51
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Kim J, Oberdoerffer P, Khurana S. The histone variant macroH2A1 is a splicing-modulated caretaker of genome integrity and tumor growth. Mol Cell Oncol 2018; 5:e1441629. [PMID: 30250894 DOI: 10.1080/23723556.2018.1441629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 01/14/2018] [Indexed: 02/02/2023]
Abstract
The macroH2A1.2 histone variant facilitates the response to replication stress with implications for genome maintenance and cell growth. A mutually exclusive splice variant, macroH2A1.1, has opposing effects on DNA repair outcome and proliferation. Here we discuss the potential impact of splicing-modulated macroH2A1 chromatin organization for cell function and malignant transformation.
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Affiliation(s)
- Jeongkyu Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Simran Khurana
- National Institute for Allergy and infectious Diseases, NIH, Bethesda, MD, USA
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52
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Haque N, Ouda R, Chen C, Ozato K, Hogg JR. ZFR coordinates crosstalk between RNA decay and transcription in innate immunity. Nat Commun 2018; 9:1145. [PMID: 29559679 PMCID: PMC5861047 DOI: 10.1038/s41467-018-03326-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/05/2018] [Indexed: 12/29/2022] Open
Abstract
Control of type I interferon production is crucial to combat infection while preventing deleterious inflammatory responses, but the extent of the contribution of post-transcriptional mechanisms to innate immune regulation is unclear. Here, we show that human zinc finger RNA-binding protein (ZFR) represses the interferon response by regulating alternative pre-mRNA splicing. ZFR expression is tightly controlled during macrophage development; monocytes express truncated ZFR isoforms, while macrophages induce full-length ZFR to modulate macrophage-specific alternative splicing. Interferon-stimulated genes are constitutively activated by ZFR depletion, and immunostimulation results in hyper-induction of interferon β (IFNβ/IFNB1). Through whole-genome analyses, we show that ZFR controls interferon signaling by preventing aberrant splicing and nonsense-mediated decay of histone variant macroH2A1/H2AFY mRNAs. Together, our data suggest that regulation of ZFR in macrophage differentiation guards against aberrant interferon responses and reveal a network of mRNA processing and decay that shapes the transcriptional response to infection. Type I interferon signaling is critical for the control of infection. Here the authors show that zinc finger RNA-binding protein (ZFR) can control type I interferon responses, and that this control is itself regulated by distinct ZFR truncation patterns that differ between monocytes and macrophages.
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Affiliation(s)
- Nazmul Haque
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Room 2341, Bethesda, MD, 20892, USA.
| | - Ryota Ouda
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive, Room 2A01, Bethesda, MD, 20892, USA
| | - Chao Chen
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive, Room 2A01, Bethesda, MD, 20892, USA
| | - Keiko Ozato
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive, Room 2A01, Bethesda, MD, 20892, USA
| | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Room 2341, Bethesda, MD, 20892, USA.
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53
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Post-Translational Modifications of H2A Histone Variants and Their Role in Cancer. Cancers (Basel) 2018; 10:cancers10030059. [PMID: 29495465 PMCID: PMC5876634 DOI: 10.3390/cancers10030059] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/19/2018] [Accepted: 02/25/2018] [Indexed: 12/12/2022] Open
Abstract
Histone variants are chromatin components that replace replication-coupled histones in a fraction of nucleosomes and confer particular characteristics to chromatin. H2A variants represent the most numerous and diverse group among histone protein families. In the nucleosomal structure, H2A-H2B dimers can be removed and exchanged more easily than the stable H3-H4 core. The unstructured N-terminal histone tails of all histones, but also the C-terminal tails of H2A histones protrude out of the compact structure of the nucleosome core. These accessible tails are the preferential target sites for a large number of post-translational modifications (PTMs). While some PTMs are shared between replication-coupled H2A and H2A variants, many modifications are limited to a specific histone variant. The present review focuses on the H2A variants H2A.Z, H2A.X, and macroH2A, and summarizes their functions in chromatin and how these are linked to cancer development and progression. H2A.Z primarily acts as an oncogene and macroH2A and H2A.X as tumour suppressors. We further focus on the regulation by PTMs, which helps to understand a degree of context dependency.
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54
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Zhang Z, Li X, Xiao Q, Wang Z. MiR-574-5p mediates the cell cycle and apoptosis in thyroid cancer cells via Wnt/β-catenin signaling by repressing the expression of Quaking proteins. Oncol Lett 2018; 15:5841-5848. [PMID: 29556311 DOI: 10.3892/ol.2018.8067] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 11/29/2017] [Indexed: 12/24/2022] Open
Abstract
Thyroid cancer is the most frequently occurring type of endocrine tumor, with a rapidly increasing incidence rate. MicroRNA (miR)-574-5p is a candidate oncogene in various types of cancer. The present study identified that miR-574-5p affected the cell cycle distribution and apoptosis of BCPAP and FTC133 thyroid cancer cells via β-catenin/Wnt signaling by targeting Quaking proteins (QKIs). An MTT assay demonstrated that the knockdown of miR-574-5p suppressed the proliferation of the thyroid cancer cells. Fluorescence-activated cell sorting analysis demonstrated that the inhibition of miR-574-5p induced the G1/S phase arrest and apoptosis of the cells. Reverse transcription-quantitative polymerase chain reaction and western blot analyses revealed that the knockdown of miR-574-5p significantly upregulated the mRNA and protein expression levels of QKIs. Furthermore, western blot analysis identified that the knockdown of miR-574-5p also repressed the Wnt/β-catenin pathway via downregulating the expression of β-catenin, cyclin D1 and survivin, and upregulating the phosphorylation of β-catenin. The further depletion of QKIs in combination with the knockdown of miR-574-5p not only increased the expression of β-catenin, cyclin D1 and survivin, but also rescued the apoptosis of thyroid cancer cells induced by the miR-574-5p knockdown. In conclusion, these findings indicated that the aberrant upregulation of miR-574-5p may be oncogenic, through regulating the Wnt/β-catenin pathway by targeting QKIs.
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Affiliation(s)
- Zhejia Zhang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Qian Xiao
- Department of Mental Hygiene Clinics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Zhiming Wang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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55
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Lo Re O, Fusilli C, Rappa F, Van Haele M, Douet J, Pindjakova J, Rocha SW, Pata I, Valčíková B, Uldrijan S, Yeung RS, Peixoto CA, Roskams T, Buschbeck M, Mazza T, Vinciguerra M. Induction of cancer cell stemness by depletion of macrohistone H2A1 in hepatocellular carcinoma. Hepatology 2018; 67:636-650. [PMID: 28913935 DOI: 10.1002/hep.29519] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/07/2017] [Accepted: 09/06/2017] [Indexed: 12/18/2022]
Abstract
Hepatocellular carcinomas (HCC) contain a subpopulation of cancer stem cells (CSCs), which exhibit stem cell-like features and are responsible for tumor relapse, metastasis, and chemoresistance. The development of effective treatments for HCC will depend on a molecular-level understanding of the specific pathways driving CSC emergence and stemness. MacroH2A1 is a variant of the histone H2A and an epigenetic regulator of stem-cell function, where it promotes differentiation and, conversely, acts as a barrier to somatic-cell reprogramming. Here, we focused on the role played by the histone variant macroH2A1 as a potential epigenetic factor promoting CSC differentiation. In human HCC sections we uncovered a significant correlation between low frequencies of macroH2A1 staining and advanced, aggressive HCC subtypes with poorly differentiated tumor phenotypes. Using HCC cell lines, we found that short hairpin RNA-mediated macroH2A1 knockdown induces acquisition of CSC-like features, including the growth of significantly larger and less differentiated tumors when injected into nude mice. MacroH2A1-depleted HCC cells also exhibited reduced proliferation, resistance to chemotherapeutic agents, and stem-like metabolic changes consistent with enhanced hypoxic responses and increased glycolysis. The loss of macroH2A1 increased expression of a panel of stemness-associated genes and drove hyperactivation of the nuclear factor kappa B p65 pathway. Blocking phosphorylation of nuclear factor kappa B p65 on Ser536 inhibited the emergence of CSC-like features in HCC cells knocked down for macroH2A1. Conclusion: The absence of histone variant macroH2A1 confers a CSC-like phenotype to HCC cells in vitro and in vivo that depends on Ser536 phosphorylation of nuclear factor kappa B p65; this pathway may hold valuable targets for the development of CSC-focused treatments for HCC. (Hepatology 2018;67:636-650).
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Affiliation(s)
- Oriana Lo Re
- Center for Translational Medicine, International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Caterina Fusilli
- IRCCS Casa Sollievo della Sofferenza, UO of Bioinformatics, San Giovanni Rotondo (FG), Italy
| | - Francesca Rappa
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Palermo, Italy
| | - Matthias Van Haele
- Translational Cell & Tissue Research Unit, Department of Imaging & Pathology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Julien Douet
- Josep Carreras Institute for Leukaemia Research, Campus ICO-GTP, Campus Can Ruti, Badalona, Spain.,Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Campus Can Ruti, Badalona, Spain
| | - Jana Pindjakova
- Center for Translational Medicine, International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | | | | | - Barbora Valčíková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Stjepan Uldrijan
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Center of Biomolecular and Cellular Engineering, International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Raymond S Yeung
- Department of Surgery.,Northwest Liver Research Program, University of Washington, Seattle, WA
| | - Christina Alves Peixoto
- Laboratório de Ultraestrutura, Centro de Pesquisa Aggeu Magalhães (FIOCRUZ), Recife, Pernambuco, Brazil
| | - Tania Roskams
- Translational Cell & Tissue Research Unit, Department of Imaging & Pathology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Marcus Buschbeck
- Josep Carreras Institute for Leukaemia Research, Campus ICO-GTP, Campus Can Ruti, Badalona, Spain.,Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Campus Can Ruti, Badalona, Spain
| | - Tommaso Mazza
- IRCCS Casa Sollievo della Sofferenza, UO of Bioinformatics, San Giovanni Rotondo (FG), Italy
| | - Manlio Vinciguerra
- Center for Translational Medicine, International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.,Institute for Liver and Digestive Health, University College London, Royal Free Hospital, London, UK
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56
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Hodge DQ, Cui J, Gamble MJ, Guo W. Histone Variant MacroH2A1 Plays an Isoform-Specific Role in Suppressing Epithelial-Mesenchymal Transition. Sci Rep 2018; 8:841. [PMID: 29339820 PMCID: PMC5770377 DOI: 10.1038/s41598-018-19364-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/27/2017] [Indexed: 02/06/2023] Open
Abstract
Epithelial-Mesenchymal Transition (EMT) is a biological program that plays key roles in various developmental and pathological processes. Although much work has been done on signaling pathways and transcription factors regulating EMT, the epigenetic regulation of EMT remains not well understood. Histone variants have been recognized as a key group of epigenetic regulators. Among them, macroH2A1 is involved in stem cell reprogramming and cancer progression. We postulated that macroH2A1 may play a role in EMT, a process involving reprogramming of cellular states. In this study, we demonstrate that expression of macroH2A1 is dramatically reduced during EMT induction in immortalized human mammary epithelial cells (HMLE). Moreover, ectopic expression of the macroH2A1.1 isoform, but not macroH2A1.2, can suppress EMT induction and reduce the stem-like cell population in HMLE. Interestingly, macroH2A1.1 overexpression cannot revert stable mesenchymal cells back to the epithelial state, suggesting a stage-specific role of macroH2A1.1 in EMT. We further pinpointed that the function of macroH2A1.1 in EMT suppression is dependent on its ability to bind the NAD+ metabolite PAR, in agreement with the inability to suppress EMT by macroH2A1.2, which lacks the PAR binding domain. Thus, our work discovered a previously unrecognized isoform-specific function of macroH2A1 in regulating EMT induction.
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Affiliation(s)
- Dayle Q Hodge
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Jihong Cui
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Matthew J Gamble
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wenjun Guo
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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57
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Quénet D. Histone Variants and Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:1-39. [DOI: 10.1016/bs.ircmb.2017.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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58
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QKI5-mediated alternative splicing of the histone variant macroH2A1 regulates gastric carcinogenesis. Oncotarget 2017; 7:32821-34. [PMID: 27092877 PMCID: PMC5078054 DOI: 10.18632/oncotarget.8739] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/28/2016] [Indexed: 12/18/2022] Open
Abstract
Alternative pre-mRNA splicing is a key mechanism for increasing proteomic diversity and modulating gene expression. Emerging evidence indicated that the splicing program is frequently dysregulated during tumorigenesis. Cancer cells produce protein isoforms that can promote growth and survival. The RNA-binding protein QKI5 is a critical regulator of alternative splicing in expanding lists of primary human tumors and tumor cell lines. However, its biological role and regulatory mechanism are poorly defined in gastric cancer (GC) development and progression. In this study, we demonstrated that the downregulation of QKI5 was associated with pTNM stage and pM state of GC patients. Re-introduction of QKI5 could inhibit GC cell proliferation, migration, and invasion in vitro and in vivo, which might be due to the altered splicing pattern of macroH2A1 pre-mRNA, leading to the accumulation of macroH2A1.1 isoform. Furthermore, QKI5 could inhibit cyclin L1 expression via promoting macroH2A1.1 production. Thus, this study identified a novel regulatory axis involved in gastric tumorigenesis and provided a new strategy for GC therapy.
