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Zhang Y, Chen K, Tang SC, Cai Y, Nambu A, See YX, Fu C, Raju A, Lebeau B, Ling Z, Chan JJ, Tay Y, Mutwil M, Lakshmanan M, Tucker-Kellogg G, Chng WJ, Tenen DG, Osato M, Tergaonkar V, Fullwood MJ. Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth. Nat Struct Mol Biol 2024:10.1038/s41594-024-01391-7. [PMID: 39304765 DOI: 10.1038/s41594-024-01391-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 06/28/2024] [Indexed: 09/22/2024]
Abstract
Human silencers have been shown to regulate developmental gene expression. However, the functional importance of human silencers needs to be elucidated, such as whether they can form 'super-silencers' and whether they are linked to cancer progression. Here, we show two silencer components of the FGF18 gene can cooperate through compensatory chromatin interactions to form a super-silencer. Double knockout of two silencers exhibited synergistic upregulation of FGF18 expression and changes in cell identity. To perturb the super-silencers, we applied combinational treatment of an enhancer of zeste homolog 2 inhibitor GSK343, and a repressor element 1-silencing transcription factor inhibitor, X5050 ('GR'). Interestingly, GR led to severe loss of topologically associated domains and loops, which were associated with reduced CTCF and TOP2A mRNA levels. Moreover, GR synergistically upregulated super-silencer-controlled genes related to cell cycle, apoptosis and DNA damage, leading to anticancer effects in vivo. Overall, our data demonstrated a super-silencer example and showed that GR can disrupt super-silencers, potentially leading to cancer ablation.
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Affiliation(s)
- Ying Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Kaijing Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Seng Chuan Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yichao Cai
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Akiko Nambu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yi Xiang See
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chaoyu Fu
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Anandhkumar Raju
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Benjamin Lebeau
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zixun Ling
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jia Jia Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Manikandan Lakshmanan
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Greg Tucker-Kellogg
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Computational Biology Programme, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research (N2CR), Centre for Translational Medicine, Singapore, Singapore
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Health System (NUHS), Singapore, Singapore
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Harvard Stem Cells Institute, Harvard Medical School, Boston, MA, USA
| | - Motomi Osato
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vinay Tergaonkar
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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2
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Rahman F, Augoustides V, Tyler E, Daugird TA, Arthur C, Legant WR. Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.27.605159. [PMID: 39211261 PMCID: PMC11360932 DOI: 10.1101/2024.07.27.605159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The nucleus coordinates many different processes. Visualizing how these are spatially organized requires imaging protein complexes, epigenetic marks, and DNA across scales from single molecules to the whole nucleus. To accomplish this, we developed a multiplexed imaging protocol to localize 13 different nuclear targets with nanometer precision in single cells. We show that nuclear specification into active and repressive states exists along a spectrum of length scales, emerging below one micron and becoming strengthened at the nanoscale with unique organizational principles in both heterochromatin and euchromatin. HP1-α was positively correlated with DNA at the microscale but uncorrelated at the nanoscale. RNA Polymerase II, p300, and CDK9 were positively correlated at the microscale but became partitioned below 300 nm. Perturbing histone acetylation or transcription disrupted nanoscale organization but had less effect at the microscale. We envision that our imaging and analysis pipeline will be useful to reveal the organizational principles not only of the cell nucleus but also other cellular compartments.
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3
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Pedersen SS, Ingerslev LR, Olsen M, Prause M, Billestrup N. Butyrate functions as a histone deacetylase inhibitor to protect pancreatic beta cells from IL-1β-induced dysfunction. FEBS J 2024; 291:566-583. [PMID: 37985375 DOI: 10.1111/febs.17005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/06/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
Butyrate, a gut microbial metabolite, has beneficial effects on glucose homeostasis and has become an attractive drug candidate for type 2 diabetes (T2D). Recently, we showed that butyrate protects pancreatic beta cells against cytokine-induced dysfunction. In this study, we explored the underlying mechanisms of butyrate action. Pancreatic mouse islets were exposed to a non-cytotoxic concentration of interleukin-1β (IL-1β) for 10 days to mimic low-grade inflammation in T2D. Similar to the effect of butyrate, an isoform-selective histone deacetylase 3 (HDAC3) inhibitor normalized IL-1β-reduced glucose-stimulated insulin secretion and insulin content. In contrast, free fatty acid receptor 2 and 3 (FFAR2/3) agonists failed to normalize IL-1β-induced beta cell dysfunction. Furthermore, butyrate inhibited HDAC activity and increased the acetylation of histone H3 and H4 by 3- and 10-fold, respectively. Genome-wide analysis of histone H3 lysine 27 acetylation (H3K27ac) revealed that butyrate mainly increased H3K27ac at promoter regions (74%), while H3K27ac peaks regulated by IL-1β were more equally distributed at promoters (38%), introns (23%) and intergenic regions (23%). Gene ontology analysis showed that butyrate increased IL-1β-reduced H3K27ac levels near several genes related to hormone secretion and reduced IL-1β-increased H3K27ac levels near genes associated with inflammatory responses. Butyrate alone increased H3K27ac near many genes related to MAPK signaling, hormone secretion, and differentiation, and decreased H3K27ac at genes involved in cell replication. Together, these results suggest that butyrate prevents IL-1β-induced pancreatic islet dysfunction by inhibition of HDACs resulting in changes in H3K27ac levels at genes relevant for beta cell function and inflammatory responses.
