DNA Elements (ENCODE) ChIP-seq studies have been systematically screened to find transcription factors with inferred DNA binding sites located in discordantly open/closed chromatin in malignant tissue (compared with non-cancer control tissue). We have combined this with tests for corresponding up-/downregulation of the transcription factors' putative target genes to obtain an integrated measure of cancer-specific regulatory activity to identify likely transcriptional drivers of prostate cancer. RESULTS Generally, we find that the degree to which transcription factors preferentially bind regions of chromatin that become more accessible during prostate carcinogenesis is significantly associated to the level of systematic upregulation of their targets, at the level of gene expression. Our approach has yielded 11 transcription factors that show strong cancer-specific transcriptional activation of targets, including the novel candidates KAT2A and TRIM28, alongside established drivers of prostate cancer MYC, ETS1, GABP and YY1. CONCLUSIONS This approach to integrated epigenetic and transcriptional profiling using publicly available data represents a cheap and powerful technique for identifying potential drivers of human disease. In our application to prostate adenocarcinoma data, the fact that well-known drivers are amongst the top candidates suggests that the discovery of novel candidate drivers may unlock pathways to future medicines. Data download instructions and code to reproduce this work are available at GitHub under 'edcurry/PRAD-compartments'.
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Affiliation(s)
- Poppy Simmonds
- Division of Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK.,Centre for Cell, Gene & Tissue Therapeutics, UCL Medical School, Royal Free Hospital, Pond Street, London, NW3 2QG, UK
| | - Erick Loomis
- Helix, 1 Circle Star Way, San Carlos, CA, 94070, USA
| | - Edward Curry
- Division of Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK.
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20
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Streubel G, Fitzpatrick DJ, Oliviero G, Scelfo A, Moran B, Das S, Munawar N, Watson A, Wynne K, Negri GL, Dillon ET, Jammula S, Hokamp K, O'Connor DP, Pasini D, Cagney G, Bracken AP. Fam60a defines a variant Sin3a‐Hdac complex in embryonic stem cells required for self‐renewal. EMBO J 2017. [DOI: https://doi.org/10.15252/embj.201696307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
| | | | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Andrea Scelfo
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Bruce Moran
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Sudipto Das
- Department of Molecular and Cellular Therapeutics Royal College of Surgeons in Ireland Dublin 2 Ireland
| | - Nayla Munawar
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Gian Luca Negri
- Department of Molecular Oncology British Columbia Cancer Research Center Vancouver BC Canada
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - SriGanesh Jammula
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Karsten Hokamp
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
| | - Darran P O'Connor
- Department of Molecular and Cellular Therapeutics Royal College of Surgeons in Ireland Dublin 2 Ireland
| | - Diego Pasini
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
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21
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Streubel G, Fitzpatrick DJ, Oliviero G, Scelfo A, Moran B, Das S, Munawar N, Watson A, Wynne K, Negri GL, Dillon ET, Jammula S, Hokamp K, O'Connor DP, Pasini D, Cagney G, Bracken AP. Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for self-renewal. EMBO J 2017; 36:2216-2232. [PMID: 28554894 DOI: 10.15252/embj.201696307] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/18/2017] [Accepted: 04/22/2017] [Indexed: 12/15/2022] Open
Abstract
Sin3a is the central scaffold protein of the prototypical Hdac1/2 chromatin repressor complex, crucially required during early embryonic development for the growth of pluripotent cells of the inner cell mass. Here, we compare the composition of the Sin3a-Hdac complex between pluripotent embryonic stem (ES) and differentiated cells by establishing a method that couples two independent endogenous immunoprecipitations with quantitative mass spectrometry. We define the precise composition of the Sin3a complex in multiple cell types and identify the Fam60a subunit as a key defining feature of a variant Sin3a complex present in ES cells, which also contains Ogt and Tet1. Fam60a binds on H3K4me3-positive promoters in ES cells, together with Ogt, Tet1 and Sin3a, and is essential to maintain the complex on chromatin. Finally, we show that depletion of Fam60a phenocopies the loss of Sin3a, leading to reduced proliferation, an extended G1-phase and the deregulation of lineage genes. Taken together, Fam60a is an essential core subunit of a variant Sin3a complex in ES cells that is required to promote rapid proliferation and prevent unscheduled differentiation.
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Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Andrea Scelfo
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Bruce Moran
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Sudipto Das
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Nayla Munawar
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Gian Luca Negri
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC, Canada
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - SriGanesh Jammula
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Darran P O'Connor
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Diego Pasini
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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22
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Witteveen JS, Willemsen MH, Dombroski TCD, van Bakel NHM, Nillesen WM, van Hulten JA, Jansen EJR, Verkaik D, Veenstra-Knol HE, van Ravenswaaij-Arts CMA, Wassink-Ruiter JSK, Vincent M, David A, Le Caignec C, Schieving J, Gilissen C, Foulds N, Rump P, Strom T, Cremer K, Zink AM, Engels H, de Munnik SA, Visser JE, Brunner HG, Martens GJM, Pfundt R, Kleefstra T, Kolk SM. Haploinsufficiency of MeCP2-interacting transcriptional co-repressor SIN3A causes mild intellectual disability by affecting the development of cortical integrity. Nat Genet 2016; 48:877-87. [PMID: 27399968 DOI: 10.1038/ng.3619] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 06/15/2016] [Indexed: 12/13/2022]
Abstract
Numerous genes are associated with neurodevelopmental disorders such as intellectual disability and autism spectrum disorder (ASD), but their dysfunction is often poorly characterized. Here we identified dominant mutations in the gene encoding the transcriptional repressor and MeCP2 interactor switch-insensitive 3 family member A (SIN3A; chromosome 15q24.2) in individuals who, in addition to mild intellectual disability and ASD, share striking features, including facial dysmorphisms, microcephaly and short stature. This phenotype is highly related to that of individuals with atypical 15q24 microdeletions, linking SIN3A to this microdeletion syndrome. Brain magnetic resonance imaging showed subtle abnormalities, including corpus callosum hypoplasia and ventriculomegaly. Intriguingly, in vivo functional knockdown of Sin3a led to reduced cortical neurogenesis, altered neuronal identity and aberrant corticocortical projections in the developing mouse brain. Together, our data establish that haploinsufficiency of SIN3A is associated with mild syndromic intellectual disability and that SIN3A can be considered to be a key transcriptional regulator of cortical brain development.