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59
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Kim J, Sturgill D, Sebastian R, Khurana S, Tran AD, Edwards GB, Kruswick A, Burkett S, Hosogane EK, Hannon WW, Weyemi U, Bonner WM, Luger K, Oberdoerffer P. Replication Stress Shapes a Protective Chromatin Environment across Fragile Genomic Regions. Mol Cell 2017; 69:36-47.e7. [PMID: 29249653 DOI: 10.1016/j.molcel.2017.11.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/05/2017] [Accepted: 11/15/2017] [Indexed: 12/14/2022]
Abstract
Recent integrative epigenome analyses highlight the importance of functionally distinct chromatin states for accurate cell function. How these states are established and maintained is a matter of intense investigation. Here, we present evidence for DNA damage as an unexpected means to shape a protective chromatin environment at regions of recurrent replication stress (RS). Upon aberrant fork stalling, DNA damage signaling and concomitant H2AX phosphorylation coordinate the FACT-dependent deposition of macroH2A1.2, a histone variant that promotes DNA repair by homologous recombination (HR). MacroH2A1.2, in turn, facilitates the accumulation of the tumor suppressor and HR effector BRCA1 at replication forks to protect from RS-induced DNA damage. Consequently, replicating primary cells steadily accrue macroH2A1.2 at fragile regions, whereas macroH2A1.2 loss in these cells triggers DNA damage signaling-dependent senescence, a hallmark of RS. Altogether, our findings demonstrate that recurrent DNA damage contributes to the chromatin landscape to ensure the epigenomic integrity of dividing cells.
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Affiliation(s)
- Jeongkyu Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Robin Sebastian
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Simran Khurana
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Andy D Tran
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Garrett B Edwards
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Alex Kruswick
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sandra Burkett
- Molecular Cytogenetics Core Facility, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Eri K Hosogane
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - William W Hannon
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Urbain Weyemi
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William M Bonner
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Karolin Luger
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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60
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Lo Re O, Vinciguerra M. Histone MacroH2A1: A Chromatin Point of Intersection between Fasting, Senescence and Cellular Regeneration. Genes (Basel) 2017; 8:genes8120367. [PMID: 29206173 PMCID: PMC5748685 DOI: 10.3390/genes8120367] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 12/22/2022] Open
Abstract
Histone variants confer chromatin unique properties. They have specific genomic distribution, regulated by specific deposition and removal machineries. Histone variants, mostly of canonical histones H2A, H2B and H3, have important roles in early embryonic development, in lineage commitment of stem cells, in the converse process of somatic cell reprogramming to pluripotency and, in some cases, in the modulation of animal aging and life span. MacroH2A1 is a variant of histone H2A, present in two alternatively exon-spliced isoforms macroH2A1.1 and macroH2A1.2, regulating cell plasticity and proliferation, during pluripotency and tumorigenesis. Furthermore, macroH2A1 participates in the formation of senescence-associated heterochromatic foci (SAHF) in senescent cells, and multiple lines of evidence in genetically modified mice suggest that macroH2A1 integrates nutritional cues from the extracellular environment to transcriptional programs. Here, we review current molecular evidence based on next generation sequencing data, cell assays and in vivo models supporting different mechanisms that could mediate the function of macroH2A1 in health span and life span. We will further discuss context-dependent and isoform-specific functions. The aim of this review is to provide guidance to assess histone variant macroH2A1 potential as a therapeutic intervention point.
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Affiliation(s)
- Oriana Lo Re
- Center for Translational Medicine, International Clinical Research Center, St'Anne University Hospital, Brno 656 91, Czech Republic.
- Faculty of Medicine, Masaryk University, Brno 656 91, Czech Republic.
| | - Manlio Vinciguerra
- Center for Translational Medicine, International Clinical Research Center, St'Anne University Hospital, Brno 656 91, Czech Republic.
- Faculty of Medicine, Masaryk University, Brno 656 91, Czech Republic.
- Division of Medicine, Institute for Liver and Digestive Health, University College London (UCL), London WC1E 6BT, UK.
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61
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Mukohyama J, Shimono Y, Minami H, Kakeji Y, Suzuki A. Roles of microRNAs and RNA-Binding Proteins in the Regulation of Colorectal Cancer Stem Cells. Cancers (Basel) 2017; 9:cancers9100143. [PMID: 29064439 PMCID: PMC5664082 DOI: 10.3390/cancers9100143] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/17/2017] [Accepted: 10/17/2017] [Indexed: 12/28/2022] Open
Abstract
Colorectal cancer stem cells (CSCs) are responsible for the initiation, progression and metastasis of human colorectal cancers, and have been characterized by the expression of cell surface markers, such as CD44, CD133, CD166 and LGR5. MicroRNAs (miRNAs) are differentially expressed between CSCs and non-tumorigenic cancer cells, and play important roles in the maintenance and regulation of stem cell properties of CSCs. RNA binding proteins (RBPs) are emerging epigenetic regulators of various RNA processing events, such as splicing, localization, stabilization and translation, and can regulate various types of stem cells. In this review, we summarize current evidences on the roles of miRNA and RBPs in the regulation of colorectal CSCs. Understanding the epigenetic regulation of human colorectal CSCs will help to develop biomarkers for colorectal cancers and to identify targets for CSC-targeting therapies.
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Affiliation(s)
- Junko Mukohyama
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan.
- Division of Gastrointestinal Surgery, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan.
- Department of Pathology and Cell Biology, Department of Medicine (Division of Digestive and Liver Diseases) and Herbert Irving Comprehensive Cancer Center (HICCC), Columbia University, New York, NY 10032, USA.
| | - Yohei Shimono
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan.
- Division of Medical Oncology/Hematology, Kobe University Graduate School of Medicine, Kobe, Hyogo 6500017, Japan.
| | - Hironobu Minami
- Division of Medical Oncology/Hematology, Kobe University Graduate School of Medicine, Kobe, Hyogo 6500017, Japan.
| | - Yoshihiro Kakeji
- Division of Gastrointestinal Surgery, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan.
| | - Akira Suzuki
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan.
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62
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Fagg WS, Liu N, Fair JH, Shiue L, Katzman S, Donohue JP, Ares M. Autogenous cross-regulation of Quaking mRNA processing and translation balances Quaking functions in splicing and translation. Genes Dev 2017; 31:1894-1909. [PMID: 29021242 PMCID: PMC5695090 DOI: 10.1101/gad.302059.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/11/2017] [Indexed: 12/18/2022]
Abstract
Quaking protein isoforms arise from a single Quaking gene and bind the same RNA motif to regulate splicing, translation, decay, and localization of a large set of RNAs. However, the mechanisms by which Quaking expression is controlled to ensure that appropriate amounts of each isoform are available for such disparate gene expression processes are unknown. Here we explore how levels of two isoforms, nuclear Quaking-5 (Qk5) and cytoplasmic Qk6, are regulated in mouse myoblasts. We found that Qk5 and Qk6 proteins have distinct functions in splicing and translation, respectively, enforced through differential subcellular localization. We show that Qk5 and Qk6 regulate distinct target mRNAs in the cell and act in distinct ways on their own and each other's transcripts to create a network of autoregulatory and cross-regulatory feedback controls. Morpholino-mediated inhibition of Qk translation confirms that Qk5 controls Qk RNA levels by promoting accumulation and alternative splicing of Qk RNA, whereas Qk6 promotes its own translation while repressing Qk5. This Qk isoform cross-regulatory network responds to additional cell type and developmental controls to generate a spectrum of Qk5/Qk6 ratios, where they likely contribute to the wide range of functions of Quaking in development and cancer.
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Affiliation(s)
- W Samuel Fagg
- Sinsheimer Laboratories, Department of Molecular, Cell, and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz. Santa Cruz, California 95064, USA.,Department of Surgery, Transplant Division, Shriners Hospital for Children, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Naiyou Liu
- Department of Surgery, Transplant Division, Shriners Hospital for Children, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Jeffrey Haskell Fair
- Department of Surgery, Transplant Division, Shriners Hospital for Children, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Lily Shiue
- Sinsheimer Laboratories, Department of Molecular, Cell, and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz. Santa Cruz, California 95064, USA
| | - Sol Katzman
- Sinsheimer Laboratories, Department of Molecular, Cell, and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz. Santa Cruz, California 95064, USA
| | - John Paul Donohue
- Sinsheimer Laboratories, Department of Molecular, Cell, and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz. Santa Cruz, California 95064, USA
| | - Manuel Ares
- Sinsheimer Laboratories, Department of Molecular, Cell, and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz. Santa Cruz, California 95064, USA
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63
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Sharma M, Anirudh CR. Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein. Sci Rep 2017; 7:12567. [PMID: 28974714 PMCID: PMC5626755 DOI: 10.1038/s41598-017-12930-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/20/2017] [Indexed: 01/08/2023] Open
Abstract
STAR proteins are evolutionary conserved mRNA-binding proteins that post-transcriptionally regulate gene expression at all stages of RNA metabolism. These proteins possess conserved STAR domain that recognizes identical RNA regulatory elements as YUAAY. Recently reported crystal structures show that STAR domain is composed of N-terminal QUA1, K-homology domain (KH) and C-terminal QUA2, and mRNA binding is mediated by KH-QUA2 domain. Here, we present simulation studies done to investigate binding of mRNA to STAR protein, mammalian Quaking protein (QKI). We carried out conventional MD simulations of STAR domain in presence and absence of mRNA, and studied the impact of mRNA on the stability, dynamics and underlying allosteric mechanism of STAR domain. Our unbiased simulations results show that presence of mRNA stabilizes the overall STAR domain by reducing the structural deviations, correlating the ‘within-domain’ motions, and maintaining the native contacts information. Absence of mRNA not only influenced the essential modes of motion of STAR domain, but also affected the connectivity of networks within STAR domain. We further explored the dissociation of mRNA from STAR domain using umbrella sampling simulations, and the results suggest that mRNA binding to STAR domain occurs in multi-step: first conformational selection of mRNA backbone conformations, followed by induced fit mechanism as nucleobases interact with STAR domain.
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Affiliation(s)
- Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS Nagar, Punjab, India.
| | - C R Anirudh
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS Nagar, Punjab, India
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64
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Cedeno RJ, Nakauka-Ddamba A, Yousefi M, Sterling S, Leu NA, Li N, Pehrson JR, Lengner CJ. The histone variant macroH2A confers functional robustness to the intestinal stem cell compartment. PLoS One 2017; 12:e0185196. [PMID: 28934364 PMCID: PMC5608326 DOI: 10.1371/journal.pone.0185196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/07/2017] [Indexed: 12/20/2022] Open
Abstract
A stem cell's epigenome directs cell fate during development, homeostasis, and regeneration. Epigenetic dysregulation can lead to inappropriate cell fate decisions, aberrant cell function, and even cancer. The histone variant macroH2A has been shown to influence gene expression, guide cell fate, and safeguard against genotoxic stress. Interestingly, mice lacking functional macroH2A histones (hereafter referred to as macroH2A DKO) are viable and fertile; yet suffer from increased perinatal death and reduced weight and size compared to wildtype (WT). Here, we ask whether the ostensible reduced vigor of macroH2A DKO mice extends to intestinal stem cell (ISC) function during homeostasis, regeneration, and oncogenesis. Lgr5-eGFP-IRES-CreERT2 or Hopx-CreERT2::Rosa26-LSL-tdTomato ISC reporter mice or the C57BL/6J-Apcmin/J murine intestinal adenoma model were bred into a macroH2A DKO or strain-matched WT background and assessed for ISC functionality, regeneration and tumorigenesis. High-dose (12Gy) whole-body γ-irradiation was used as an injury model. We show that macroH2A is dispensable for intestinal homeostasis and macroH2A DKO mice have similar numbers of active crypt-base columnar ISCs (CBCs). MacroH2A DKO intestine exhibits impaired regeneration following injury, despite having significantly more putative reserve ISCs. DKO reserve ISCs disproportionately undergo apoptosis compared to WT after DNA damage infliction. Interestingly, a macroH2A DKO background does not significantly increase tumorigenesis in the Apcmin model of intestinal adenoma. We conclude that macroH2A influences reserve ISC number and function during homeostasis and regeneration. These data suggest macroH2A enhances reserve ISC survival after DNA damage and thus confers functional robustness to the intestinal epithelium.