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Affiliation(s)
- Signe Schultz Pedersen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Lars Roed Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Mathias Olsen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Michala Prause
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Nils Billestrup
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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4
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Al-Hasani K, Marikar SN, Kaipananickal H, Maxwell S, Okabe J, Khurana I, Karagiannis T, Liang JJ, Mariana L, Loudovaris T, Kay T, El-Osta A. EZH2 inhibitors promote β-like cell regeneration in young and adult type 1 diabetes donors. Signal Transduct Target Ther 2024; 9:2. [PMID: 38161208 PMCID: PMC10757994 DOI: 10.1038/s41392-023-01707-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 10/16/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024] Open
Abstract
β-cells are a type of endocrine cell found in pancreatic islets that synthesize, store and release insulin. In type 1 diabetes (T1D), T-cells of the immune system selectively destroy the insulin-producing β-cells. Destruction of these cells leads to a lifelong dependence on exogenous insulin administration for survival. Consequently, there is an urgent need to identify novel therapies that stimulate β-cell growth and induce β-cell function. We and others have shown that pancreatic ductal progenitor cells are a promising source for regenerating β-cells for T1D owing to their inherent differentiation capacity. Default transcriptional suppression is refractory to exocrine reaction and tightly controls the regenerative potential by the EZH2 methyltransferase. In the present study, we show that transient stimulation of exocrine cells, derived from juvenile and adult T1D donors to the FDA-approved EZH2 inhibitors GSK126 and Tazemetostat (Taz) influence a phenotypic shift towards a β-like cell identity. The transition from repressed to permissive chromatin states are dependent on bivalent H3K27me3 and H3K4me3 chromatin modification. Targeting EZH2 is fundamental to β-cell regenerative potential. Reprogrammed pancreatic ductal cells exhibit insulin production and secretion in response to a physiological glucose challenge ex vivo. These pre-clinical studies underscore the potential of small molecule inhibitors as novel modulators of ductal progenitor differentiation and a promising new approach for the restoration of β-like cell function.
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Affiliation(s)
- Keith Al-Hasani
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, 3004, VIC, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
| | - Safiya Naina Marikar
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, 3004, VIC, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
| | - Harikrishnan Kaipananickal
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, 3004, VIC, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
| | - Scott Maxwell
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, 3004, VIC, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
| | - Jun Okabe
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, 3004, VIC, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
| | - Ishant Khurana
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, 3004, VIC, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
| | - Thomas Karagiannis
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, 3004, VIC, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia
| | - Julia J Liang
- School of Science, STEM College, RMIT University, Melbourne, 3001, VIC, Australia
| | - Lina Mariana
- Immunology and Diabetes Unit, St Vincent's Institute of Medical Research, Fitzroy, 3065, VIC, Australia
| | - Thomas Loudovaris
- Immunology and Diabetes Unit, St Vincent's Institute of Medical Research, Fitzroy, 3065, VIC, Australia
| | - Thomas Kay
- Immunology and Diabetes Unit, St Vincent's Institute of Medical Research, Fitzroy, 3065, VIC, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, 3004, VIC, Australia.
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia.
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, 3004, VIC, Australia.
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR.
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, 3/F Lui Che Woo Clinical Sciences Building, 30-32- Ngan Shing Street, Sha Tin, Hong Kong SAR.
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR.
- Biomedical Laboratory Science, Department of Technology, Faculty of Health, University College Copenhagen, Copenhagen, Denmark.