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Affiliation(s)
- Josefine S Witteveen
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Thaís C D Dombroski
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Nick H M van Bakel
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Willy M Nillesen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Josephus A van Hulten
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Eric J R Jansen
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Dave Verkaik
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Hermine E Veenstra-Knol
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | | | - Marie Vincent
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, Nantes, France
| | - Albert David
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, Nantes, France
| | - Cedric Le Caignec
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, Nantes, France.,Laboratoire de Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Faculté de Médecine, INSERM UMRS 957, Nantes, France
| | - Jolanda Schieving
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Nicola Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton National Health Service Foundation Trust, Princess Anne Hospital, Southampton, UK.,Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Patrick Rump
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tim Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Sonja A de Munnik
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Jasper E Visser
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Neurology, Amphia Hospital Breda, Berda, the Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Gerard J M Martens
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Sharon M Kolk
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
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23
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Abstract
Human retinoblastoma gene RB1 is the first tumor suppressor gene (TSG) isolated by positional cloning in 1986. RB is extensively studied for its ability to regulate cell cycle by binding to E2F1 and inhibiting the transcriptional activity of the latter. In human embryonic stem cells (ESCs), only a minute trace of RB is found in complex with E2F1. Increased activity of RB triggers differentiation, cell cycle arrest, and cell death. On the other hand, inactivation of the entire RB family (RB1, RBL1, and RBL2) in human ESC induces G2/M arrest and cell death. These observations indicate that both loss and overactivity of RB could be lethal for the stemness of cells. A question arises why inactive RB is required for the survival and stemness of cells? To shed some light on this question, we analyzed the RB-binding proteins. In this review we have focused on 27 RB-binding partners that may have potential roles in different aspects of stem cell biology.
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Affiliation(s)
- M Mushtaq
- Karolinska Institutet, Stockholm, Sweden
| | | | - E V Kashuba
- Karolinska Institutet, Stockholm, Sweden; R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, NASU, Kyiv, Ukraine.
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24
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Ito T, Tsuji G, Ohno F, Uchi H, Nakahara T, Hashimoto-Hachiya A, Yoshida Y, Yamamoto O, Oda Y, Furue M. Activation of the OVOL1-OVOL2 Axis in the Hair Bulb and in Pilomatricoma. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:1036-43. [PMID: 26873447 DOI: 10.1016/j.ajpath.2015.12.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 11/25/2015] [Accepted: 12/07/2015] [Indexed: 12/27/2022]
Abstract
OVOL1 and OVOL2, ubiquitously conserved genes encoding C2H2 zinc finger transcription factors in mammals, control epithelial cell proliferation, and differentiation, including those in skin. OVOL1 and OVOL2 expression is coordinately mediated via the Wnt signaling pathway, and OVOL1 negatively regulates OVOL2 expression in a transcriptional manner. Our previous study of OVOL1 expression in human skin revealed that OVOL1 is preferentially expressed in the inner root sheath of the hair follicle. Therefore, we hypothesized that the OVOL1-OVOL2 axis is involved in normal and neoplastic follicular differentiation. Immunohistochemical analysis showed that OVOL1 and OVOL2 were strongly expressed in a mutually exclusive manner in the cytoplasm of inner root sheath cells and matrix cells, respectively, in normal follicles. OVOL2 was also expressed in pilomatricoma, with only partial expression of OVOL1. Cultured human keratinocytes expressed OVOL1 and OVOL2 on both the mRNA and protein levels. The expression of OVOL2 was higher in keratinocytes transfected with siRNA of OVOL1. Ketoconazole, a hair growth stimulant, up-regulated the expression of OVOL1 but did not affect OVOL2 expression. These results indicated that the OVOL1-OVOL2 axis may actively contribute to cell differentiation and proliferation in the hair bulb, suggesting that the OVOL1 and OVOL2 may be therapeutic targets of hair disorders, including alopecia, and play important roles in the tumorigenesis of pilomatricoma.
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Affiliation(s)
- Takamichi Ito
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Gaku Tsuji
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Fumitaka Ohno
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroshi Uchi
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Nakahara
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Division of Skin Surface Sensing, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Akiko Hashimoto-Hachiya
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuichi Yoshida
- Division of Dermatology, Department of Medicine of Sensory and Motor Organs, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Osamu Yamamoto
- Division of Dermatology, Department of Medicine of Sensory and Motor Organs, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masutaka Furue
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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25
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Matsumura H, Mohri Y, Binh NT, Morinaga H, Fukuda M, Ito M, Kurata S, Hoeijmakers J, Nishimura EK. Hair follicle aging is driven by transepidermal elimination of stem cells via COL17A1 proteolysis. Science 2016; 351:aad4395. [PMID: 26912707 DOI: 10.1126/science.aad4395] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/17/2015] [Indexed: 12/12/2022]
Abstract
Hair thinning and loss are prominent aging phenotypes but have an unknown mechanism. We show that hair follicle stem cell (HFSC) aging causes the stepwise miniaturization of hair follicles and eventual hair loss in wild-type mice and in humans. In vivo fate analysis of HFSCs revealed that the DNA damage response in HFSCs causes proteolysis of type XVII collagen (COL17A1/BP180), a critical molecule for HFSC maintenance, to trigger HFSC aging, characterized by the loss of stemness signatures and by epidermal commitment. Aged HFSCs are cyclically eliminated from the skin through terminal epidermal differentiation, thereby causing hair follicle miniaturization. The aging process can be recapitulated by Col17a1 deficiency and prevented by the forced maintenance of COL17A1 in HFSCs, demonstrating that COL17A1 in HFSCs orchestrates the stem cell-centric aging program of the epithelial mini-organ.