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Affiliation(s)
- Ryan James Cedeno
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America.,Cell and Molecular Biology Graduate Program, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States of America
| | - Angela Nakauka-Ddamba
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Maryam Yousefi
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America.,Cell and Molecular Biology Graduate Program, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States of America
| | - Stephanie Sterling
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America.,Center for Animal Transgenesis, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Nicolae Adrian Leu
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America.,Center for Animal Transgenesis, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Ning Li
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - John R Pehrson
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Christopher Joachim Lengner
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America.,Center for Animal Transgenesis, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America.,Center for Molecular Studies in Digestive and Liver Disease, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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65
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Yu S, Wang X, Geng P, Tang X, Xiang L, Lu X, Li J, Ruan Z, Chen J, Xie G, Wang Z, Ou J, Peng Y, Luo X, Zhang X, Dong Y, Pang X, Miao H, Chen H, Liang H. Melatonin regulates PARP1 to control the senescence-associated secretory phenotype (SASP) in human fetal lung fibroblast cells. J Pineal Res 2017; 63. [PMID: 28247536 DOI: 10.1111/jpi.12405] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/24/2017] [Indexed: 02/05/2023]
Abstract
Cellular senescence is an important tumor-suppressive mechanism. However, acquisition of a senescence-associated secretory phenotype (SASP) in senescent cells has deleterious effects on the tissue microenvironment and, paradoxically, promotes tumor progression. In a drug screen, we identified melatonin as a novel SASP suppressor in human cells. Strikingly, melatonin blunts global SASP gene expression upon oncogene-induced senescence (OIS). Moreover, poly(ADP-ribose) polymerase-1 (PARP-1), a sensor of DNA damage, was identified as a new melatonin-dependent regulator of SASP gene induction upon OIS. Here, we report two different but potentially coherent epigenetic strategies for melatonin regulation of SASP. The interaction between the telomeric repeat-containing RNA (TERRA) and PARP-1 stimulates the SASP, which was attenuated by 67.9% (illustrated by the case of IL8) by treatment with melatonin. Through binding to macroH2A1.1, PARP-1 recruits CREB-binding protein (CBP) to mediate acetylation of H2BK120, which positively regulates the expression of target SASP genes, and this process is interrupted by melatonin. Consequently, the findings provide novel insight into melatonin's epigenetic role via modulating PARP-1 in suppression of SASP gene expression in OIS-induced senescent cells. Our studies identify melatonin as a novel anti-SASP molecule, define PARP-1 as a new target by which melatonin regulates SASP, and establish a new epigenetic paradigm for a pharmacological mechanism by which melatonin interrupts PARP-1 interaction with the telomeric long noncoding RNA(lncRNA) or chromatin.
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Affiliation(s)
- Songtao Yu
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Xiaojiao Wang
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Peiliang Geng
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Xudong Tang
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Lisha Xiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Xin Lu
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Jianjun Li
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Zhihua Ruan
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Jianfang Chen
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Ganfeng Xie
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Zhe Wang
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Juanjuan Ou
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Yuan Peng
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Xi Luo
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Xuan Zhang
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Yan Dong
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Xueli Pang
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Hongming Miao
- Department of Biochemistry and Molecular Biology, The Third Military Medical University, Chongqing, China
| | - Hongshan Chen
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Houjie Liang
- Department of Oncology, Southwest Hospital, Third Military Medical University, Chongqing, China
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66
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Asadipour M, Hassan-Zadeh V, Aryaeian N, Shahram F, Mahmoudi M. Histone variants expression in peripheral blood mononuclear cells of patients with rheumatoid arthritis. Int J Rheum Dis 2017; 21:1831-1837. [DOI: 10.1111/1756-185x.13126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Maryam Asadipour
- Department of Cell and Molecular Biology; Kish International Campus; University of Tehran; Kish Iran
| | - Vahideh Hassan-Zadeh
- Department of Cell and Molecular Biology; Faculty of Biology; College of Science; University of Tehran; Tehran Iran
| | - Naheed Aryaeian
- Department of Nutrition; School of Public Health; Iran University of Medical Sciences; Tehran Iran
| | - Farhad Shahram
- Rheumatology Research Center (RRC); Tehran University of Medical Sciences; Tehran Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center (RRC); Tehran University of Medical Sciences; Tehran Iran
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67
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Zhou X, Li X, Sun C, Shi C, Hua D, Yu L, Wen Y, Hua F, Wang Q, Zhou Q, Yu S. Quaking-5 suppresses aggressiveness of lung cancer cells through inhibiting β-catenin signaling pathway. Oncotarget 2017; 8:82174-82184. [PMID: 29137254 PMCID: PMC5669880 DOI: 10.18632/oncotarget.19066] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 06/11/2017] [Indexed: 12/30/2022] Open
Abstract
Quaking-5 (QKI-5) belongs to the STAR (signal transduction and activation of RNA) family of RNA binding proteins and functions as a tumor suppressor in several human malignancies. In this study, we attempt to elucidate the role of QKI-5 in the pro-metastasis processes of lung cancer (LC) cells and the underlying mechanisms. We confirmed that QKI-5 was decreased in human LC tissues and cell lines, especially in high-metastatic cells. Moreover, QKI expression was positively correlated with LC patients’ survival. Functional studies verified that QKI-5 suppressed migration, invasion and TGF-β1-induced epithelial-mesenchymal transition (EMT) of LC cells. Mechanistically, we affirmed that QKI-5 reduced β-catenin level in LC cells via suppressing its translation and promoting its degradation, whereas QKI-5 promoter hypermethylation suppressed QKI-5 expression. Our findings indicate that QKI-5 inhibits pro-metastasis processes of LC cells through interdicting β-catenin signaling pathway, and that QKI-5 promoter hypermethylation is a crucial epigenetic regulation reducing QKI-5 expression in LC cells, and reveal that QKI-5 is a potential prognostic biomarker for LC patients.
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Affiliation(s)
- Xuexia Zhou
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of The Nervous System, Key Laboratory of Post-Trauma Neuro-Repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Xuebing Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Cuiyun Sun
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of The Nervous System, Key Laboratory of Post-Trauma Neuro-Repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Cuijuan Shi
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of The Nervous System, Key Laboratory of Post-Trauma Neuro-Repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Dan Hua
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of The Nervous System, Key Laboratory of Post-Trauma Neuro-Repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Lin Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences of Tianjin Medical University, Tianjin 300070, China
| | - Yanjun Wen
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of The Nervous System, Key Laboratory of Post-Trauma Neuro-Repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Feng Hua
- Department of Surgery, Shandong Cancer Hospital and Institute, Jinan 250117, China
| | - Qian Wang
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of The Nervous System, Key Laboratory of Post-Trauma Neuro-Repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qinghua Zhou
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Shizhu Yu
- Department of Neuropathology, Tianjin Key Laboratory of Injuries, Variations and Regeneration of The Nervous System, Key Laboratory of Post-Trauma Neuro-Repair and Regeneration in Central Nervous System of Education Ministry, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
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68
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Buschbeck M, Hake SB. Variants of core histones and their roles in cell fate decisions, development and cancer. Nat Rev Mol Cell Biol 2017; 18:299-314. [DOI: 10.1038/nrm.2016.166] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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69
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Pazienza V, Panebianco C, Rappa F, Memoli D, Borghesan M, Cannito S, Oji A, Mazza G, Tamburrino D, Fusai G, Barone R, Bolasco G, Villarroya F, Villarroya J, Hatsuzawa K, Cappello F, Tarallo R, Nakanishi T, Vinciguerra M. Histone macroH2A1.2 promotes metabolic health and leanness by inhibiting adipogenesis. Epigenetics Chromatin 2016; 9:45. [PMID: 27800025 PMCID: PMC5078890 DOI: 10.1186/s13072-016-0098-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 10/17/2016] [Indexed: 12/13/2022] Open
Abstract
Background Obesity has tremendous impact on the health systems. Its epigenetic bases are unclear. MacroH2A1 is a variant of histone H2A, present in two alternatively exon-spliced isoforms macroH2A1.1 and macroH2A1.2, regulating cell plasticity and proliferation, during pluripotency and tumorigenesis. Their role in adipose tissue plasticity is unknown. Results Here, we show evidence that macroH2A1.1 protein levels in the visceral adipose tissue of obese humans positively correlate with BMI, while macroH2A1.2 is nearly absent. We thus introduced a constitutive GFP-tagged transgene for macroH2A1.2 in mice, and we characterized their metabolic health upon being fed a standard chow diet or a high fat diet. Despite unchanged food intake, these mice exhibit lower adipose mass and improved glucose metabolism both under a chow and an obesogenic diet. In the latter regimen, transgenic mice display smaller pancreatic islets and significantly less inflammation. MacroH2A1.2 overexpression in the mouse adipose tissue induced dramatic changes in the transcript levels of key adipogenic genes; genomic analyses comparing pre-adipocytes to mature adipocytes uncovered only minor changes in macroH2A1.2 genomic distribution upon adipogenic differentiation and suggested differential cooperation with transcription factors. MacroH2A1.2 overexpression markedly inhibited adipogenesis, while overexpression of macroH2A1.1 had opposite effects. Conclusions MacroH2A1.2 is an unprecedented chromatin component powerfully promoting metabolic health by modulating anti-adipogenic transcriptional networks in the differentiating adipose tissue. Strategies aiming at enhancing macroH2A1.2 expression might counteract excessive adiposity in humans. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0098-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valerio Pazienza
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, 71013 San Giovanni Rotondo, Italy
| | - Concetta Panebianco
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, 71013 San Giovanni Rotondo, Italy
| | - Francesca Rappa
- Department of Experimental Biomedicine and Clinical Neurosciences, Section of Human Anatomy, University of Palermo, 90127 Palermo, Italy ; Department of Legal, Society and Sport Sciences, University of Palermo, 90133 Palermo, Italy ; Euro-Mediterranean Institute of Science and Technology (IEMEST), 90146 Palermo, Italy
| | - Domenico Memoli
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, 84081 Baronissi, SA Italy
| | - Michela Borghesan
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, 71013 San Giovanni Rotondo, Italy ; Institute for Liver and Digestive Health, University College London (UCL), Royal Free Hospital, London, NW3 2PF UK
| | - Sara Cannito
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, 71013 San Giovanni Rotondo, Italy
| | - Asami Oji
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 5650871 Japan
| | - Giuseppe Mazza
- Institute for Liver and Digestive Health, University College London (UCL), Royal Free Hospital, London, NW3 2PF UK
| | - Domenico Tamburrino
- Centre for HPB Surgery and Liver Transplantation, Royal Free Hospital, London, NW3 2QG UK
| | - Giuseppe Fusai
- Centre for HPB Surgery and Liver Transplantation, Royal Free Hospital, London, NW3 2QG UK
| | - Rosario Barone
- Department of Experimental Biomedicine and Clinical Neurosciences, Section of Human Anatomy, University of Palermo, 90127 Palermo, Italy ; Euro-Mediterranean Institute of Science and Technology (IEMEST), 90146 Palermo, Italy
| | - Giulia Bolasco
- Mouse Biology Unit, European Molecular Biology Laboratory (EMBL), 00015 Monterotondo, Italy
| | - Francesc Villarroya
- Departament de Bioquimica i Biologia Molecular, Institut de Biomedicina de la Universitat de Barcelona (IBUB), and CIBER Fisiopatologia de la Obesidad y Nutricion, University of Barcelona, Barcelona, 08007 Spain ; Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBEROBN) ISCIII, Madrid, Spain
| | - Joan Villarroya
- Departament de Bioquimica i Biologia Molecular, Institut de Biomedicina de la Universitat de Barcelona (IBUB), and CIBER Fisiopatologia de la Obesidad y Nutricion, University of Barcelona, Barcelona, 08007 Spain ; Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBEROBN) ISCIII, Madrid, Spain
| | | | - Francesco Cappello
- Department of Experimental Biomedicine and Clinical Neurosciences, Section of Human Anatomy, University of Palermo, 90127 Palermo, Italy ; Euro-Mediterranean Institute of Science and Technology (IEMEST), 90146 Palermo, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, 84081 Baronissi, SA Italy
| | - Tomoko Nakanishi
- Faculty of Medicine, Tottori University, Yonago, 683-8503 Japan ; The Institute of Medical Sciences, University of Tokyo, Tokyo, 108-8639 Japan
| | - Manlio Vinciguerra
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, 71013 San Giovanni Rotondo, Italy ; Euro-Mediterranean Institute of Science and Technology (IEMEST), 90146 Palermo, Italy ; Institute for Liver and Digestive Health, University College London (UCL), Royal Free Hospital, London, NW3 2PF UK ; Center for Translational Medicine (CTM), International Clinical Research Center (ICRC), St. Anne's University Hospital, Brno, 656 91 Czech Republic
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70
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Zhang RL, Yang JP, Peng LX, Zheng LS, Xie P, Wang MY, Cao Y, Zhang ZL, Zhou FJ, Qian CN, Bao YX. RNA-binding protein QKI-5 inhibits the proliferation of clear cell renal cell carcinoma via post-transcriptional stabilization of RASA1 mRNA. Cell Cycle 2016; 15:3094-3104. [PMID: 27767378 DOI: 10.1080/15384101.2016.1235103] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a common pathological subtype of renal cancer. Although the recent application of molecular-targeted agents has modestly improved the prognosis of ccRCC patients, their outcome is still poor. It is therefore important to characterize the molecular and biological mechanisms responsible for the development of ccRCC. Approximately 25% ccRCC patients involves the loss of RNA-binding protein QKI at 6q26, but the role of QKI in ccRCC is unknown. Here, we found that QKI-5 was frequently downregulated in ccRCC patients and its down-regulation was significantly associated with clinical features including T status, M status, and differentiation grade, and poorer patient prognosis. Moreover, QKI-5 inhibited the proliferation of kidney cancer cells both in vitro and in vivo. The subsequent functional studies showed that QKI-5 stabilized RASA1 mRNA via directly binding to the QKI response element region of RASA1, which in turn prevented the activation of the Ras-MAPK signaling pathway, suppressed cellular proliferation and induced cell cycle arrest. Overall, our data demonstrate a suppressive role of QKI in ccRCC tumourigenesis that involves the QKI-mediated post-transcriptional regulation of the Ras-MAPK signaling pathway.