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5
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Teichmann E, Blessing E, Hinz B. Non-Psychoactive Phytocannabinoids Inhibit Inflammation-Related Changes of Human Coronary Artery Smooth Muscle and Endothelial Cells. Cells 2023; 12:2389. [PMID: 37830604 PMCID: PMC10571842 DOI: 10.3390/cells12192389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023] Open
Abstract
Atherosclerosis is associated with vascular smooth muscle cell proliferation, chronic vascular inflammation, and leukocyte adhesion. In view of the cardioprotective effects of cannabinoids described in recent years, the present study investigated the impact of the non-psychoactive phytocannabinoids cannabidiol (CBD) and tetrahydrocannabivarin (THCV) on proliferation and migration of human coronary artery smooth muscle cells (HCASMC) and on inflammatory markers in human coronary artery endothelial cells (HCAEC). In HCASMC, CBD and THCV at nontoxic concentrations exhibited inhibitory effects on platelet-derived growth factor-triggered proliferation (CBD) and migration (CBD, THCV). When interleukin (IL)-1β- and lipopolysaccharide (LPS)-stimulated HCAEC were examined, both cannabinoids showed a concentration-dependent decrease in the expression of vascular cell adhesion molecule-1 (VCAM-1), which was mediated independently of classical cannabinoid receptors and was not accompanied by a comparable inhibition of intercellular adhesion molecule-1. Further inhibitor experiments demonstrated that reactive oxygen species, p38 mitogen-activated protein kinase activation, histone deacetylase, and nuclear factor κB (NF-κB) underlie IL-1β- and LPS-induced expression of VCAM-1. In this context, CBD and THCV were shown to inhibit phosphorylation of NF-κB regulators in LPS- but not IL-1β-stimulated HCAEC. Stimulation of HCAEC with IL-1β and LPS was associated with increased adhesion of monocytes, which, however, could not be significantly abolished by CBD and THCV. In summary, the results highlight the potential of the non-psychoactive cannabinoids CBD and THCV to regulate inflammation-related changes in HCASMC and HCAEC. Considering their effect on both cell types studied, further preclinical studies could address the use of CBD and THCV in drug-eluting stents for coronary interventions.
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Affiliation(s)
| | | | - Burkhard Hinz
- Institute of Pharmacology and Toxicology, Rostock University Medical Center, Schillingallee 70, 18057 Rostock, Germany; (E.T.); (E.B.)
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6
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Oger F, Moreno M, Derhourhi M, Thiroux B, Berberian L, Bourouh C, Durand E, Amanzougarene S, Badreddine A, Blanc E, Molendi-Coste O, Pineau L, Pasquetti G, Rolland L, Carney C, Bornaque F, Courty E, Gheeraert C, Eeckhoute J, Dombrowicz D, Kerr-Conte J, Pattou F, Staels B, Froguel P, Bonnefond A, Annicotte JS. Pharmacological HDAC inhibition impairs pancreatic β-cell function through an epigenome-wide reprogramming. iScience 2023; 26:107231. [PMID: 37496675 PMCID: PMC10366467 DOI: 10.1016/j.isci.2023.107231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/05/2023] [Accepted: 06/23/2023] [Indexed: 07/28/2023] Open
Abstract
Histone deacetylases enzymes (HDACs) are chromatin modifiers that regulate gene expression through deacetylation of lysine residues within specific histone and non-histone proteins. A cell-specific gene expression pattern defines the identity of insulin-producing pancreatic β cells, yet molecular networks driving this transcriptional specificity are not fully understood. Here, we investigated the HDAC-dependent molecular mechanisms controlling pancreatic β-cell identity and function using the pan-HDAC inhibitor trichostatin A through chromatin immunoprecipitation assays and RNA sequencing experiments. We observed that TSA alters insulin secretion associated with β-cell specific transcriptome programming in both mouse and human β-cell lines, as well as on human pancreatic islets. We also demonstrated that this alternative β-cell transcriptional program in response to HDAC inhibition is related to an epigenome-wide remodeling at both promoters and enhancers. Our data indicate that HDAC activity could be required to protect against loss of β-cell identity with unsuitable expression of genes associated with alternative cell fates.