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Affiliation(s)
- Hiroyuki Matsumura
- Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Yasuaki Mohri
- Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Nguyen Thanh Binh
- Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan. Department of Stem Cell Medicine, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-0934, Japan
| | - Hironobu Morinaga
- Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Makoto Fukuda
- Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Mayumi Ito
- Departments of Dermatology and Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Sotaro Kurata
- Beppu Garden-Hill Clinic, Kurata Clinic, Beppu city, Oita 8740831, Japan
| | - Jan Hoeijmakers
- Department of Genetics, Cancer Genomics Center, Erasmus MC, Room Ee 722, Dr. Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Emi K Nishimura
- Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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26
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Childress P, Stayrook KR, Alvarez MB, Wang Z, Shao Y, Hernandez-Buquer S, Mack JK, Grese ZR, He Y, Horan D, Pavalko FM, Warden SJ, Robling AG, Yang FC, Allen MR, Krishnan V, Liu Y, Bidwell JP. Genome-Wide Mapping and Interrogation of the Nmp4 Antianabolic Bone Axis. Mol Endocrinol 2015; 29:1269-85. [PMID: 26244796 DOI: 10.1210/me.2014-1406] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
PTH is an osteoanabolic for treating osteoporosis but its potency wanes. Disabling the transcription factor nuclear matrix protein 4 (Nmp4) in healthy, ovary-intact mice enhances bone response to PTH and bone morphogenetic protein 2 and protects from unloading-induced osteopenia. These Nmp4(-/-) mice exhibit expanded bone marrow populations of osteoprogenitors and supporting CD8(+) T cells. To determine whether the Nmp4(-/-) phenotype persists in an osteoporosis model we compared PTH response in ovariectomized (ovx) wild-type (WT) and Nmp4(-/-) mice. To identify potential Nmp4 target genes, we performed bioinformatic/pathway profiling on Nmp4 chromatin immunoprecipitation sequencing (ChIP-seq) data. Mice (12 w) were ovx or sham operated 4 weeks before the initiation of PTH therapy. Skeletal phenotype analysis included microcomputed tomography, histomorphometry, serum profiles, fluorescence-activated cell sorting and the growth/mineralization of cultured WT and Nmp4(-/-) bone marrow mesenchymal stem progenitor cells (MSPCs). ChIP-seq data were derived using MC3T3-E1 preosteoblasts, murine embryonic stem cells, and 2 blood cell lines. Ovx Nmp4(-/-) mice exhibited an improved response to PTH coupled with elevated numbers of osteoprogenitors and CD8(+) T cells, but were not protected from ovx-induced bone loss. Cultured Nmp4(-/-) MSPCs displayed enhanced proliferation and accelerated mineralization. ChIP-seq/gene ontology analyses identified target genes likely under Nmp4 control as enriched for negative regulators of biosynthetic processes. Interrogation of mRNA transcripts in nondifferentiating and osteogenic differentiating WT and Nmp4(-/-) MSPCs was performed on 90 Nmp4 target genes and differentiation markers. These data suggest that Nmp4 suppresses bone anabolism, in part, by regulating IGF-binding protein expression. Changes in Nmp4 status may lead to improvements in osteoprogenitor response to therapeutic cues.
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Affiliation(s)
- Paul Childress
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Keith R Stayrook
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Marta B Alvarez
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Zhiping Wang
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Yu Shao
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Selene Hernandez-Buquer
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Justin K Mack
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Zachary R Grese
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Yongzheng He
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Daniel Horan
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Fredrick M Pavalko
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Stuart J Warden
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Alexander G Robling
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Feng-Chun Yang
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Matthew R Allen
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Venkatesh Krishnan
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Yunlong Liu
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
| | - Joseph P Bidwell
- Department of Anatomy and Cell Biology (P.C., S.H.-B., D.H., A.G.R., M.R.A., J.P.B.), Indiana University School of Medicine, Indianapolis, Indiana 46202; Lilly Research Laboratories (K.R.S., J.K.M., Z.R.G., V.K.), Eli Lilly and Company, Indianapolis, Indiana 46202; Orthopaedic Surgery (M.B.A.), Indiana University School of Medicine; Department of Medical and Molecular Genetics (Z.W., Y.S., Y.L., J.P.B.), Indiana University School of Medicine; Center for Computational Biology and Bioinformatics (Z.W., Y.L.), Indiana University School of Medicine; Department of Pediatrics (Y.H., F.-C.Y.), Indiana University School of Medicine; Herman B Wells Center for Pediatric Research (Y.H., F.-C.Y.); Cellular and Integrative Physiology (F.M.P.); Center for Translational Musculoskeletal Research (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University; and Department of Physical Therapy (S.J.W.), School of Health and Rehabilitation Sciences, Indiana University, Indianapolis, Indiana 46202
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Kadamb R, Mittal S, Bansal N, Saluja D. Stress-mediated Sin3B activation leads to negative regulation of subset of p53 target genes. Biosci Rep 2015; 35:e00234. [PMID: 26181367 PMCID: PMC4613689 DOI: 10.1042/bsr20150122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/03/2015] [Accepted: 06/19/2015] [Indexed: 11/28/2022] Open
Abstract
The multiprotein SWI-independent 3 (Sin3)-HDAC (histone deacetylase) corepressor complex mediates gene repression through its interaction with DNA-binding factors and recruitment of chromatin-modifying proteins on to the promoters of target gene. Previously, an increased expression of Sin3B and tumour suppressor protein, p53 has been established upon adriamycin treatment. We, now provide evidence that Sin3B expression is significantly up-regulated under variety of stress conditions and this response is not stress-type specific. We observed that Sin3B expression is significantly up-regulated both at transcript and at protein level upon DNA damage induced by bleomycin drug, a radiomimetic agent. This increase in Sin3B expression upon stress is found to be p53-dependent and is associated with enhanced interaction of Sin3B with Ser(15) phosphorylated p53. Binding of Sin3-HDAC repressor complex on to the promoters of p53 target genes influences gene regulation by altering histone modifications (H3K9me3 and H3K27me3) at target genes. Furthermore, knockdown of Sin3B by shRNA severely compromises p53-mediated gene repression under stress conditions. Taken together, these results suggest that stress-induced Sin3B activation is p53-dependent and is essential for p53-mediated repression of its selective target genes. The present study has an implication in understanding the transrepression mechanism of p53 under DNA damaging conditions.