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Affiliation(s)
- Rui-Li Zhang
- a Cancer Center, The First Affiliated Hospital of Xinjiang Medical University , Urumqi , China.,b Key Laboratory of Infection and Cancer , Urumqi , China
| | - Jun-Ping Yang
- c Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine , Guangzhou , Guangdong , China
| | - Li-Xia Peng
- c Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine , Guangzhou , Guangdong , China
| | - Li-Sheng Zheng
- c Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine , Guangzhou , Guangdong , China
| | - Ping Xie
- c Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine , Guangzhou , Guangdong , China
| | - Meng-Yao Wang
- c Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine , Guangzhou , Guangdong , China
| | - Yun Cao
- c Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine , Guangzhou , Guangdong , China.,d Department of Pathology , Sun Yat-sen University Cancer Center , Guangzhou , Guangdong , China
| | - Zhi-Ling Zhang
- c Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine , Guangzhou , Guangdong , China.,e Department of Urology , Sun Yat-sen University Cancer Center , Guangzhou , Guangdong , China
| | - Fang-Jian Zhou
- c Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine , Guangzhou , Guangdong , China.,e Department of Urology , Sun Yat-sen University Cancer Center , Guangzhou , Guangdong , China
| | - Chao-Nan Qian
- c Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine , Guangzhou , Guangdong , China.,f Department of Nasopharyngeal Carcinoma , Sun Yat-sen University Cancer Center , Guangzhou , Guangdong , China
| | - Yong-Xing Bao
- a Cancer Center, The First Affiliated Hospital of Xinjiang Medical University , Urumqi , China.,b Key Laboratory of Infection and Cancer , Urumqi , China
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71
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Jueliger S, Lyons J, Cannito S, Pata I, Pata P, Shkolnaya M, Lo Re O, Peyrou M, Villarroya F, Pazienza V, Rappa F, Cappello F, Azab M, Taverna P, Vinciguerra M. Efficacy and epigenetic interactions of novel DNA hypomethylating agent guadecitabine (SGI-110) in preclinical models of hepatocellular carcinoma. Epigenetics 2016; 11:709-720. [PMID: 27646854 PMCID: PMC5094635 DOI: 10.1080/15592294.2016.1214781] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a deadly malignancy characterized at the epigenetic level by global DNA hypomethylation and focal hypermethylation on the promoter of tumor suppressor genes. In most cases it develops on a background of liver steatohepatitis, fibrosis, and cirrhosis. Guadecitabine (SGI-110) is a second-generation hypomethylating agent, which inhibits DNA methyltransferases. Guadecitabine is formulated as a dinucleotide of decitabine and deoxyguanosine that is resistant to cytidine deaminase (CDA) degradation and results in prolonged in vivo exposure to decitabine following small volume subcutaneous administration of guadecitabine. Here we found that guadecitabine is an effective demethylating agent and is able to prevent HCC progression in pre-clinical models. In a xenograft HCC HepG2 model, guadecitabine impeded tumor growth and inhibited angiogenesis, while it could not prevent liver fibrosis and inflammation in a mouse model of steatohepatitis. Demethylating efficacy of guadecitabine on LINE-1 elements was found to be the highest 8 d post-infusion in blood samples of mice. Analysis of a panel of human HCC vs. normal tissue revealed a signature of hypermethylated tumor suppressor genes (CDKN1A, CDKN2A, DLEC1, E2F1, GSTP1, OPCML, E2F1, RASSF1, RUNX3, and SOCS1) as detected by methylation-specific PCR. A pronounced demethylating effect of guadecitabine was obtained also in the promoters of a subset of tumor suppressors genes (CDKN2A, DLEC1, and RUNX3) in HepG2 and Huh-7 HCC cells. Finally, we analyzed the role of macroH2A1, a variant of histone H2A, an oncogene upregulated in human cirrhosis/HCC that synergizes with DNA methylation in suppressing tumor suppressor genes, and it prevents the inhibition of cell growth triggered by decitabine in HCC cells. Guadecitabine, in contrast to decitabine, blocked growth in HCC cells overexpressing macroH2A1 histones and with high CDA levels, despite being unable to fully demethylate CDKN2A, RUNX3, and DLEC1 promoters altered by macroH2A1. Collectively, our findings in human and mice models reveal novel epigenetic anti-HCC effects of guadecitabine, which might be effective specifically in advanced states of the disease.
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Affiliation(s)
| | - John Lyons
- a Astex Pharmaceuticals , Cambridge , UK
| | - Sara Cannito
- b Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo , Italy.,c Institute for Liver and Digestive Health, University College London (UCL), Royal Free Hospital , London , UK
| | - Illar Pata
- d Department of Gene Technology , Tallinn University of Technology (TTU), IVEX Lab , Tallinn , Estonia
| | - Pille Pata
- d Department of Gene Technology , Tallinn University of Technology (TTU), IVEX Lab , Tallinn , Estonia
| | - Marianna Shkolnaya
- d Department of Gene Technology , Tallinn University of Technology (TTU), IVEX Lab , Tallinn , Estonia
| | - Oriana Lo Re
- e Center for Translational Medicine (CTM), International Clinical Research Center (ICRC), St. Anne's University Hospital , Brno , Czech Republic
| | - Marion Peyrou
- f Departament de Bioquímica i Biologia Molecular , Institute of Biomedicine (IBUB), University of Barcelona , Barcelona , Spain
| | - Francesc Villarroya
- f Departament de Bioquímica i Biologia Molecular , Institute of Biomedicine (IBUB), University of Barcelona , Barcelona , Spain
| | - Valerio Pazienza
- b Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo , Italy
| | - Francesca Rappa
- g Department of Experimental Biomedicine and Clinical Neurosciences , Section of Human Anatomy, University of Palermo , Palermo , Italy.,h Euro-Mediterranean Institute of Science and Technology (IEMEST) , Palermo , Italy
| | - Francesco Cappello
- g Department of Experimental Biomedicine and Clinical Neurosciences , Section of Human Anatomy, University of Palermo , Palermo , Italy.,h Euro-Mediterranean Institute of Science and Technology (IEMEST) , Palermo , Italy
| | | | | | - Manlio Vinciguerra
- b Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo , Italy.,c Institute for Liver and Digestive Health, University College London (UCL), Royal Free Hospital , London , UK.,e Center for Translational Medicine (CTM), International Clinical Research Center (ICRC), St. Anne's University Hospital , Brno , Czech Republic.,h Euro-Mediterranean Institute of Science and Technology (IEMEST) , Palermo , Italy
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de Miguel FJ, Pajares MJ, Martínez-Terroba E, Ajona D, Morales X, Sharma RD, Pardo FJ, Rouzaut A, Rubio A, Montuenga LM, Pio R. A large-scale analysis of alternative splicing reveals a key role of QKI in lung cancer. Mol Oncol 2016; 10:1437-1449. [PMID: 27555542 DOI: 10.1016/j.molonc.2016.08.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 01/14/2023] Open
Abstract
Increasing interest has been devoted in recent years to the understanding of alternative splicing in cancer. In this study, we performed a genome-wide analysis to identify cancer-associated splice variants in non-small cell lung cancer. We discovered and validated novel differences in the splicing of genes known to be relevant to lung cancer biology, such as NFIB, ENAH or SPAG9. Gene enrichment analyses revealed an important contribution of alternative splicing to cancer-related molecular functions, especially those involved in cytoskeletal dynamics. Interestingly, a substantial fraction of the altered genes found in our analysis were targets of the protein quaking (QKI), pointing to this factor as one of the most relevant regulators of alternative splicing in non-small cell lung cancer. We also found that ESYT2, one of the QKI targets, is involved in cytoskeletal organization. ESYT2-short variant inhibition in lung cancer cells resulted in a cortical distribution of actin whereas inhibition of the long variant caused an increase of endocytosis, suggesting that the cancer-associated splicing pattern of ESYT2 has a profound impact in the biology of cancer cells. Finally, we show that low nuclear QKI expression in non-small cell lung cancer is an independent prognostic factor for disease-free survival (HR = 2.47; 95% CI = 1.11-5.46, P = 0.026). In conclusion, we identified several splicing variants with functional relevance in lung cancer largely regulated by the splicing factor QKI, a tumor suppressor associated with prognosis in lung cancer.
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Affiliation(s)
- Fernando J de Miguel
- Program in Solid Tumors and Biomarkers, CIMA, 31008 Pamplona, Spain; Department of Biochemistry and Genetics, School of Science, University of Navarra, 31008 Pamplona, Spain
| | - María J Pajares
- Program in Solid Tumors and Biomarkers, CIMA, 31008 Pamplona, Spain; Department of Histology and Pathology, School of Medicine, University of Navarra, 31008 Pamplona, Spain; Navarra's Health Research Institute (IDISNA), 31008 Pamplona, Spain
| | - Elena Martínez-Terroba
- Program in Solid Tumors and Biomarkers, CIMA, 31008 Pamplona, Spain; Department of Histology and Pathology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Daniel Ajona
- Program in Solid Tumors and Biomarkers, CIMA, 31008 Pamplona, Spain; Department of Biochemistry and Genetics, School of Science, University of Navarra, 31008 Pamplona, Spain; Navarra's Health Research Institute (IDISNA), 31008 Pamplona, Spain
| | - Xabier Morales
- Program in Immunology and Immunotherapy, CIMA, 31008 Pamplona, Spain
| | - Ravi D Sharma
- Group of Bioinformatics, CEIT and TECNUN, University of Navarra, 20018 San Sebastian, Spain
| | - Francisco J Pardo
- Department of Pathology, Clinica Universidad de Navarra, 31080 Pamplona, Spain
| | - Ana Rouzaut
- Department of Biochemistry and Genetics, School of Science, University of Navarra, 31008 Pamplona, Spain; Navarra's Health Research Institute (IDISNA), 31008 Pamplona, Spain; Program in Immunology and Immunotherapy, CIMA, 31008 Pamplona, Spain
| | - Angel Rubio
- Group of Bioinformatics, CEIT and TECNUN, University of Navarra, 20018 San Sebastian, Spain
| | - Luis M Montuenga
- Program in Solid Tumors and Biomarkers, CIMA, 31008 Pamplona, Spain; Department of Histology and Pathology, School of Medicine, University of Navarra, 31008 Pamplona, Spain; Navarra's Health Research Institute (IDISNA), 31008 Pamplona, Spain.
| | - Ruben Pio
- Program in Solid Tumors and Biomarkers, CIMA, 31008 Pamplona, Spain; Department of Biochemistry and Genetics, School of Science, University of Navarra, 31008 Pamplona, Spain; Navarra's Health Research Institute (IDISNA), 31008 Pamplona, Spain.