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Affiliation(s)
- Frédérik Oger
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, F-59000 Lille, France
| | - Maeva Moreno
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, F-59000 Lille, France
| | - Mehdi Derhourhi
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, F-59000 Lille, France
| | - Bryan Thiroux
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, F-59000 Lille, France
| | - Lionel Berberian
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, F-59000 Lille, France
| | - Cyril Bourouh
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, F-59000 Lille, France
| | - Emmanuelle Durand
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, F-59000 Lille, France
| | - Souhila Amanzougarene
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, F-59000 Lille, France
| | - Alaa Badreddine
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, F-59000 Lille, France
| | - Etienne Blanc
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, F-59000 Lille, France
| | - Olivier Molendi-Coste
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011 - EGID, F-59000 Lille, France
| | - Laurent Pineau
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011 - EGID, F-59000 Lille, France
| | - Gianni Pasquetti
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1190 - EGID, F-59000 Lille, France
| | - Laure Rolland
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 – RID-AGE-Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000 Lille, France
| | - Charlène Carney
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, F-59000 Lille, France
| | - Florine Bornaque
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 – RID-AGE-Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000 Lille, France
| | - Emilie Courty
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 – RID-AGE-Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000 Lille, France
| | - Céline Gheeraert
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011 - EGID, F-59000 Lille, France
| | - Jérôme Eeckhoute
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011 - EGID, F-59000 Lille, France
| | - David Dombrowicz
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011 - EGID, F-59000 Lille, France
| | - Julie Kerr-Conte
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1190 - EGID, F-59000 Lille, France
| | - François Pattou
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1190 - EGID, F-59000 Lille, France
| | - Bart Staels
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011 - EGID, F-59000 Lille, France
| | - Philippe Froguel
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, F-59000 Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Amélie Bonnefond
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, CNRS, U1283 - UMR 8199 - EGID, F-59000 Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jean-Sébastien Annicotte
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 – RID-AGE-Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000 Lille, France
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7
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Khurana I, Kaipananickal H, Maxwell S, Birkelund S, Syreeni A, Forsblom C, Okabe J, Ziemann M, Kaspi A, Rafehi H, Jørgensen A, Al-Hasani K, Thomas MC, Jiang G, Luk AO, Lee HM, Huang Y, Thewjitcharoen Y, Nakasatien S, Himathongkam T, Fogarty C, Njeim R, Eid A, Hansen TW, Tofte N, Ottesen EC, Ma RC, Chan JC, Cooper ME, Rossing P, Groop PH, El-Osta A. Reduced methylation correlates with diabetic nephropathy risk in type 1 diabetes. J Clin Invest 2023; 133:160959. [PMID: 36633903 PMCID: PMC9927943 DOI: 10.1172/jci160959] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
Diabetic nephropathy (DN) is a polygenic disorder with few risk variants showing robust replication in large-scale genome-wide association studies. To understand the role of DNA methylation, it is important to have the prevailing genomic view to distinguish key sequence elements that influence gene expression. This is particularly challenging for DN because genome-wide methylation patterns are poorly defined. While methylation is known to alter gene expression, the importance of this causal relationship is obscured by array-based technologies since coverage outside promoter regions is low. To overcome these challenges, we performed methylation sequencing using leukocytes derived from participants of the Finnish Diabetic Nephropathy (FinnDiane) type 1 diabetes (T1D) study (n = 39) that was subsequently replicated in a larger validation cohort (n = 296). Gene body-related regions made up more than 60% of the methylation differences and emphasized the importance of methylation sequencing. We observed differentially methylated genes associated with DN in 3 independent T1D registries originating from Denmark (n = 445), Hong Kong (n = 107), and Thailand (n = 130). Reduced DNA methylation at CTCF and Pol2B sites was tightly connected with DN pathways that include insulin signaling, lipid metabolism, and fibrosis. To define the pathophysiological significance of these population findings, methylation indices were assessed in human renal cells such as podocytes and proximal convoluted tubule cells. The expression of core genes was associated with reduced methylation, elevated CTCF and Pol2B binding, and the activation of insulin-signaling phosphoproteins in hyperglycemic cells. These experimental observations also closely parallel methylation-mediated regulation in human macrophages and vascular endothelial cells.