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Affiliation(s)
- Rama Kadamb
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
| | - Shilpi Mittal
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
| | - Nidhi Bansal
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
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Yuan T, Jiao Y, de Jong S, Ophoff RA, Beck S, Teschendorff AE. An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging. PLoS Genet 2015; 11:e1004996. [PMID: 25692570 PMCID: PMC4334892 DOI: 10.1371/journal.pgen.1004996] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/10/2015] [Indexed: 12/21/2022] Open
Abstract
Recent studies have demonstrated that the DNA methylome changes with age. This epigenetic drift may have deep implications for cellular differentiation and disease development. However, it remains unclear how much of this drift is functional or caused by underlying changes in cell subtype composition. Moreover, no study has yet comprehensively explored epigenetic drift at different genomic length scales and in relation to regulatory elements. Here we conduct an in-depth analysis of epigenetic drift in blood tissue. We demonstrate that most of the age-associated drift is independent of the increase in the granulocyte to lymphocyte ratio that accompanies aging and that enrichment of age-hypermethylated CpG islands increases upon adjustment for cellular composition. We further find that drift has only a minimal impact on in-cis gene expression, acting primarily to stabilize pre-existing baseline expression levels. By studying epigenetic drift at different genomic length scales, we demonstrate the existence of mega-base scale age-associated hypomethylated blocks, covering approximately 14% of the human genome, and which exhibit preferential hypomethylation in age-matched cancer tissue. Importantly, we demonstrate the feasibility of integrating Illumina 450k DNA methylation with ENCODE data to identify transcription factors with key roles in cellular development and aging. Specifically, we identify REST and regulatory factors of the histone methyltransferase MLL complex, whose function may be disrupted in aging. In summary, most of the epigenetic drift seen in blood is independent of changes in blood cell type composition, and exhibits patterns at different genomic length scales reminiscent of those seen in cancer. Integration of Illumina 450k with appropriate ENCODE data may represent a fruitful approach to identify transcription factors with key roles in aging and disease. Two well-known features of aging are the gradual decline of the body’s ability to regenerate tissues, as well as an increased incidence of diseases like cancer and Alzheimers. One of the most recent exciting findings which may underlie the aging process is a gradual modification of DNA, called epigenetic drift, which is effected by the covalent addition and removal of methyl groups, which in turn can deregulate the activity of nearby genes. However, this study presents the most convincing evidence to date that epigenetic drift acts to stabilize the activity levels of nearby genes. This study shows that instead, epigenetic drift may act primarly to disrupt DNA binding patterns of proteins which regulate the activity of many genes, and moreover identifies specific regulatory proteins with key roles in cancer and Alzheimers. The study also performs the most comprehensive analysis of epigenetic drift at different spatial scales, demonstrating that epigenetic drift on the largest length scales is highly reminiscent of those seen in cancer. In summary, this work substantially supports the view that epigenetic drift may contribute to the age-associated increased risk of diseases like cancer and Alzheimers, by disrupting master regulators of genomewide gene activity.
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Affiliation(s)
- Tian Yuan
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, Shanghai, China
| | - Yinming Jiao
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, Shanghai, China
| | - Simone de Jong
- Center for Neurobehavioral Genetics, Los Angeles, California, USA
| | - Roel A. Ophoff
- Center for Neurobehavioral Genetics, Los Angeles, California, USA
| | - Stephan Beck
- Medical Genomics Group, UCL Cancer Institute, University College London, London, United Kingdom
| | - Andrew E. Teschendorff
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, Shanghai, China
- Statistical Genomics Group, UCL Cancer Institute, University College London, London, United Kingdom
- * E-mail: (AET), (AET)
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30
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A role for the serine/arginine-rich (SR) protein B52/SRSF6 in cell growth and myc expression in Drosophila. Genetics 2015; 199:1201-11. [PMID: 25680814 PMCID: PMC4391563 DOI: 10.1534/genetics.115.174391] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/11/2015] [Indexed: 11/18/2022] Open
Abstract
Serine-/arginine-rich (SR) proteins are RNA-binding proteins that are primarily involved in alternative splicing. Expression of some SR proteins is frequently upregulated in tumors, and previous reports have demonstrated that these proteins can directly participate in cell transformation. Identifying factors that can rescue the effects of SR overexpression in vivo is, therefore, of potential therapeutic interest. Here, we analyzed phenotypes induced by overexpression of the SR protein B52 during Drosophila development and identified several proteins that can rescue these phenotypes. Using the mechanosensory bristle lineage as a developmental model, we show that B52 expression level influences cell growth, but not differentiation, in this lineage. In particular, B52 overexpression increases cell growth, upregulates myc transcription, and gives rise to flies lacking thoracic bristles. Using a genetic screen, we identified several suppressors of the phenotypes induced by overexpression of B52 in vivo in two different organs. We show that upregulation of brain tumor (brat), a tumor suppressor and post-transcriptional repressor of myc, and downregulation of lilliputian (lilli), a subunit of the superelongation complex involved in transcription elongation, efficiently rescue the phenotypes induced by B52 overexpression. Our results demonstrate a role of this SR protein in cell growth and identify candidate proteins that may overcome the effects of SR protein overexpression in mammals.
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Sawicka A, Hartl D, Goiser M, Pusch O, Stocsits RR, Tamir IM, Mechtler K, Seiser C. H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress. Genome Res 2014; 24:1808-20. [PMID: 25135956 PMCID: PMC4216922 DOI: 10.1101/gr.176255.114] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 08/14/2014] [Indexed: 12/26/2022]
Abstract
The selectivity of transcriptional responses to extracellular cues is reflected by the deposition of stimulus-specific chromatin marks. Although histone H3 phosphorylation is a target of numerous signaling pathways, its role in transcriptional regulation remains poorly understood. Here, for the first time, we report a genome-wide analysis of H3S28 phosphorylation in a mammalian system in the context of stress signaling. We found that this mark targets as many as 50% of all stress-induced genes, underlining its importance in signal-induced transcription. By combining ChIP-seq, RNA-seq, and mass spectrometry we identified the factors involved in the biological interpretation of this histone modification. We found that MSK1/2-mediated phosphorylation of H3S28 at stress-responsive promoters contributes to the dissociation of HDAC corepressor complexes and thereby to enhanced local histone acetylation and subsequent transcriptional activation of stress-induced genes. Our data reveal a novel function of the H3S28ph mark in the activation of mammalian genes in response to MAP kinase pathway activation.
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Affiliation(s)
- Anna Sawicka
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
| | - Dominik Hartl
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
| | - Malgorzata Goiser
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, 1030 Vienna, Austria; Research Institute of Molecular Pathology, 1030 Vienna, Austria
| | - Oliver Pusch
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Ido M Tamir
- Campus Science Support Facilities GmbH, 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology, 1030 Vienna, Austria; Protein Chemistry Facility, IMBA Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Christian Seiser
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, 1030 Vienna, Austria;
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32
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Rinaldi L, Benitah SA. Epigenetic regulation of adult stem cell function. FEBS J 2014; 282:1589-604. [PMID: 25060320 DOI: 10.1111/febs.12946] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/17/2014] [Accepted: 07/22/2014] [Indexed: 01/09/2023]
Abstract
Understanding the cellular and molecular mechanisms that specify cell lineages throughout development, and that maintain tissue homeostasis during adulthood, is paramount towards our understanding of why we age or develop pathologies such as cancer. Epigenetic mechanisms ensure that genetically identical cells acquire different fates during embryonic development and are therefore essential for the proper progression of development. How they do so is still a matter of intense investigation, but there is sufficient evidence indicating that they act in a concerted manner with inductive signals and tissue-specific transcription factors to promote and stabilize fate changes along the three germ layers during development. In consequence, it is generally hypothesized that epigenetic mechanisms are also required for the continuous maintenance of cell fate during adulthood. However, in vivo models in which different epigenetic factors have been depleted in different tissues do not show overt changes in cell lineage, thus not strongly supporting this view. Instead, the function of some of these factors appears to be primarily associated with tissue functionality, and a strong causal relationship has been established between their misregulation and a diseased state. In this review, we summarize our current knowledge of the role of epigenetic factors in adult stem cell function and tissue homeostasis.