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73
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Konstantinov NK, Ulff-Møller CJ, Dimitrov S. Histone variants and melanoma: facts and hypotheses. Pigment Cell Melanoma Res 2016; 29:426-33. [DOI: 10.1111/pcmr.12467] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 02/10/2016] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - Stefan Dimitrov
- Institut Albert Bonniot; U823, INSERM/Université Joseph Fourier; Grenoble Cedex 9 France
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74
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Inoue D, Bradley RK, Abdel-Wahab O. Spliceosomal gene mutations in myelodysplasia: molecular links to clonal abnormalities of hematopoiesis. Genes Dev 2016; 30:989-1001. [PMID: 27151974 PMCID: PMC4863743 DOI: 10.1101/gad.278424.116] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Genomic analyses of the myeloid malignancies and clonal disorders of hematopoiesis that may give rise to these disorders have identified that mutations in genes encoding core spliceosomal proteins and accessory regulatory splicing factors are among the most common targets of somatic mutations. These spliceosomal mutations often occur in a mutually exclusive manner with one another and, in aggregate, account for the most frequent class of mutations in patients with myelodysplastic syndromes (MDSs) in particular. Although substantial progress has been made in understanding the effects of several of these mutations on splicing and splice site recognition, functional connections linking the mechanistic changes in splicing induced by these mutations to the phenotypic consequences of clonal and aberrant hematopoiesis are not yet well defined. This review describes our current understanding of the mechanistic and biological effects of spliceosomal gene mutations in MDSs as well as the regulation of splicing throughout normal hematopoiesis.
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Affiliation(s)
- Daichi Inoue
- Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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75
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Rivera-Casas C, Gonzalez-Romero R, Cheema MS, Ausió J, Eirín-López JM. The characterization of macroH2A beyond vertebrates supports an ancestral origin and conserved role for histone variants in chromatin. Epigenetics 2016; 11:415-25. [PMID: 27082816 DOI: 10.1080/15592294.2016.1172161] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Histone variants play a critical role in chromatin structure and epigenetic regulation. These "deviant" proteins have been historically considered as the evolutionary descendants of ancestral canonical histones, helping specialize the nucleosome structure during eukaryotic evolution. Such view is now challenged by 2 major observations: first, canonical histones present extremely unique features not shared with any other genes; second, histone variants are widespread across many eukaryotic groups. The present work further supports the ancestral nature of histone variants by providing the first in vivo characterization of a functional macroH2A histone (a variant long defined as a specific refinement of vertebrate chromatin) in a non-vertebrate organism (the mussel Mytilus) revealing its recruitment into heterochromatic fractions of actively proliferating tissues. Combined with in silico analyses of genomic data, these results provide evidence for the widespread presence of macroH2A in metazoan animals, as well as in the holozoan Capsaspora, supporting an evolutionary origin for this histone variant lineage before the radiation of Filozoans (including Filasterea, Choanoflagellata and Metazoa). Overall, the results presented in this work help configure a new evolutionary scenario in which histone variants, rather than modern "deviants" of canonical histones, would constitute ancient components of eukaryotic chromatin.
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Affiliation(s)
- Ciro Rivera-Casas
- a Department of Biological Sciences, Chromatin Structure and Evolution (Chromevol) Group , Florida International University , North Miami , FL , USA
| | - Rodrigo Gonzalez-Romero
- a Department of Biological Sciences, Chromatin Structure and Evolution (Chromevol) Group , Florida International University , North Miami , FL , USA
| | - Manjinder S Cheema
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , British Columbia , Canada
| | - Juan Ausió
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , British Columbia , Canada
| | - José M Eirín-López
- a Department of Biological Sciences, Chromatin Structure and Evolution (Chromevol) Group , Florida International University , North Miami , FL , USA
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76
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Altered primary chromatin structures and their implications in cancer development. Cell Oncol (Dordr) 2016; 39:195-210. [PMID: 27007278 DOI: 10.1007/s13402-016-0276-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cancer development is a complex process involving both genetic and epigenetic changes. Genetic changes in oncogenes and tumor-suppressor genes are generally considered as primary causes, since these genes may directly regulate cellular growth. In addition, it has been found that changes in epigenetic factors, through mutation or altered gene expression, may contribute to cancer development. In the nucleus of eukaryotic cells DNA and histone proteins form a structure called chromatin which consists of nucleosomes that, like beads on a string, are aligned along the DNA strand. Modifications in chromatin structure are essential for cell type-specific activation or repression of gene transcription, as well as other processes such as DNA repair, DNA replication and chromosome segregation. Alterations in epigenetic factors involved in chromatin dynamics may accelerate cell cycle progression and, ultimately, result in malignant transformation. Abnormal expression of remodeler and modifier enzymes, as well as histone variants, may confer to cancer cells the ability to reprogram their genomes and to yield, maintain or exacerbate malignant hallmarks. At the end, genetic and epigenetic alterations that are encountered in cancer cells may culminate in chromatin changes that may, by altering the quantity and quality of gene expression, promote cancer development. METHODS During the last decade a vast number of studies has uncovered epigenetic abnormalities that are associated with the (anomalous) packaging and remodeling of chromatin in cancer genomes. In this review I will focus on recently published work dealing with alterations in the primary structure of chromatin resulting from imprecise arrangements of nucleosomes along DNA, and its functional implications for cancer development. CONCLUSIONS The primary chromatin structure is regulated by a variety of epigenetic mechanisms that may be deregulated through gene mutations and/or gene expression alterations. In recent years, it has become evident that changes in chromatin structure may coincide with the occurrence of cancer hallmarks. The functional interrelationships between such epigenetic alterations and cancer development are just becoming manifest and, therefore, the oncology community should continue to explore the molecular mechanisms governing the primary chromatin structure, both in normal and in cancer cells, in order to improve future approaches for cancer detection, prevention and therapy, as also for circumventing drug resistance.
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77
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Histone variants: nuclear function and disease. Curr Opin Genet Dev 2016; 37:82-89. [PMID: 26826795 DOI: 10.1016/j.gde.2015.12.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/17/2015] [Accepted: 12/19/2015] [Indexed: 11/23/2022]
Abstract
Histone variants have emerged as important contributors to the regulation of chromatin structure and therefore of almost all DNA-based processes. Hence, these specialized proteins play important roles in transcriptional regulation, cell cycle progression, DNA repair, chromatin stability, chromosome segregation and apoptosis. Due to their evident biological significance, it is not surprising that mutations or the deregulation of their expression levels can have severe implications for cellular functions that ultimately might contribute to or even drive disease development, most notably cancer. Besides the histones themselves, their respective chaperone/remodeling complexes needed for precise variant chromatin deposition, are consequently frequent targets in neoplasms and diverse diseases. In this review, we briefly summarize current understanding on the function of human/mammalian histone variants and their regulatory networks and highlight their roles in cancer development.
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78
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Borghesan M, Fusilli C, Rappa F, Panebianco C, Rizzo G, Oben JA, Mazzoccoli G, Faulkes C, Pata I, Agodi A, Rezaee F, Minogue S, Warren A, Peterson A, Sedivy JM, Douet J, Buschbeck M, Cappello F, Mazza T, Pazienza V, Vinciguerra M. DNA Hypomethylation and Histone Variant macroH2A1 Synergistically Attenuate Chemotherapy-Induced Senescence to Promote Hepatocellular Carcinoma Progression. Cancer Res 2016; 76:594-606. [PMID: 26772755 DOI: 10.1158/0008-5472.can-15-1336] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022]
Abstract
Aging is a major risk factor for progression of liver diseases to hepatocellular carcinoma (HCC). Cellular senescence contributes to age-related tissue dysfunction, but the epigenetic basis underlying drug-induced senescence remains unclear. macroH2A1, a variant of histone H2A, is a marker of senescence-associated heterochromatic foci that synergizes with DNA methylation to silence tumor-suppressor genes in human fibroblasts. In this study, we investigated the relationship between macroH2A1 splice variants, macroH2A1.1 and macroH2A1.2, and liver carcinogenesis. We found that protein levels of both macroH2A1 isoforms were increased in the livers of very elderly rodents and humans, and were robust immunohistochemical markers of human cirrhosis and HCC. In response to the chemotherapeutic and DNA-demethylating agent 5-aza-deoxycytidine (5-aza-dC), transgenic expression of macroH2A1 isoforms in HCC cell lines prevented the emergence of a senescent-like phenotype and induced synergistic global DNA hypomethylation. Conversely, macroH2A1 depletion amplified the antiproliferative effects of 5-aza-dC in HCC cells, but failed to enhance senescence. Senescence-associated secretory phenotype and whole-transcriptome analyses implicated the p38 MAPK/IL8 pathway in mediating macroH2A1-dependent escape of HCC cells from chemotherapy-induced senescence. Furthermore, chromatin immunoprecipitation sequencing revealed that this hepatic antisenescence state also required active transcription that could not be attributed to genomic occupancy of these histones. Collectively, our findings reveal a new mechanism by which drug-induced senescence is epigenetically regulated by macroH2A1 and DNA methylation and suggest macroH2A1 as a novel biomarker of hepatic senescence that could potentially predict prognosis and disease progression.
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Affiliation(s)
- Michela Borghesan
- Institute for Liver and Digestive Health, Royal Free Hospital, University College London, London, United Kingdom. Division of Internal Medicine, Department of Medical Sciences, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Caterina Fusilli
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza"-Mendel Laboratory, Rome, Italy
| | - Francesca Rappa
- Department of Experimental Biomedicine and Clinical Neurosciences, Section of Human Anatomy, University of Palermo, Palermo, Italy
| | - Concetta Panebianco
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Giovanni Rizzo
- Institute for Liver and Digestive Health, Royal Free Hospital, University College London, London, United Kingdom
| | - Jude A Oben
- Institute for Liver and Digestive Health, Royal Free Hospital, University College London, London, United Kingdom
| | - Gianluigi Mazzoccoli
- Division of Internal Medicine, Department of Medical Sciences, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Chris Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Illar Pata
- Department of Gene Technology, Tallinn University of Technology (TTU), IVEX Lab, Tallinn, Estonia
| | - Antonella Agodi
- Department GF Ingrassia, University of Catania, Catania, Italy
| | - Farhad Rezaee
- Department of Cell Biology, University Medical Center Groningen, Groningen, the Netherlands
| | - Shane Minogue
- Institute for Liver and Digestive Health, Royal Free Hospital, University College London, London, United Kingdom
| | - Alessandra Warren
- Institute for Liver and Digestive Health, Royal Free Hospital, University College London, London, United Kingdom. Centre for Education and Research on Aging (CERA) and the ANZAC Research Institute, Concord RG Hospital, University of Sydney, Sydney, Australia
| | - Abigail Peterson
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Julien Douet
- Institute for Predictive and Personalized Medicine of Cancer, Campus Can Ruti, Badalona, Spain. Josep Carreras Institute for Leukaemia Research, Campus ICO-HGTP, Campus Can Ruti, Badalona, Spain
| | - Marcus Buschbeck
- Institute for Predictive and Personalized Medicine of Cancer, Campus Can Ruti, Badalona, Spain. Josep Carreras Institute for Leukaemia Research, Campus ICO-HGTP, Campus Can Ruti, Badalona, Spain
| | - Francesco Cappello
- Department of Experimental Biomedicine and Clinical Neurosciences, Section of Human Anatomy, University of Palermo, Palermo, Italy. Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza"-Mendel Laboratory, Rome, Italy
| | - Valerio Pazienza
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Manlio Vinciguerra
- Institute for Liver and Digestive Health, Royal Free Hospital, University College London, London, United Kingdom. Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy. Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy. School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom.
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79
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Hollar D. Epigenetic Significance of Chromatin Organization During Cellular Aging and Organismal Lifespan. EPIGENETICS, THE ENVIRONMENT, AND CHILDREN’S HEALTH ACROSS LIFESPANS 2016. [PMCID: PMC7153164 DOI: 10.1007/978-3-319-25325-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David Hollar
- Pfeiffer University, Morrisville, North Carolina USA
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80
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Camicia R, Winkler HC, Hassa PO. Novel drug targets for personalized precision medicine in relapsed/refractory diffuse large B-cell lymphoma: a comprehensive review. Mol Cancer 2015; 14:207. [PMID: 26654227 PMCID: PMC4676894 DOI: 10.1186/s12943-015-0474-2] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 08/26/2015] [Indexed: 02/07/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a clinically heterogeneous lymphoid malignancy and the most common subtype of non-Hodgkin's lymphoma in adults, with one of the highest mortality rates in most developed areas of the world. More than half of DLBLC patients can be cured with standard R-CHOP regimens, however approximately 30 to 40 % of patients will develop relapsed/refractory disease that remains a major cause of morbidity and mortality due to the limited therapeutic options.Recent advances in gene expression profiling have led to the identification of at least three distinct molecular subtypes of DLBCL: a germinal center B cell-like subtype, an activated B cell-like subtype, and a primary mediastinal B-cell lymphoma subtype. Moreover, recent findings have not only increased our understanding of the molecular basis of chemotherapy resistance but have also helped identify molecular subsets of DLBCL and rational targets for drug interventions that may allow for subtype/subset-specific molecularly targeted precision medicine and personalized combinations to both prevent and treat relapsed/refractory DLBCL. Novel agents such as lenalidomide, ibrutinib, bortezomib, CC-122, epratuzumab or pidilizumab used as single-agent or in combination with (rituximab-based) chemotherapy have already demonstrated promising activity in patients with relapsed/refractory DLBCL. Several novel potential drug targets have been recently identified such as the BET bromodomain protein (BRD)-4, phosphoribosyl-pyrophosphate synthetase (PRPS)-2, macrodomain-containing mono-ADP-ribosyltransferase (ARTD)-9 (also known as PARP9), deltex-3-like E3 ubiquitin ligase (DTX3L) (also known as BBAP), NF-kappaB inducing kinase (NIK) and transforming growth factor beta receptor (TGFβR).This review highlights the new insights into the molecular basis of relapsed/refractory DLBCL and summarizes the most promising drug targets and experimental treatments for relapsed/refractory DLBCL, including the use of novel agents such as lenalidomide, ibrutinib, bortezomib, pidilizumab, epratuzumab, brentuximab-vedotin or CAR T cells, dual inhibitors, as well as mechanism-based combinatorial experimental therapies. We also provide a comprehensive and updated list of current drugs, drug targets and preclinical and clinical experimental studies in DLBCL. A special focus is given on STAT1, ARTD9, DTX3L and ARTD8 (also known as PARP14) as novel potential drug targets in distinct molecular subsets of DLBCL.