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Affiliation(s)
- Ishant Khurana
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Harikrishnan Kaipananickal
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Scott Maxwell
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Sørine Birkelund
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,University College Copenhagen, Faculty of Health, Department of Technology, Biomedical Laboratory Science, Copenhagen, Denmark
| | - Anna Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jun Okabe
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Mark Ziemann
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Haloom Rafehi
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Anne Jørgensen
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Steno Diabetes Center Copenhagen, Herlev, Denmark
| | - Keith Al-Hasani
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Merlin C. Thomas
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | | | - Andrea O.Y. Luk
- Department of Medicine and Therapeutics,,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Heung Man Lee
- Department of Medicine and Therapeutics,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Huang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | | | | | | | - Christopher Fogarty
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Rachel Njeim
- Department of Anatomy, Cell Biology and Physiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Assaad Eid
- Department of Anatomy, Cell Biology and Physiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | | | - Nete Tofte
- Steno Diabetes Center Copenhagen, Herlev, Denmark
| | | | - Ronald C.W. Ma
- Department of Medicine and Therapeutics,,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Juliana C.N. Chan
- Department of Medicine and Therapeutics,,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Mark E. Cooper
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, Herlev, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Per-Henrik Groop
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory and,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia.,University College Copenhagen, Faculty of Health, Department of Technology, Biomedical Laboratory Science, Copenhagen, Denmark.,Hong Kong Institute of Diabetes and Obesity,,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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8
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Genomic or Non-Genomic? A Question about the Pleiotropic Roles of Vitamin D in Inflammatory-Based Diseases. Nutrients 2023; 15:nu15030767. [PMID: 36771473 PMCID: PMC9920355 DOI: 10.3390/nu15030767] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
Vitamin D (vit D) is widely known for its role in calcium metabolism and its importance for the bone system. However, various studies have revealed a myriad of extra-skeletal functions, including cell differentiation and proliferation, antibacterial, antioxidant, immunomodulatory, and anti-inflammatory properties in various cells and tissues. Vit D mediates its function via regulation of gene expression by binding to its receptor (VDR) which is expressed in almost all cells within the body. This review summarizes the pleiotropic effects of vit D, emphasizing its anti-inflammatory effect on different organ systems. It also provides a comprehensive overview of the genetic and epigenetic effects of vit D and VDR on the expression of genes pertaining to immunity and anti-inflammation. We speculate that in the context of inflammation, vit D and its receptor VDR might fulfill their roles as gene regulators through not only direct gene regulation but also through epigenetic mechanisms.
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9
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Royce SG, Licciardi PV, Beh RC, Bourke JE, Donovan C, Hung A, Khurana I, Liang JJ, Maxwell S, Mazarakis N, Pitsillou E, Siow YY, Snibson KJ, Tobin MJ, Ververis K, Vongsvivut J, Ziemann M, Samuel CS, Tang MLK, El-Osta A, Karagiannis TC. Sulforaphane prevents and reverses allergic airways disease in mice via anti-inflammatory, antioxidant, and epigenetic mechanisms. Cell Mol Life Sci 2022; 79:579. [DOI: 10.1007/s00018-022-04609-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 11/30/2022]
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10
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Inhibition of pancreatic EZH2 restores progenitor insulin in T1D donor. Signal Transduct Target Ther 2022; 7:248. [PMID: 35864094 PMCID: PMC9304326 DOI: 10.1038/s41392-022-01034-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 01/02/2023] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease that selectively destroys insulin-producing β-cells in the pancreas. An unmet need in diabetes management, current therapy is focussed on transplantation. While the reprogramming of progenitor cells into functional insulin-producing β-cells has also been proposed this remains controversial and poorly understood. The challenge is determining why default transcriptional suppression is refractory to exocrine reactivation. After the death of a 13-year-old girl with established insulin-dependent T1D, pancreatic cells were harvested in an effort to restore and understand exocrine competence. The pancreas showed classic silencing of β-cell progenitor genes with barely detectable insulin (Ins) transcript. GSK126, a highly selective inhibitor of EZH2 methyltransferase activity influenced H3K27me3 chromatin content and transcriptional control resulting in the expression of core β-cell markers and ductal progenitor genes. GSK126 also reinstated Ins gene expression despite absolute β-cell destruction. These studies show the refractory nature of chromatin characterises exocrine suppression influencing β-cell plasticity. Additional regeneration studies are warranted to determine if the approach of this n-of-1 study generalises to a broader T1D population.