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Affiliation(s)
- Lorenzo Rinaldi
- Centre for Genomic Regulation, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain
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Garcia-Sanz P, Quintanilla A, Lafita MC, Moreno-Bueno G, García-Gutierrez L, Tabor V, Varela I, Shiio Y, Larsson LG, Portillo F, Leon J. Sin3b interacts with Myc and decreases Myc levels. J Biol Chem 2014; 289:22221-36. [PMID: 24951594 DOI: 10.1074/jbc.m113.538744] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Myc expression is deregulated in many human cancers. A yeast two-hybrid screen has revealed that the transcriptional repressor Sin3b interacts with Myc protein. Endogenous Myc and Sin3b co-localize and interact in the nuclei of human and rat cells, as assessed by co-immunoprecipitation, immunofluorescence, and proximity ligation assay. The interaction is Max-independent. A conserved Myc region (amino acids 186-203) is required for the interaction with Sin3 proteins. Histone deacetylase 1 is recruited to Myc-Sin3b complexes, and its deacetylase activity is required for the effects of Sin3b on Myc. Myc and Sin3a/b co-occupied many sites on the chromatin of human leukemia cells, although the presence of Sin3 was not associated with gene down-regulation. In leukemia cells and fibroblasts, Sin3b silencing led to Myc up-regulation, whereas Sin3b overexpression induced Myc deacetylation and degradation. An analysis of Sin3b expression in breast tumors revealed an association between low Sin3b expression and disease progression. The data suggest that Sin3b decreases Myc protein levels upon Myc deacetylation. As Sin3b is also required for transcriptional repression by Mxd-Max complexes, our results suggest that, at least in some cell types, Sin3b limits Myc activity through two complementary activities: Mxd-dependent gene repression and reduction of Myc levels.
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Affiliation(s)
- Pablo Garcia-Sanz
- From the Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas, Universidad de Cantabria, Sociedad para el Desarrollo de Cantabria and the Departamento de Biología Molecular, Universidad de Cantabria, Santander 39011, Spain, the Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas, Instituto de Investigación Hospital Universitario La Paz (IdiPaz), Facultad de Medicina, Universidad Autónoma de Madrid, 28046 Madrid, Spain, the Fundación M. D. Anderson Internacional, Madrid, Spain
| | - Andrea Quintanilla
- From the Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas, Universidad de Cantabria, Sociedad para el Desarrollo de Cantabria and the Departamento de Biología Molecular, Universidad de Cantabria, Santander 39011, Spain
| | - M Carmen Lafita
- From the Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas, Universidad de Cantabria, Sociedad para el Desarrollo de Cantabria and the Departamento de Biología Molecular, Universidad de Cantabria, Santander 39011, Spain
| | - Gema Moreno-Bueno
- the Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas, Instituto de Investigación Hospital Universitario La Paz (IdiPaz), Facultad de Medicina, Universidad Autónoma de Madrid, 28046 Madrid, Spain, the Fundación M. D. Anderson Internacional, Madrid, Spain
| | - Lucia García-Gutierrez
- From the Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas, Universidad de Cantabria, Sociedad para el Desarrollo de Cantabria and the Departamento de Biología Molecular, Universidad de Cantabria, Santander 39011, Spain
| | - Vedrana Tabor
- the Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm SE-17177, Sweden, and
| | - Ignacio Varela
- From the Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas, Universidad de Cantabria, Sociedad para el Desarrollo de Cantabria and the Departamento de Biología Molecular, Universidad de Cantabria, Santander 39011, Spain
| | - Yuzuru Shiio
- the Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, Texas 78229-3900
| | - Lars-Gunnar Larsson
- the Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm SE-17177, Sweden, and
| | - Francisco Portillo
- the Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas, Instituto de Investigación Hospital Universitario La Paz (IdiPaz), Facultad de Medicina, Universidad Autónoma de Madrid, 28046 Madrid, Spain,
| | - Javier Leon
- From the Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas, Universidad de Cantabria, Sociedad para el Desarrollo de Cantabria and the Departamento de Biología Molecular, Universidad de Cantabria, Santander 39011, Spain,
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Hsa-miR-520d induces hepatoma cells to form normal liver tissues via a stemness-mediated process. Sci Rep 2014; 4:3852. [PMID: 24458129 PMCID: PMC3900933 DOI: 10.1038/srep03852] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 01/06/2014] [Indexed: 01/07/2023] Open
Abstract
The human ncRNA gene RGM249 regulates the extent of differentiation of cancer cells and the conversion of 293FT cells to hiPSCs. To identify the factors underlying this process, we investigated the effects of lentivirally inducing miR-520d expression in 293FT and HLF cells in vitro. Subsequently, we evaluated tumor formation in a xenograft model. Transformed HLF cells were Oct4 and Nanog positive within 24 h, showed p53 upregulation and hTERT downregulation, and mostly lost their migration abilities. After lentiviral infection, the cells were intraperitoneally injected into mice, resulting in benign teratomas (6%), the absence of tumors (87%) or differentiation into benign liver tissues (7%) at the injection site after 1 month. We are the first to demonstrate the loss of malignant properties in cancer cells in vivo through the expression of a single microRNA (miRNA). This miRNA successfully converted 293FT and hepatoma cells to hiPSC-like cells. The regulation of malignancy by miR-520d appears to be through the conversion of cancer cells to normal stem cells, maintaining p53 upregulation.