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Affiliation(s)
- Rosalba Camicia
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Stem Cell Research Laboratory, NHS Blood and Transplant, Nuffield Division of Clinical, Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK.,MRC-UCL Laboratory for Molecular Cell Biology Unit, University College London, Gower Street, London, WC1E6BT, UK
| | - Hans C Winkler
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute of Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland
| | - Paul O Hassa
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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81
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Fu Y, Lv P, Yan G, Fan H, Cheng L, Zhang F, Dang Y, Wu H, Wen B. MacroH2A1 associates with nuclear lamina and maintains chromatin architecture in mouse liver cells. Sci Rep 2015; 5:17186. [PMID: 26603343 PMCID: PMC4658601 DOI: 10.1038/srep17186] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/26/2015] [Indexed: 12/26/2022] Open
Abstract
In the interphase nucleus, chromatin is organized into three-dimensional conformation to coordinate genome functions. The lamina-chromatin association is important to facilitate higher-order chromatin in mammalian cells, but its biological significances and molecular mechanisms remain poorly understood. One obstacle is that the list of lamina-associated proteins remains limited, presumably due to the inherent insolubility of lamina proteins. In this report, we identified 182 proteins associated with lamin B1 (a constitutive component of lamina) in mouse hepatocytes, by adopting virus-based proximity-dependent biotin identification. These proteins are functionally related to biological processes such as chromatin organization. As an example, we validated the association between lamin B1 and core histone macroH2A1, a histone associated with repressive chromatin. Furthermore, we mapped Lamina-associated domains (LADs) in mouse liver cells and found that boundaries of LADs are enriched for macroH2A. More interestingly, knocking-down of macroH2A1 resulted in the release of heterochromatin foci marked by histone lysine 9 trimethylation (H3K9me3) and the decondensation of global chromatin structure. However, down-regulation of lamin B1 led to redistribution of macroH2A1. Taken together, our data indicated that macroH2A1 is associated with lamina and is required to maintain chromatin architecture in mouse liver cells.
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Affiliation(s)
- Yuhua Fu
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Pin Lv
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Guoquan Yan
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Chemistry, Fudan University, Shanghai, 200433
| | - Hui Fan
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lu Cheng
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yongjun Dang
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Bo Wen
- Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
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82
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Mattiroli F, D'Arcy S, Luger K. The right place at the right time: chaperoning core histone variants. EMBO Rep 2015; 16:1454-66. [PMID: 26459557 DOI: 10.15252/embr.201540840] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/17/2015] [Indexed: 12/13/2022] Open
Abstract
Histone proteins dynamically regulate chromatin structure and epigenetic signaling to maintain cell homeostasis. These processes require controlled spatial and temporal deposition and eviction of histones by their dedicated chaperones. With the evolution of histone variants, a network of functionally specific histone chaperones has emerged. Molecular details of the determinants of chaperone specificity for different histone variants are only slowly being resolved. A complete understanding of these processes is essential to shed light on the genuine biological roles of histone variants, their chaperones, and their impact on chromatin dynamics.
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Affiliation(s)
- Francesca Mattiroli
- Department of Molecular and Radiobiological Sciences, Howard Hughes Medical Institute, Colorado State University, Fort Collins, CO, USA
| | - Sheena D'Arcy
- Department of Molecular and Radiobiological Sciences, Howard Hughes Medical Institute, Colorado State University, Fort Collins, CO, USA
| | - Karolin Luger
- Department of Molecular and Radiobiological Sciences, Howard Hughes Medical Institute, Colorado State University, Fort Collins, CO, USA
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83
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Santoro SW, Dulac C. Histone variants and cellular plasticity. Trends Genet 2015; 31:516-27. [PMID: 26299477 PMCID: PMC5111554 DOI: 10.1016/j.tig.2015.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 06/15/2015] [Accepted: 07/15/2015] [Indexed: 11/27/2022]
Abstract
The broad diversity of cell types within vertebrates arises from a unique genetic blueprint by combining intrinsic cellular information with developmental and other extrinsic signals. Lying at the interface between cellular signals and the DNA is the chromatin, a dynamic nucleoprotein complex that helps to mediate gene regulation. The most basic subunit of chromatin, the nucleosome, consists of DNA wrapped around histones, a set of proteins that play crucial roles as scaffolding molecules and regulators of gene expression. Growing evidence indicates that canonical histones are commonly replaced by protein variants before and during cellular transitions. We highlight exciting new results suggesting that histone variants are essential players in the control of cellular plasticity during development and in the adult nervous system.
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Affiliation(s)
- Stephen W Santoro
- Neuroscience Program, Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA.
| | - Catherine Dulac
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
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84
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Chen H, Ruiz PD, McKimpson WM, Novikov L, Kitsis RN, Gamble MJ. MacroH2A1 and ATM Play Opposing Roles in Paracrine Senescence and the Senescence-Associated Secretory Phenotype. Mol Cell 2015; 59:719-31. [PMID: 26300260 DOI: 10.1016/j.molcel.2015.07.011] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/28/2015] [Accepted: 07/15/2015] [Indexed: 01/07/2023]
Abstract
Oncogene-induced senescence (OIS) is a tumor-suppressive mechanism typified by stable proliferative arrest, a persistent DNA damage response, and the senescence-associated secretory phenotype (SASP), which helps to maintain the senescent state and triggers bystander senescence in a paracrine fashion. Here, we demonstrate that the tumor suppressive histone variant macroH2A1 is a critical component of the positive feedback loop that maintains SASP gene expression and triggers the induction of paracrine senescence. MacroH2A1 undergoes dramatic genome-wide relocalization during OIS, including its removal from SASP gene chromatin. The removal of macroH2A1 from SASP genes results from a negative feedback loop activated by SASP-mediated endoplasmic reticulum (ER) stress. ER stress leads to increased reactive oxygen species and persistent DNA damage response including activation of ATM, which mediates removal macroH2A1 from SASP genes. Together, our findings indicate that macroH2A1 is a critical control point for the regulation of SASP gene expression during senescence.
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Affiliation(s)
- Hongshan Chen
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Penelope D Ruiz
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Wendy M McKimpson
- Department of Cell Biology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Leonid Novikov
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Richard N Kitsis
- Department of Cell Biology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Matthew J Gamble
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA.
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85
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Park SJ, Shim JW, Park HS, Eum DY, Park MT, Mi Yi J, Choi SH, Kim SD, Son TG, Lu W, Kim ND, Yang K, Heo K. MacroH2A1 downregulation enhances the stem-like properties of bladder cancer cells by transactivation of Lin28B. Oncogene 2015; 35:1292-301. [PMID: 26028027 PMCID: PMC4791524 DOI: 10.1038/onc.2015.187] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 04/01/2015] [Accepted: 04/24/2015] [Indexed: 12/18/2022]
Abstract
The histone variant, macroH2A1, has an important role in embryonic stem cell differentiation and tumor progression in various types of tumors. However, the regulatory roles of macroH2A1 on bladder cancer progression have not been fully elucidated. Here, we show that macroH2A1 knockdown promotes stem-like properties of bladder cancer cells. The knockdown of macroH2A1 in bladder cancer cells increased tumorigenicity, radioresistance, degeneration of reactive oxygen species, increased sphere formation capability and an increase in the proportion of side populations. We found that macroH2A1 is required for the suppression of Lin28B identified as a novel downstream target of macroH2A1 in bladder cancer. Loss of macroH2A1 expression significantly correlated with the elevated levels of Lin28B expression and subsequently inhibited the mature let-7 microRNA expression. Furthermore, the stable overexpression of Lin28B enhances the several phenotypes, including tumorigenicity and sphere-forming ability, which are induced by macroH2A1 depletion. Importantly, Lin28B expression was regulated by macroH2A1-mediated reciprocal binding of p300 and EZH2/SUV39H1. Our results suggest that Lin28B/let-7 pathway is tightly regulated by macroH2A1 and its cofactors, and have a pivotal role in the bladder tumor progression and the regulation of stem-like characteristics of bladder cancer cells.
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Affiliation(s)
- S-J Park
- Research Center, Dongnam Institute of Radiological and Medical Science (DIRAMS), Busan, Republic of Korea.,Department of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - J W Shim
- Research Center, Dongnam Institute of Radiological and Medical Science (DIRAMS), Busan, Republic of Korea
| | - H S Park
- Research Center, Dongnam Institute of Radiological and Medical Science (DIRAMS), Busan, Republic of Korea
| | - D-Y Eum
- Research Center, Dongnam Institute of Radiological and Medical Science (DIRAMS), Busan, Republic of Korea
| | - M-T Park
- Research Center, Dongnam Institute of Radiological and Medical Science (DIRAMS), Busan, Republic of Korea
| | - J Mi Yi
- Research Center, Dongnam Institute of Radiological and Medical Science (DIRAMS), Busan, Republic of Korea
| | - S H Choi
- Research Center, Dongnam Institute of Radiological and Medical Science (DIRAMS), Busan, Republic of Korea
| | - S D Kim
- Research Center, Dongnam Institute of Radiological and Medical Science (DIRAMS), Busan, Republic of Korea
| | - T G Son
- Research Center, Dongnam Institute of Radiological and Medical Science (DIRAMS), Busan, Republic of Korea
| | - W Lu
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - N D Kim
- Department of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - K Yang
- Research Center, Dongnam Institute of Radiological and Medical Science (DIRAMS), Busan, Republic of Korea.,Department of Radiation Oncology, Dongnam Institute of Radiological & Medical Sciences, Busan, Republic of Korea.,Department of Radiation Oncology, Korea Institute of Radiological & Medical Sciences, Seoul, Republic of Korea
| | - K Heo
- Research Center, Dongnam Institute of Radiological and Medical Science (DIRAMS), Busan, Republic of Korea
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86
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Danan-Gotthold M, Golan-Gerstl R, Eisenberg E, Meir K, Karni R, Levanon EY. Identification of recurrent regulated alternative splicing events across human solid tumors. Nucleic Acids Res 2015; 43:5130-44. [PMID: 25908786 PMCID: PMC4446417 DOI: 10.1093/nar/gkv210] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 03/02/2015] [Indexed: 12/21/2022] Open
Abstract
Cancer is a complex disease that involves aberrant gene expression regulation. Discriminating the modified expression patterns driving tumor biology from the many that have no or little contribution is important for understanding cancer molecular basis. Recurrent deregulation patterns observed in multiple cancer types are enriched for such driver events. Here, we studied splicing alterations in hundreds of matched tumor and normal RNA-seq samples of eight solid cancer types. We found hundreds of cassette exons for which splicing was altered in multiple cancer types and identified a set of highly frequent altered splicing events. Specific splicing regulators, including RBFOX2, MBNL1/2 and QKI, appear to account for many splicing alteration events in multiple cancer types. Together, our results provide a first global analysis of regulated splicing alterations in cancer and identify common events with a potential causative role in solid tumor development.
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Affiliation(s)
- Miri Danan-Gotthold
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Regina Golan-Gerstl
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Ein Karem, 91120 Jerusalem, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Keren Meir
- Department of Pathology, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Ein Karem, 91120 Jerusalem, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
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87
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Monteiro FL, Baptista T, Amado F, Vitorino R, Jerónimo C, Helguero LA. Expression and functionality of histone H2A variants in cancer. Oncotarget 2015; 5:3428-43. [PMID: 25003966 PMCID: PMC4116493 DOI: 10.18632/oncotarget.2007] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Regulation of gene expression includes the replacement of canonical histones for non-allelic histone variants, as well as their multiple targeting by postranslational modifications. H2A variants are highly conserved between species suggesting they execute important functions that cannot be accomplished by canonical histones. Altered expression of many H2A variants is associated to cancer. MacroH2A variants are enriched in heterocromatic foci and are necessary for chromatin condensation. MacroH2A1.1 and macroH2A1.2 are two mutually exclusive isoforms. MacroH2A1.1 and macroH2A2 inhibit proliferation and are associated with better cancer prognosis; while macroH2A1.2 is associated to cancer progression. H2AX variant functions as a sensor of DNA damage and defines the cellular response towards DNA repair or apoptosis; therefore, screening approaches and therapeutic options targeting H2AX have been proposed. H2A.Z is enriched in euchromatin, acting as a proto-oncogene with established roles in hormone responsive cancers and overexpressed in endocrine-resistant disease. Other H2A family members have also been found altered in cancer, but their function remains unknown. Substantial progress has been made to understand histone H2A variants, their contribution to normal cellular function and to cancer development and progression. Yet, implementation of high resolution mass spectrometry is needed to further our knowledge on highly homologous H2A variants expression and function.