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11
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Miller AL, Fuller-Carter PI, Masarini K, Samardzija M, Carter KW, Rashwan R, Lim XR, Brunet AA, Chopra A, Ram R, Grimm C, Ueffing M, Carvalho LS, Trifunović D. Increased H3K27 trimethylation contributes to cone survival in a mouse model of cone dystrophy. Cell Mol Life Sci 2022; 79:409. [PMID: 35810394 PMCID: PMC9271452 DOI: 10.1007/s00018-022-04436-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 11/30/2022]
Abstract
Inherited retinal diseases (IRDs) are a heterogeneous group of blinding disorders, which result in dysfunction or death of the light-sensing cone and rod photoreceptors. Despite individual IRDs (Inherited retinal disease) being rare, collectively, they affect up to 1:2000 people worldwide, causing a significant socioeconomic burden, especially when cone-mediated central vision is affected. This study uses the Pde6ccpfl1 mouse model of achromatopsia, a cone-specific vision loss IRD (Inherited retinal disease), to investigate the potential gene-independent therapeutic benefits of a histone demethylase inhibitor GSK-J4 on cone cell survival. We investigated the effects of GSK-J4 treatment on cone cell survival in vivo and ex vivo and changes in cone-specific gene expression via single-cell RNA sequencing. A single intravitreal GSK-J4 injection led to transcriptional changes in pathways involved in mitochondrial dysfunction, endoplasmic reticulum stress, among other key epigenetic pathways, highlighting the complex interplay between methylation and acetylation in healthy and diseased cones. Furthermore, continuous administration of GSK-J4 in retinal explants increased cone survival. Our results suggest that IRD (Inherited retinal disease)-affected cones respond positively to epigenetic modulation of histones, indicating the potential of this approach in developing a broad class of novel therapies to slow cone degeneration.
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Affiliation(s)
- Annie L Miller
- Retinal Genomics and Therapy Group, Lions Eye Institute Ltd, 2 Verdun Street, Nedlands, WA, 6009, Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Paula I Fuller-Carter
- Retinal Genomics and Therapy Group, Lions Eye Institute Ltd, 2 Verdun Street, Nedlands, WA, 6009, Australia
| | - Klaudija Masarini
- Institute for Ophthalmic Research, Tübingen University, Elfriede-Aulhorn-Straße 7, 72076, Tübingen, Germany
| | - Marijana Samardzija
- Lab for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zürich, University of Zürich, Zurich, Switzerland
| | - Kim W Carter
- Analytical Computing Solutions, Willetton, WA, 6155, Australia
| | - Rabab Rashwan
- Retinal Genomics and Therapy Group, Lions Eye Institute Ltd, 2 Verdun Street, Nedlands, WA, 6009, Australia
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, Egypt
| | - Xin Ru Lim
- Retinal Genomics and Therapy Group, Lions Eye Institute Ltd, 2 Verdun Street, Nedlands, WA, 6009, Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Alicia A Brunet
- Retinal Genomics and Therapy Group, Lions Eye Institute Ltd, 2 Verdun Street, Nedlands, WA, 6009, Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, TN, USA
| | - Ramesh Ram
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Christian Grimm
- Lab for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zürich, University of Zürich, Zurich, Switzerland
| | - Marius Ueffing
- Institute for Ophthalmic Research, Tübingen University, Elfriede-Aulhorn-Straße 7, 72076, Tübingen, Germany
| | - Livia S Carvalho
- Retinal Genomics and Therapy Group, Lions Eye Institute Ltd, 2 Verdun Street, Nedlands, WA, 6009, Australia.
- Centre for Ophthalmology and Visual Science, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia.
| | - Dragana Trifunović
- Institute for Ophthalmic Research, Tübingen University, Elfriede-Aulhorn-Straße 7, 72076, Tübingen, Germany.