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35
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Kheradpour P, Kellis M. Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res 2013; 42:2976-87. [PMID: 24335146 PMCID: PMC3950668 DOI: 10.1093/nar/gkt1249] [Citation(s) in RCA: 313] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Recent advances in technology have led to a dramatic increase in the number of available transcription factor ChIP-seq and ChIP-chip data sets. Understanding the motif content of these data sets is an important step in understanding the underlying mechanisms of regulation. Here we provide a systematic motif analysis for 427 human ChIP-seq data sets using motifs curated from the literature and also discovered de novo using five established motif discovery tools. We use a systematic pipeline for calculating motif enrichment in each data set, providing a principled way for choosing between motif variants found in the literature and for flagging potentially problematic data sets. Our analysis confirms the known specificity of 41 of the 56 analyzed factor groups and reveals motifs of potential cofactors. We also use cell type-specific binding to find factors active in specific conditions. The resource we provide is accessible both for browsing a small number of factors and for performing large-scale systematic analyses. We provide motif matrices, instances and enrichments in each of the ENCODE data sets. The motifs discovered here have been used in parallel studies to validate the specificity of antibodies, understand cooperativity between data sets and measure the variation of motif binding across individuals and species.
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Affiliation(s)
- Pouya Kheradpour
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA and Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02139, USA
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36
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Winter M, Moser MA, Meunier D, Fischer C, Machat G, Mattes K, Lichtenberger BM, Brunmeir R, Weissmann S, Murko C, Humer C, Meischel T, Brosch G, Matthias P, Sibilia M, Seiser C. Divergent roles of HDAC1 and HDAC2 in the regulation of epidermal development and tumorigenesis. EMBO J 2013; 32:3176-91. [PMID: 24240174 PMCID: PMC3981143 DOI: 10.1038/emboj.2013.243] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 10/21/2013] [Indexed: 12/26/2022] Open
Abstract
The histone deacetylases HDAC1 and HDAC2 remove acetyl moieties from lysine residues of histones and other proteins and are important regulators of gene expression. By deleting different combinations of Hdac1 and Hdac2 alleles in the epidermis, we reveal a dosage-dependent effect of HDAC1/HDAC2 activity on epidermal proliferation and differentiation. Conditional ablation of either HDAC1 or HDAC2 in the epidermis leads to no obvious phenotype due to compensation by the upregulated paralogue. Strikingly, deletion of a single Hdac2 allele in HDAC1 knockout mice results in severe epidermal defects, including alopecia, hyperkeratosis, hyperproliferation and spontaneous tumour formation. These mice display impaired Sin3A co-repressor complex function, increased levels of c-Myc protein, p53 expression and apoptosis in hair follicles (HFs) and misregulation of HF bulge stem cells. Surprisingly, ablation of HDAC1 but not HDAC2 in a skin tumour model leads to accelerated tumour development. Our data reveal a crucial function of HDAC1/HDAC2 in the control of lineage specificity and a novel role of HDAC1 as a tumour suppressor in the epidermis.
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Affiliation(s)
- Mircea Winter
- Max F. Perutz Laboratories, Department of Medical Biochemistry, Vienna Biocenter, Medical University of Vienna, Vienna, Austria
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37
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Mulay K, Aggarwal E, White VA. Periocular sebaceous gland carcinoma: A comprehensive review. Saudi J Ophthalmol 2013; 27:159-65. [PMID: 24227981 DOI: 10.1016/j.sjopt.2013.05.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Sebaceous gland carcinoma (SGC) is a rare tumour occurring at periocular and extra-ocular sites. SGC can be a challenging diagnosis for both clinicians and pathologists. High recurrence rates and a tendency for intra-epithelial spread, locoregional and distant metastases make it important for SGC to be suspected and be included in the differential diagnosis of an eyelid lesion. Early diagnosis, that may sometimes need ancillary testing, and prompt management using a multimodal approach can help reduce morbidity and mortality in patients with SGC.
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Affiliation(s)
- Kaustubh Mulay
- National Reporting Centre for Ophthalmic Pathology, Centre For Sight, Hyderabad, India
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38
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First International Symposium "Epigenetic Control of Skin Development and Regeneration": how chromatin regulators orchestrate skin functions. J Invest Dermatol 2013; 133:1918-21. [PMID: 23856928 DOI: 10.1038/jid.2013.126] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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39
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Kadamb R, Mittal S, Bansal N, Batra H, Saluja D. Sin3: insight into its transcription regulatory functions. Eur J Cell Biol 2013; 92:237-46. [PMID: 24189169 DOI: 10.1016/j.ejcb.2013.09.001] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/27/2013] [Accepted: 09/11/2013] [Indexed: 10/26/2022] Open
Abstract
Sin3, a large acidic protein, shares structural similarity with the helix-loop-helix dimerization domain of proteins of the Myc family of transcription factors. Sin3/HDAC corepressor complex functions in transcriptional regulation of several genes and is therefore implicated in the regulation of key biological processes. Knockdown studies have confirmed the role of Sin3 in cellular proliferation, differentiation, apoptosis and cell cycle regulation, emphasizing Sin3 as an essential regulator of critical cellular events in normal and pathological processes. The present review covers the diverse functions of this master transcriptional regulator as well as illustrates the redundant and distinct functions of its two mammalian isoforms.
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Affiliation(s)
- Rama Kadamb
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India.
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40
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Bao X, Tang J, Lopez-Pajares V, Tao S, Qu K, Crabtree GR, Khavari PA. ACTL6a enforces the epidermal progenitor state by suppressing SWI/SNF-dependent induction of KLF4. Cell Stem Cell 2013; 12:193-203. [PMID: 23395444 DOI: 10.1016/j.stem.2012.12.014] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 10/05/2012] [Accepted: 12/04/2012] [Indexed: 10/27/2022]
Abstract
Somatic progenitors suppress differentiation to maintain tissue self-renewal. The mammalian SWI/SNF chromatin-remodeling complex regulates nucleosome packaging to control differentiation in embryonic and adult stem cells. Catalytic Brg1 and Brm subunits are required for these processes; however, the roles of SWI/SNF regulatory subunits are not fully understood. Here, we show that ACTL6a/BAF53A modulates the SWI/SNF complex to suppress differentiation in epidermis. Conditional loss of ACTL6a resulted in terminal differentiation, cell-cycle exit, and hypoplasia, whereas ectopic expression of ACTL6a promoted the progenitor state. A significant portion of genes regulated by ACTL6a were found to also be targets of KLF4, a known activator of epidermal differentiation. Mechanistically, we show that ACTL6a prevents SWI/SNF complex binding to promoters of KLF4 and other differentiation genes and that SWI/SNF catalytic subunits are required for full induction of KLF4 targets. Thus, ACTL6a controls the epidermal progenitor state by sequestering SWI/SNF to prevent activation of differentiation programs.