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Affiliation(s)
- Fátima Liliana Monteiro
- Mass Specrometry Center, Organic Chemistry and Natural Products Unit (QOPNA), Department of Chemistry, Universidade de Aveiro., Aveiro, Portugal
| | | | | | | | | | - Luisa A Helguero
- Mass Specrometry Center, Organic Chemistry and Natural Products Unit (QOPNA), Dep. of Chemistry, Universidade de Aveiro., Aveiro, Portugal
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88
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Abstract
Genetic and epigenetic changes are at the root of all cancers. The epigenetic component involves alterations of the post-synthetic modifications of DNA (methylation) and histones (histone posttranslational modifications, PTMs) as well as of those of their molecular "writers," "readers," and "erasers." Noncoding RNAs (ncRNA) can also play a role. Here, we focus on the involvement of histone alterations in cancer, in particular that of the histone variant H2A.Z in the etiology of prostate cancer. The structural mechanisms putatively responsible for the contribution of H2A.Z to oncogenic gene expression programs are first described, followed by what is currently known about the involvement of this histone variant in the regulation of androgen receptor regulated gene expression. The implications of this and their relevance to oncogene deregulation in different stages of prostate cancer, including the progression toward androgen independence, are discussed. This review underscores the increasing awareness of the epigenetic contribution of histone variants to oncogenic progression.
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Affiliation(s)
- Deanna Dryhurst
- Department of Biochemistry and Microbiology, University of Victoria, Petch building, 258a, Victoria, British Columbia Canada V8W 3P6
- ImmunoPrecise Antibodies Ltd., 3204-4464 Markham St., Victoria, British Columbia Canada V8Z 7X8
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Petch building, 258a, Victoria, British Columbia Canada V8W 3P6
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89
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Chen FC. Alternative RNA structure-coupled gene regulations in tumorigenesis. Int J Mol Sci 2014; 16:452-75. [PMID: 25551597 PMCID: PMC4307256 DOI: 10.3390/ijms16010452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/16/2014] [Indexed: 12/11/2022] Open
Abstract
Alternative RNA structures (ARSs), or alternative transcript isoforms, are critical for regulating cellular phenotypes in humans. In addition to generating functionally diverse protein isoforms from a single gene, ARS can alter the sequence contents of 5'/3' untranslated regions (UTRs) and intronic regions, thus also affecting the regulatory effects of these regions. ARS may introduce premature stop codon(s) into a transcript, and render the transcript susceptible to nonsense-mediated decay, which in turn can influence the overall gene expression level. Meanwhile, ARS can regulate the presence/absence of upstream open reading frames and microRNA targeting sites in 5'UTRs and 3'UTRs, respectively, thus affecting translational efficiencies and protein expression levels. Furthermore, since ARS may alter exon-intron structures, it can influence the biogenesis of intronic microRNAs and indirectly affect the expression of the target genes of these microRNAs. The connections between ARS and multiple regulatory mechanisms underline the importance of ARS in determining cell fate. Accumulating evidence indicates that ARS-coupled regulations play important roles in tumorigenesis. Here I will review our current knowledge in this field, and discuss potential future directions.
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Affiliation(s)
- Feng-Chi Chen
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 350, Taiwan.
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90
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Podrini C, Koffas A, Chokshi S, Vinciguerra M, Lelliott CJ, White JK, Adissu HA, Williams R, Greco A. MacroH2A1 isoforms are associated with epigenetic markers for activation of lipogenic genes in fat-induced steatosis. FASEB J 2014; 29:1676-87. [PMID: 25526730 DOI: 10.1096/fj.14-262717] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/24/2014] [Indexed: 01/14/2023]
Abstract
The importance of epigenetic changes in the development of hepatic steatosis is largely unknown. The histone variant macroH2A1 under alternative splicing gives rise to macroH2A1.1 and macroH2A1.2. In this study, we show that the macroH2A1 isoforms play an important role in the regulation of lipid accumulation in hepatocytes. Hepatoma cell line and immortalized human hepatocytes transiently transfected or knocked down with macroH2A1 isoforms were used as in vitro model of fat-induced steatosis. Gene expressions were analyzed by quantitative PCR array and Western blot. Chromatin immunoprecipitation analysis was performed to check the association of histone H3 lysine 27 trimethylation (H3K27me3) and histone H3 lysine 4 trimethylation (H3K4me3) with the promoter of lipogenic genes. Livers from knockout mice that are resistant to lipid deposition despite a high-fat diet were used for histopathology. We found that macroH2A1.2 is regulated by fat uptake and that its overexpression caused an increase in lipid uptake, triglycerides, and lipogenic genes compared with macroH2A1.1. This suggests that macroH2A1.2 is important for lipid uptake, whereas macroH2A1.1 was found to be protective. The result was supported by a high positivity for macroH2A1.1 in knockout mice for genes targeted by macroH2A1 (Atp5a1 and Fam73b), that under a high-fat diet presented minimal lipidosis. Moreover, macroH2A1 isoforms differentially regulate the expression of lipogenic genes by modulating the association of the active (H3K4me3) and repressive (H3K27me3) histone marks on their promoters. This study underlines the importance of the replacement of noncanonical histones in the regulation of genes involved in lipid metabolism in the progression of steatosis.
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Affiliation(s)
- Christine Podrini
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Apostolos Koffas
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Shilpa Chokshi
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Manlio Vinciguerra
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Christopher J Lelliott
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Jacqueline K White
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Hibret A Adissu
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Roger Williams
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Azzura Greco
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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91
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Rouleau SG, Beaudoin JD, Bisaillon M, Perreault JP. Small antisense oligonucleotides against G-quadruplexes: specific mRNA translational switches. Nucleic Acids Res 2014; 43:595-606. [PMID: 25510493 PMCID: PMC4288198 DOI: 10.1093/nar/gku1311] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
G-quadruplexes (G4) are intricate RNA structures found throughout the transcriptome. Because they are associated with a variety of biological cellular mechanisms, these fascinating structural motifs are seen as potential therapeutic targets against many diseases. While screening of chemical compounds specific to G4 motifs has yielded interesting results, no single compound successfully discriminates between G4 motifs based on nucleotide sequences alone. This level of specificity is best attained using antisense oligonucleotides (ASO). Indeed, oligonucleotide-based strategies are already used to modulate DNA G4 folding in vitro. Here, we report that, in human cells, the use of short ASO to promote and inhibit RNA G4 folding affects the translation of specific mRNAs, including one from the 5'UTR of the H2AFY gene, a histone variant associated with cellular differentiation and cancer. These results suggest that the relatively high specificity of ASO-based strategies holds significant potential for applications aimed at modulating G4-motif folding.
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Affiliation(s)
- Samuel G Rouleau
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Québec, J1E 4K8, Canada
| | - Jean-Denis Beaudoin
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Québec, J1E 4K8, Canada
| | - Martin Bisaillon
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Québec, J1E 4K8, Canada
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Québec, J1E 4K8, Canada
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92
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An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J Neurosci 2014; 34:11929-47. [PMID: 25186741 DOI: 10.1523/jneurosci.1860-14.2014] [Citation(s) in RCA: 3539] [Impact Index Per Article: 353.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The major cell classes of the brain differ in their developmental processes, metabolism, signaling, and function. To better understand the functions and interactions of the cell types that comprise these classes, we acutely purified representative populations of neurons, astrocytes, oligodendrocyte precursor cells, newly formed oligodendrocytes, myelinating oligodendrocytes, microglia, endothelial cells, and pericytes from mouse cerebral cortex. We generated a transcriptome database for these eight cell types by RNA sequencing and used a sensitive algorithm to detect alternative splicing events in each cell type. Bioinformatic analyses identified thousands of new cell type-enriched genes and splicing isoforms that will provide novel markers for cell identification, tools for genetic manipulation, and insights into the biology of the brain. For example, our data provide clues as to how neurons and astrocytes differ in their ability to dynamically regulate glycolytic flux and lactate generation attributable to unique splicing of PKM2, the gene encoding the glycolytic enzyme pyruvate kinase. This dataset will provide a powerful new resource for understanding the development and function of the brain. To ensure the widespread distribution of these datasets, we have created a user-friendly website (http://web.stanford.edu/group/barres_lab/brain_rnaseq.html) that provides a platform for analyzing and comparing transciption and alternative splicing profiles for various cell classes in the brain.
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93
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Yang P, Yin K, Zhong D, Liao Q, Li K. Inhibition of osteosarcoma cell progression by MacroH2A via the downregulation of cyclin D and cyclin‑dependent kinase genes. Mol Med Rep 2014; 11:1905-10. [PMID: 25378143 DOI: 10.3892/mmr.2014.2903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Accepted: 10/20/2014] [Indexed: 11/06/2022] Open
Abstract
MacroH2A is a histone modification factor the activity of which has been acutely studied in cancer progression, and a number of studies have shown that the progression of certain types of cancer is under regulation by MacroH2A. However, information regarding the underlying molecular mechanisms of MacroH2A inhibition on the cell cycle remains elusive, and elucidating this process may aid in the production of novel treatment strategies. The aim of the current study was to investigate the inhibitory effects of MacroH2A on osteosarcoma cell progression, and the possible molecular mechanisms of this process. MacroH2A overexpression and interference vectors were designed and transfected into U2‑OS osteosarcoma cells. The cells underwent reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR), western blot analysis and immunofluorescence assays. The apoptosis rate and cell cycle stage were assayed using flow cytometry. The results revealed that the overexpression of MacroH2A inhibited the progression of U2‑OS osteosarcoma cells, and the cells were arrested at the G2/M stage of the cell cycle. The molecular mechanism by which MacroH2A suppresses the cell progression involves the inhibition of the expression of cyclin D and cyclin‑dependent kinase (CDK) genes, including cyclin D1, cyclin D2, CDK4, CDK6 and CDK8. Taken together, the present results revealed that MacroH2A is an important modifier of chromatin that downregulates the progression of osteosarcoma cells and triggers disturbance of the cell cycle via the downregulation of cyclin D and CDK genes.
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Affiliation(s)
- Pu Yang
- Department of Orthopedic Surgery, The Xiangya Hospital of Central South University, Changsha, Hunan 410008, P.R. China
| | - Ke Yin
- Department of Orthopedic Surgery, The Xiangya Hospital of Central South University, Changsha, Hunan 410008, P.R. China
| | - Da Zhong
- Department of Orthopedic Surgery, The Xiangya Hospital of Central South University, Changsha, Hunan 410008, P.R. China
| | - Qiande Liao
- Department of Orthopedic Surgery, The Xiangya Hospital of Central South University, Changsha, Hunan 410008, P.R. China
| | - Kanghua Li
- Department of Orthopedic Surgery, The Xiangya Hospital of Central South University, Changsha, Hunan 410008, P.R. China
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94
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Chen H, Ruiz PD, Novikov L, Casill AD, Park JW, Gamble MJ. MacroH2A1.1 and PARP-1 cooperate to regulate transcription by promoting CBP-mediated H2B acetylation. Nat Struct Mol Biol 2014; 21:981-9. [PMID: 25306110 PMCID: PMC4221384 DOI: 10.1038/nsmb.2903] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 09/16/2014] [Indexed: 12/29/2022]
Abstract
The histone variant macroH2A1 regulates gene expression important for differentiation, stem cell reprogramming and tumor suppression. Here, we demonstrate that in primary human cells, macroH2A1 participates in two physically and functionally distinct types of chromatin either marked by H3K27me3 or nine histone acetylations. Using RNA-seq, we found that macroH2A1-regulated genes, which have roles in cancer progression, are specifically found in macroH2A1-containing acetylated chromatin. Of the two macroH2A1 variants, macroH2A1.1 and macroH2A1.2, the former is suppressed in cancer and can interact with PARP-generated poly(ADP-ribose). Through the recruitment of PARP-1, macroH2A1.1 promotes the CBP-mediated acetylation of H2B K12 and K120 which either positively or negatively regulates the expression of macroH2A1-target genes. While macroH2A1-regulated H2B acetylation is a common feature of primary cells, this regulation is typically lost in cancer cells. Consequently, our results provide important insight into macroH2A1.1’s role in cancer suppression.