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12
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Keating ST, El-Osta A. Metaboloepigenetics in cancer, immunity and cardiovascular disease. Cardiovasc Res 2022; 119:357-370. [PMID: 35389425 PMCID: PMC10064843 DOI: 10.1093/cvr/cvac058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/12/2022] [Accepted: 02/02/2022] [Indexed: 11/14/2022] Open
Abstract
The influence of cellular metabolism on epigenetic pathways are well documented but misunderstood. Scientists have long known of the metabolic impact on epigenetic determinants. More often than not, that title role for DNA methylation was portrayed by the metabolite SAM or S-adenosylmethionine. Technically speaking there are many other metabolites that drive epigenetic processes that instruct seemingly distant - yet highly connect pathways - and none more so than our understanding of the cancer epigenome. Recent studies have shown that available energy link the extracellular environment to influence cellular responses. This focused review examines the recent interest in epigenomics and casts cancer, metabolism and immunity in unfamiliar roles - cooperating. There are not only language lessons from cancer research, we have come round to appreciate that reaching into areas previously thought of as too distinct are also object lessons in understanding health and disease. The Warburg effect is one such signature of how glycolysis influences metabolic shift during oncogenesis. That shift in metabolism - now recognised as central to proliferation in cancer biology - influence core enzymes that not only control gene expression but are also central to replication, condensation and the repair of nucleic acid. These nuclear processes rely on metabolism and with glucose at center stage the role of respiration and oxidative metabolism are now synonymous with the mitochondria as the powerhouses of metaboloepigenetics. The emerging evidence for metaboloepigenetics in trained innate immunity has revealed recognisable signalling pathways with antecedent extracellular stimulation. With due consideration to immunometabolism we discuss the striking signalling similarities influencing these core pathways. The immunometabolic-epigenetic axis in cardiovascular disease has deeply etched connections with inflammation and we examine the chromatin template as a carrier of epigenetic indices that determine the expression of genes influencing atherosclerosis and vascular complications of diabetes.
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Affiliation(s)
- Samuel T Keating
- Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Assam El-Osta
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia.,Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR.,Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, 3/F Lui Che Woo Clinical Sciences Building, 30-32 Ngan Shing Street, Sha Tin, Hong Kong SAR.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR.,University College Copenhagen, Faculty of Health, Department of Technology, Biomedical Laboratory Science, Copenhagen, Denmark
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13
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Wijesooriya K, Jadaan SA, Perera KL, Kaur T, Ziemann M. Urgent need for consistent standards in functional enrichment analysis. PLoS Comput Biol 2022; 18:e1009935. [PMID: 35263338 PMCID: PMC8936487 DOI: 10.1371/journal.pcbi.1009935] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/21/2022] [Accepted: 02/18/2022] [Indexed: 11/25/2022] Open
Abstract
Gene set enrichment tests (a.k.a. functional enrichment analysis) are among the most frequently used methods in computational biology. Despite this popularity, there are concerns that these methods are being applied incorrectly and the results of some peer-reviewed publications are unreliable. These problems include the use of inappropriate background gene lists, lack of false discovery rate correction and lack of methodological detail. To ascertain the frequency of these issues in the literature, we performed a screen of 186 open-access research articles describing functional enrichment results. We find that 95% of analyses using over-representation tests did not implement an appropriate background gene list or did not describe this in the methods. Failure to perform p-value correction for multiple tests was identified in 43% of analyses. Many studies lacked detail in the methods section about the tools and gene sets used. An extension of this survey showed that these problems are not associated with journal or article level bibliometrics. Using seven independent RNA-seq datasets, we show misuse of enrichment tools alters results substantially. In conclusion, most published functional enrichment studies suffered from one or more major flaws, highlighting the need for stronger standards for enrichment analysis. Functional enrichment analysis is a commonly used technique to identify trends in large scale biological datasets. In biomedicine, functional enrichment analysis of gene expression data is frequently applied to identify disease and drug mechanisms. While enrichment tests were once primarily conducted with complicated computer scripts, web-based tools are becoming more widely used. Users can paste a list of genes into a website and receive enrichment results in a matter of seconds. Despite the popularity of these tools, there are concerns that statistical problems and incomplete reporting are compromising research quality. In this article, we conducted a systematic examination of published enrichment analyses and assessed whether (i) any statistical flaws were present and (ii) sufficient methodological detail is provided such that the study could be replicated. We found that lack of methodological detail and errors in statistical analysis were widespread, which undermines the reliability and reproducibility of these research articles. A set of best practices is urgently needed to raise the quality of published work.