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Affiliation(s)
- Xiaomin Bao
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
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41
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Cangkrama M, Ting SB, Darido C. Stem cells behind the barrier. Int J Mol Sci 2013; 14:13670-86. [PMID: 23812084 PMCID: PMC3742210 DOI: 10.3390/ijms140713670] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 06/25/2013] [Indexed: 12/17/2022] Open
Abstract
Epidermal stem cells sustain the adult skin for a lifetime through self-renewal and the production of committed progenitors. These stem cells generate progeny that will undergo terminal differentiation leading to the development of a protective epidermal barrier. Whereas the molecular mechanisms that govern epidermal barrier repair and renewal have been extensively studied, pathways controlling stem cell differentiation remain poorly understood. Asymmetric cell divisions, small non-coding RNAs (microRNAs), chromatin remodeling complexes, and multiple differentiation factors tightly control the balance of stem and progenitor cell proliferation and differentiation, and disruption of this balance leads to skin diseases. In this review, we summarize and discuss current advances in our understanding of the mechanisms regulating epidermal stem and progenitor cell differentiation, and explore new relationships for maintenance of skin barrier function.
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Affiliation(s)
- Michael Cangkrama
- Epidermal Development Laboratory, Department of Medicine, Central Clinical School, Alfred Hospital and Monash University, Prahran VIC 3004, Australia; E-Mail:
| | - Stephen B. Ting
- Stem Cell Research Group, Australian Centre for Blood Diseases, Central Clinical School, Alfred Hospital and Monash University, Prahran VIC 3004, Australia; E-Mail:
| | - Charbel Darido
- Epidermal Development Laboratory, Department of Medicine, Central Clinical School, Alfred Hospital and Monash University, Prahran VIC 3004, Australia; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +61-3-9903-0619
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42
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Hussain S, Tuorto F, Menon S, Blanco S, Cox C, Flores JV, Watt S, Kudo NR, Lyko F, Frye M. The mouse cytosine-5 RNA methyltransferase NSun2 is a component of the chromatoid body and required for testis differentiation. Mol Cell Biol 2013; 33:1561-70. [PMID: 23401851 PMCID: PMC3624257 DOI: 10.1128/mcb.01523-12] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/30/2013] [Indexed: 11/20/2022] Open
Abstract
Posttranscriptional regulatory mechanisms are crucial for protein synthesis during spermatogenesis and are often organized by the chromatoid body. Here, we identify the RNA methyltransferase NSun2 as a novel component of the chromatoid body and, further, show that NSun2 is essential for germ cell differentiation in the mouse testis. In NSun2-depleted testes, genes encoding Ddx4, Miwi, and Tudor domain-containing (Tdr) proteins are repressed, indicating that RNA-processing and posttranscriptional pathways are impaired. Loss of NSun2 specifically blocked meiotic progression of germ cells into the pachytene stage, as spermatogonial and Sertoli cells were unaffected in knockout mice. We observed the same phenotype when we simultaneously deleted NSun2 and Dnmt2, the only other cytosine-5 RNA methyltransferase characterized to date, indicating that Dnmt2 was not functionally redundant with NSun2 in spermatogonial stem cells or Sertoli cells. Specific NSun2- and Dnmt2-methylated tRNAs decreased in abundance when both methyltransferases were deleted, suggesting that RNA methylation pathways play an essential role in male germ cell differentiation.
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Affiliation(s)
- Shobbir Hussain
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Francesca Tuorto
- Division of Epigenetics, German Cancer Research Center, Heidelberg, Germany
| | - Suraj Menon
- CR-UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Sandra Blanco
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Claire Cox
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Joana V. Flores
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Stephen Watt
- CR-UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Nobuaki R. Kudo
- IRDB, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Frank Lyko
- Division of Epigenetics, German Cancer Research Center, Heidelberg, Germany
| | - Michaela Frye
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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c-MYC-induced sebaceous gland differentiation is controlled by an androgen receptor/p53 axis. Cell Rep 2013; 3:427-41. [PMID: 23403291 PMCID: PMC3778892 DOI: 10.1016/j.celrep.2013.01.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 10/28/2012] [Accepted: 01/14/2013] [Indexed: 01/02/2023] Open
Abstract
Although the sebaceous gland (SG) plays an important role in skin function, the mechanisms regulating SG differentiation and carcinoma formation are poorly understood. We previously reported that c-MYC overexpression stimulates SG differentiation. We now demonstrate roles for the androgen receptor (AR) and p53. MYC-induced SG differentiation was reduced in mice lacking a functional AR. High levels of MYC triggered a p53-dependent DNA damage response, leading to accumulation of proliferative SG progenitors and inhibition of AR signaling. Conversely, testosterone treatment or p53 deletion activated AR signaling and restored MYC-induced differentiation. Poorly differentiated human sebaceous carcinomas exhibited high p53 and low AR expression. Thus, the consequences of overactivating MYC in the SG depend on whether AR or p53 is activated, as they form a regulatory axis controlling proliferation and differentiation.
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44
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Lee B, Dai X. Transcriptional control of epidermal stem cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 786:157-73. [PMID: 23696356 DOI: 10.1007/978-94-007-6621-1_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transcriptional regulation is fundamentally important for the progression of tissue stem cells through different stages of development and differentiation. Mammalian skin epidermis is an excellent model system to study such regulatory mechanisms due to its easy accessibility, stereotypic spatial arrangement, and availability of well-established cell type/lineage differentiation markers. Moreover, epidermis is one of the few mammalian tissues the stem cells of which can be maintained and propagated in culture to generate mature cell types and a functional tissue (reviewed in [1]), offering in vitro and ex vivo platforms to probe deep into the underlying cell and molecular mechanisms of biological functions.