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Affiliation(s)
- Hongshan Chen
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, USA
| | - Penelope D Ruiz
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, USA
| | - Leonid Novikov
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, USA
| | - Alyssa D Casill
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, USA
| | - Jong Woo Park
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, USA
| | - Matthew J Gamble
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York, USA
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95
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Pazienza V, Borghesan M, Mazza T, Sheedfar F, Panebianco C, Williams R, Mazzoccoli G, Andriulli A, Nakanishi T, Vinciguerra M. SIRT1-metabolite binding histone macroH2A1.1 protects hepatocytes against lipid accumulation. Aging (Albany NY) 2014; 6:35-47. [PMID: 24473773 PMCID: PMC3927808 DOI: 10.18632/aging.100632] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Non-alcoholic-fatty-liver-disease (NAFLD) encompasses conditions associated to fat deposition in the liver, which are generally deteriorated during the aging process. MacroH2A1, a variant of histone H2A, is a key transcriptional regulator involved in tumorigenic processes and cell senescence, and featuring two alternatively splicing isoforms, macroH2A1.1 and macroH2A1.2. MacroH2A1.1 binds with high affinity O-acetyl ADP ribose, a small metabolite produced by the reaction catalysed by NAD+-dependent deacetylase SIRT1, whereas macroH2A1.2 is unable to do so. The functional significance of this binding is unknown. We previously reported that the hepatic levels of macroH2A1.1 and macroH2A1.2 are differentially expressed in mice models of NAFLD. Here we show that over-expression of macroH2A1.1, but not of macroH2A1.2, is able to protect hepatocytes against lipid accumulation. MacroH2A1.1 over-expressing cells display ameliorated glucose metabolism, reduced expression of lipidogenic genes and fatty acids content. SIRT1/macroH2A1.1-dependent epigenetic regulation of lipid metabolism may be relevant to NAFLD development.
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Affiliation(s)
- Valerio Pazienza
- Department of Medical Sciences, Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
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96
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Lei S, Long J, Li J. MacroH2A suppresses the proliferation of the B16 melanoma cell line. Mol Med Rep 2014; 10:1845-50. [PMID: 25119498 DOI: 10.3892/mmr.2014.2482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 03/27/2014] [Indexed: 11/05/2022] Open
Abstract
MacroH2A is the most frequently altered histone, which participates in cancer progression. Increasing evidence demonstrates that cancer progression could be regulated by macroH2A by affecting the cell cycle. In the present study, it was demonstrated that macroH2A suppresses melanoma cell progression and the molecular mechanisms underlying this process were examined. The interference and overexpression vectors of macroH2A were constructed and then transferred into B16 melanoma cells and, following transfection, were analyzed by quantitative polymerase chain reaction (PCR), western blot analysis and immunofluorescence assays. Apoptosis and the cell cycle stage among all the treatment groups were detected. Then, cyclin D1, cyclin D3, cyclin-dependent protein kinase (CDK) 4, CDK6 and CDK8 expression was detected in order to elucidate the effects of macroH2A on cell cycle-related genes. The results demonstrated that the overexpression of macroH2A suppressed melanoma cell progression and arrested the cells in the G2/M stage. Furthermore, macroH2A inhibits cyclin D1, cyclin D2, CDK6 and CDK8 expression in B16 melanoma cells. In conclusion, the results demonstrated that macroH2A, a critical component of chromatin, suppresses the development of melanoma (which results from a disordered cell cycle) through regulating cyclin D1, cyclin D3 and CDK6 genes.
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Affiliation(s)
- Shaorong Lei
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Jianhong Long
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Jiaguang Li
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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97
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Daubner GM, Brümmer A, Tocchini C, Gerhardy S, Ciosk R, Zavolan M, Allain FHT. Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1. Nucleic Acids Res 2014; 42:8092-105. [PMID: 24838563 PMCID: PMC4081071 DOI: 10.1093/nar/gku445] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 05/04/2014] [Accepted: 05/06/2014] [Indexed: 01/13/2023] Open
Abstract
The STAR family comprises ribonucleic acid (RNA)-binding proteins that play key roles in RNA-regulatory processes. RNA recognition is achieved by a KH domain with an additional α-helix (QUA2) that seems to extend the RNA-binding surface to six nucleotides for SF1 (Homo sapiens) and seven nucleotides for GLD-1 (Caenorhabditis elegans). To understand the structural basis of this probable difference in specificity, we determined the solution structure of GLD-1 KH-QUA2 with the complete consensus sequence identified in the tra-2 gene. Compared to SF1, the GLD-1 KH-QUA2 interface adopts a different conformation resulting indeed in an additional sequence-specific binding pocket for a uracil at the 5'end. The functional relevance of this binding pocket is emphasized by our bioinformatics analysis showing that GLD-1 binding sites with this 5'end uracil are more predictive for the functional response of the messenger RNAs to gld-1 knockout. We further reveal the importance of the KH-QUA2 interface in vitro and that its alteration in vivo affects the level of translational repression dependent on the sequence of the GLD-1 binding motif. In conclusion, we demonstrate that the QUA2 domain distinguishes GLD-1 from other members of the STAR family and contributes more generally to the modulation of RNA-binding affinity and specificity of KH domain containing proteins.
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Affiliation(s)
- Gerrit M Daubner
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Anneke Brümmer
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Cristina Tocchini
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland
| | - Stefan Gerhardy
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Rafal Ciosk
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland
| | | | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
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98
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Marsh DJ, Shah JS, Cole AJ. Histones and their modifications in ovarian cancer - drivers of disease and therapeutic targets. Front Oncol 2014; 4:144. [PMID: 24971229 PMCID: PMC4053763 DOI: 10.3389/fonc.2014.00144] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 05/27/2014] [Indexed: 01/08/2023] Open
Abstract
Epithelial ovarian cancer has the highest mortality of the gynecological malignancies. High grade serous epithelial ovarian cancer (SEOC) is the most common subtype, with the majority of women presenting with advanced disease where 5-year survival is around 25%. Platinum-based chemotherapy in combination with paclitaxel remains the most effective treatment despite platinum therapies being introduced almost 40 years ago. Advances in molecular medicine are underpinning new strategies for the treatment of cancer. Major advances have been made by international initiatives to sequence cancer genomes. For SEOC, with the exception of TP53 that is mutated in virtually 100% of these tumors, there is no other gene mutated at high frequency. There is extensive copy number variation, as well as changes in methylation patterns that will influence gene expression. To date, the role of histones and their post-translational modifications in ovarian cancer is a relatively understudied field. Post-translational histone modifications play major roles in gene expression as they direct the configuration of chromatin and so access by transcription factors. Histone modifications include methylation, acetylation, and monoubiquitination, with involvement of enzymes including histone methyltransferases, histone acetyltransferases/deacetylases, and ubiquitin ligases/deubiquitinases, respectively. Complexes such as the Polycomb repressive complex also play roles in the control of histone modifications and more recently roles for long non-coding RNA and microRNAs are emerging. Epigenomic-based therapies targeting histone modifications are being developed and offer new approaches for the treatment of ovarian cancer. Here, we discuss histone modifications and their aberrant regulation in malignancy and specifically in ovarian cancer. We review current and upcoming histone-based therapies that have the potential to inform and improve treatment strategies for women with ovarian cancer.
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Affiliation(s)
- Deborah J Marsh
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hospital, The University of Sydney , Sydney, NSW , Australia
| | - Jaynish S Shah
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hospital, The University of Sydney , Sydney, NSW , Australia
| | - Alexander J Cole
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hospital, The University of Sydney , Sydney, NSW , Australia
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99
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Lavigne AC, Castells M, Mermet J, Kocanova S, Dalvai M, Bystricky K. Increased macroH2A1.1 expression correlates with poor survival of triple-negative breast cancer patients. PLoS One 2014; 9:e98930. [PMID: 24911873 PMCID: PMC4049614 DOI: 10.1371/journal.pone.0098930] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 05/08/2014] [Indexed: 01/06/2023] Open
Abstract
PURPOSE Epithelial-Mesenchymal Transition (EMT) features appear to be key events in development and progression of breast cancer. Epigenetic modifications contribute to the establishment and maintenance of cancer subclasses, as well as to the EMT process. Whether histone variants contribute to these transformations is not known. We investigated the relative expression levels of histone macroH2A1 splice variants and correlated it with breast cancer status/prognosis/types. METHODS To detect differential expression of macroH2A1 variant mRNAs in breast cancer cells and tumor samples, we used the following databases: GEO, EMBL-EBI and publisher databases (may-august 2012). We extracted macroH2A1.1/macroH2A1 mRNA ratios and performed correlation studies on intrinsic molecular subclasses of breast cancer and on molecular characteristics of EMT. Associations between molecular and survival data were determined. RESULTS We found increased macroH2A1.1/macroH2A1 mRNA ratios to be associated with the claudin-low intrinsic subtype in breast cancer cell lines. At the molecular level this association translates into a positive correlation between macroH2A1 ratios and molecular characteristics of the EMT process. Moreover, untreated Triple Negative Breast Cancers presenting a high macroH2A1.1 mRNA ratio exhibit a poor outcome. CONCLUSION These results provide first evidence that macroH2A1.1 could be exploited as an actor in the maintenance of a transient cellular state in EMT progress towards metastatic development of breast tumors.
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Affiliation(s)
- Anne-Claire Lavigne
- Université de Toulouse; Laboratoire de Biologie Moléculaire Eucaryote (LBME); F-31062 Toulouse, France
- CNRS; LBME; F-31062 Toulouse, France
- * E-mail:
| | - Magali Castells
- Université de Toulouse; Laboratoire de Biologie Moléculaire Eucaryote (LBME); F-31062 Toulouse, France
- CNRS; LBME; F-31062 Toulouse, France
| | - Jérôme Mermet
- Université de Toulouse; Laboratoire de Biologie Moléculaire Eucaryote (LBME); F-31062 Toulouse, France
- CNRS; LBME; F-31062 Toulouse, France
| | - Silvia Kocanova
- Université de Toulouse; Laboratoire de Biologie Moléculaire Eucaryote (LBME); F-31062 Toulouse, France
- CNRS; LBME; F-31062 Toulouse, France
| | - Mathieu Dalvai
- Université de Toulouse; Laboratoire de Biologie Moléculaire Eucaryote (LBME); F-31062 Toulouse, France
- CNRS; LBME; F-31062 Toulouse, France
| | - Kerstin Bystricky
- Université de Toulouse; Laboratoire de Biologie Moléculaire Eucaryote (LBME); F-31062 Toulouse, France
- CNRS; LBME; F-31062 Toulouse, France
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100
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French CA, Rahman S, Walsh EM, Kühnle S, Grayson AR, Lemieux ME, Grunfeld N, Rubin BP, Antonescu CR, Zhang S, Venkatramani R, Dal Cin P, Howley PM. NSD3-NUT fusion oncoprotein in NUT midline carcinoma: implications for a novel oncogenic mechanism. Cancer Discov 2014; 4:928-41. [PMID: 24875858 DOI: 10.1158/2159-8290.cd-14-0014] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED NUT midline carcinoma (NMC) is an aggressive subtype of squamous cell carcinoma that typically harbors BRD4/3-NUT fusion oncoproteins that block differentiation and maintain tumor growth. In 20% of cases, NUT is fused to uncharacterized non-BRD gene(s). We established a new patient-derived NMC cell line (1221) and demonstrated that it harbors a novel NSD3-NUT fusion oncogene. We find that NSD3-NUT is both necessary and sufficient for the blockade of differentiation and maintenance of proliferation in NMC cells. NSD3-NUT binds to BRD4, and BRD bromodomain inhibitors induce differentiation and arrest proliferation of 1221 cells. We find further that NSD3 is required for the blockade of differentiation in BRD4-NUT-expressing NMCs. These findings identify NSD3 as a novel critical oncogenic component and potential therapeutic target in NMC. SIGNIFICANCE The existence of a family of fusion oncogenes in squamous cell carcinoma is unprecedented, and should lead to key insights into aberrant differentiation in NMC and possibly other squamous cell carcinomas. The involvement of the NSD3 methyltransferase as a component of the NUT fusion protein oncogenic complex identifies a new potential therapeutic target.
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Affiliation(s)
| | - Shaila Rahman
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Erica M Walsh
- Department of Pathology, Brigham and Women's Hospital
| | - Simone Kühnle
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | | | | | - Noam Grunfeld
- Department of Pathology, Brigham and Women's Hospital
| | - Brian P Rubin
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Department of Molecular Genetics, Cleveland Clinic, and Lerner Research Institute, Cleveland, Ohio
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Songlin Zhang
- Department of Pathology & Laboratory Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Rajkumar Venkatramani
- Center for Cancer and Blood Diseases, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California; and
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital
| | - Peter M Howley
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
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