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Affiliation(s)
- Briana Lee
- Department of Biological Chemistry, School of Medicine, University of California, D250 Med Sci I, Irvine 92697-1700, CA, USA
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45
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Gallagher SJ, Kofman AE, Huszar JM, Dannenberg JH, DePinho RA, Braun RE, Payne CJ. Distinct requirements for Sin3a in perinatal male gonocytes and differentiating spermatogonia. Dev Biol 2012; 373:83-94. [PMID: 23085237 DOI: 10.1016/j.ydbio.2012.10.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 09/27/2012] [Accepted: 10/08/2012] [Indexed: 01/16/2023]
Abstract
Chromatin modifier Swi-independent 3a (SIN3A), together with associated histone deacetylases, influences gene expression during development and differentiation through a variety of transcription factors in a cell-specific manner. Sin3a is essential for the maintenance of inner cell mass cells of mouse blastocysts, embryonic fibroblasts, and myoblasts, but is not required for the survival of trophectoderm or Sertoli cells. To better understand how this transcriptional regulator modulates cells at different developmental stages within a single lineage, we used conditional gene targeting in mice to ablate Sin3a from perinatal quiescent male gonocytes and from postnatal differentiating spermatogonia. Mitotic germ cells expressing stimulated by retinoic acid gene 8 (Stra8) that lacked Sin3a exhibited increased DNA damage and apoptosis, yet collectively progressed through meiosis and spermiogenesis and generated epididymal sperm at approximately 50% of control levels, sufficient for normal fertility. In contrast, perinatal gonocytes lacking Sin3a underwent rapid depletion that coincided with cell cycle reentry, exhibiting 2.5-fold increased histone H3 phosphorylation upon cycling that suggested a prophase/metaphase block; germ cells were almost entirely absent two weeks after birth, resulting in sterility. Gene expression profiling of neonatal testes containing Sin3a-deleted gonocytes identified upregulated transcripts highly associated with developmental processes and pattern formation, and downregulated transcripts involved in nuclear receptor activity, including Nr4a1 (Nur77). Interestingly, Nr4a1 levels were elevated in testes containing Stra8-expressing, Sin3a-deleted spermatogonia. SIN3A directly binds to the Nr4a1 promoter, and Nr4a1 expression is diminished upon spermatogonial differentiation in vitro. We conclude that within the male germline, Sin3a is required for the mitotic reentry of gonocytes, but is dispensable for the maintenance of differentiating spermatogonia and subsequent spermatogenic processes.
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Affiliation(s)
- Shannon J Gallagher
- Human Molecular Genetics Program, Children's Hospital of Chicago Research Center, and Department of Pediatrics and Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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46
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Chromatin regulators in mammalian epidermis. Semin Cell Dev Biol 2012; 23:897-905. [DOI: 10.1016/j.semcdb.2012.08.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 08/09/2012] [Accepted: 08/24/2012] [Indexed: 12/17/2022]
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47
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Sin3a acts through a multi-gene module to regulate invasion in Drosophila and human tumors. Oncogene 2012; 32:3184-97. [PMID: 22890320 DOI: 10.1038/onc.2012.326] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Chromatin remodeling proteins regulate multiple aspects of cell homeostasis, making them ideal candidates for misregulation in transformed cells. Here, we explore Sin3A, a member of the Sin3 family of proteins linked to tumorigenesis that are thought to regulate gene expression through their role as histone deacetylases (HDACs). We identified Drosophila Sin3a as an important mediator of oncogenic Ret receptor in a fly model of Multiple Endocrine Neoplasia Type 2. Reducing Drosophila Sin3a activity led to metastasis-like behavior and, in the presence of Diap1, secondary tumors distant from the site of origin. Genetic and Chip-Seq analyses identified previously undescribed Sin3a targets including genes involved in cell motility and actin dynamics, as well as signaling pathways including Src, Jnk and Rho. A key Sin3a oncogenic target, PP1B, regulates stability of β-Catenin/Armadillo: the outcome is to oppose T-cell factor (TCF) function and Wg/Wnt pathway signaling in both fly and mammalian cancer cells. Reducing Sin3A strongly increased the invasive behavior of A549 human lung adenocarcinoma cells. We show that Sin3A is downregulated in a variety of human tumors and that Src, JNK, RhoA and PP1B/β-Catenin are regulated in a manner analogous to our Drosophila models. Our data suggest that Sin3A influences a specific step of tumorigenesis by regulating a module of genes involved in cell invasion. Tumor progression may commonly rely on such 'modules of invasion' under the control of broad transcriptional regulators.
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Pellegrino J, Castrillon DH, David G. Chromatin associated Sin3A is essential for male germ cell lineage in the mouse. Dev Biol 2012; 369:349-55. [PMID: 22820070 DOI: 10.1016/j.ydbio.2012.07.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 07/02/2012] [Accepted: 07/10/2012] [Indexed: 01/15/2023]
Abstract
Spermatogenesis is a complex process that requires coordinated proliferation and differentiation of male germ cells. The molecular events that dictate this process are largely unknown, but are likely to involve highly regulated transcriptional control. In this study, we investigate the contribution of chromatin associated Sin3A in mouse germ cell lineage development. Genetic inactivation of Sin3A in the male germline leads to sterility that results from the early and penetrant apoptotic death observed in Sin3A-deleted germ cells, coincident with the reentry in mitosis. Sin3A-deleted testes exhibit a Sertoli-cell only phenotype, consistent with the absolute requirement for Sin3A in germ cells' development and/or viability. Interestingly, transcripts analysis revealed that the expression program of Sertoli cells is altered upon inactivation of Sin3A in germ cells. These studies identified a central role for the mammalian Sin3-HDAC complex in the germ cell lineage, and point to an exquisite transcriptional crosstalk between germ cells and their niche to support fertility in mammals.
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Affiliation(s)
- Jessica Pellegrino
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, NY, USA
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Botchkarev VA, Gdula MR, Mardaryev AN, Sharov AA, Fessing MY. Epigenetic regulation of gene expression in keratinocytes. J Invest Dermatol 2012; 132:2505-21. [PMID: 22763788 PMCID: PMC3650472 DOI: 10.1038/jid.2012.182] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nucleus is a complex and highly compartmentalized organelle, which organization undergoes major changes during cell differentiation allowing cells to become specialized and fulfill their functions.During terminal differentiation of the epidermal keratinocytes, nucleus undergoes programmed transformation from active status, associated with execution of the genetic programs of cornification and epidermal barrier formation, to fully inactive condition and becomes a part of the keratinized cells of the cornified layer. Tremendous progress achieved within the last two decades in understanding the biology of the nucleus and epigenetic mechanisms controlling gene expression allowed defining several levels in the regulation of cell differentiation-associated gene expression programs, including an accessibility of the gene regulatory regions to DNA-protein interactions, covalent DNA and histone modifications and ATP-dependent chromatin remodeling, as well as higher-order chromatin remodeling and nuclear compartmentalization of the genes and transcription machinery. Here, we integrate our current knowledge of the mechanisms controlling gene expression during terminal keratinocyte differentiation with distinct levels of chromatin organization and remodeling. We also propose the directions to further explore the role of epigenetic mechanisms and their interactions with other regulatory systems in the control of keratinocyte differentiation in normal and diseased skin.
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Abstract
Dynamic changes in the chromatin of adult stem cells are required to establish the gene expression profiles associated with stem cell self-renewal and differentiation. A complex genetic network of chromatin remodellers and epigenetic factors orchestrate these genome-wide changes in human epidermal stem cells.
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