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Affiliation(s)
- Kaumadi Wijesooriya
- Deakin University, School of Life and Environmental Sciences, Geelong, Australia
| | - Sameer A. Jadaan
- College of Health and Medical Technology, Middle Technical University, Baghdad, Iraq
| | - Kaushalya L. Perera
- Deakin University, School of Life and Environmental Sciences, Geelong, Australia
| | - Tanuveer Kaur
- Deakin University, School of Life and Environmental Sciences, Geelong, Australia
| | - Mark Ziemann
- Deakin University, School of Life and Environmental Sciences, Geelong, Australia
- * E-mail:
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14
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Minisini M, Di Giorgio E, Kerschbamer E, Dalla E, Faggiani M, Franforte E, Meyer-Almes FJ, Ragno R, Antonini L, Mai A, Fiorentino F, Rotili D, Chinellato M, Perin S, Cendron L, Weichenberger CX, Angelini A, Brancolini C. Transcriptomic and genomic studies classify NKL54 as a histone deacetylase inhibitor with indirect influence on MEF2-dependent transcription. Nucleic Acids Res 2022; 50:2566-2586. [PMID: 35150567 PMCID: PMC8934631 DOI: 10.1093/nar/gkac081] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/25/2022] [Indexed: 12/23/2022] Open
Abstract
In leiomyosarcoma class IIa HDACs (histone deacetylases) bind MEF2 and convert these transcription factors into repressors to sustain proliferation. Disruption of this complex with small molecules should antagonize cancer growth. NKL54, a PAOA (pimeloylanilide o-aminoanilide) derivative, binds a hydrophobic groove of MEF2, which is used as a docking site by class IIa HDACs. However, NKL54 could also act as HDAC inhibitor (HDACI). Therefore, it is unclear which activity is predominant. Here, we show that NKL54 and similar derivatives are unable to release MEF2 from binding to class IIa HDACs. Comparative transcriptomic analysis classifies these molecules as HDACIs strongly related to SAHA/vorinostat. Low expressed genes are upregulated by HDACIs, while abundant genes are repressed. This transcriptional resetting correlates with a reorganization of H3K27 acetylation around the transcription start site (TSS). Among the upregulated genes there are several BH3-only family members, thus explaining the induction of apoptosis. Moreover, NKL54 triggers the upregulation of MEF2 and the downregulation of class IIa HDACs. NKL54 also increases the binding of MEF2D to promoters of genes that are upregulated after treatment. In summary, although NKL54 cannot outcompete MEF2 from binding to class IIa HDACs, it supports MEF2-dependent transcription through several actions, including potentiation of chromatin binding.
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Affiliation(s)
- Martina Minisini
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Eros Di Giorgio
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Emanuela Kerschbamer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck. Via Galvani 31, 39100 Bolzano, Italy
| | - Emiliano Dalla
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Massimo Faggiani
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Elisa Franforte
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Science, Haardtring 100, 64295 Darmstadt, Germany
| | - Rino Ragno
- Rome Center for Molecular Design, Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Lorenzo Antonini
- Rome Center for Molecular Design, Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Antonello Mai
- Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Francesco Fiorentino
- Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Dante Rotili
- Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Monica Chinellato
- Department of Biology, University of Padova, Via U. Bassi, 58/B, 35121 Padova, Italy
| | - Stefano Perin
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy.,European Centre for Living Technology (ECLT), Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Via U. Bassi, 58/B, 35121 Padova, Italy
| | - Christian X Weichenberger
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck. Via Galvani 31, 39100 Bolzano, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy.,European Centre for Living Technology (ECLT), Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy
| | - Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
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15
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Martín Giménez VM, Chuffa LGA, Simão VA, Reiter RJ, Manucha W. Protective actions of vitamin D, anandamide and melatonin during vascular inflammation: Epigenetic mechanisms involved. Life Sci 2022; 288:120191. [PMID: 34856208 DOI: 10.1016/j.lfs.2021.120191] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/13/2021] [Accepted: 11/26/2021] [Indexed: 12/11/2022]
Abstract
Vascular inflammation is one of the main activating stimuli of cardiovascular disease and its uncontrolled development may worsen the progression and prognosis of these pathologies. Therefore, the search for new therapeutic options to treat this condition is undoubtedly needed. In this regard, it may be better to repurpose endogenous anti-inflammatory compounds already known, in addition to synthesizing new compounds for therapeutic purposes. It is well known that vitamin D, anandamide, and melatonin are promising endogenous substances with powerful and wide-spread anti-inflammatory properties. Currently, the epigenetic mechanisms underlying these effects are often unknown. This review summarizes the potential epigenetic mechanisms by which vitamin D, anandamide, and melatonin attenuate vascular inflammation. This information could contribute to the improvement in the therapeutic management of multiple pathologies associated with blood vessel inflammation, through the pharmacological manipulation of new target sites that until now have not been addressed.
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Affiliation(s)
- Virna Margarita Martín Giménez
- Instituto de Investigaciones en Ciencias Químicas, Facultad de Ciencias Químicas y Tecnológicas, Universidad Católica de Cuyo, Sede San Juan, Argentina
| | - Luiz Gustavo A Chuffa
- Department of Structural and Functional Biology, UNESP-São Paulo State University, Institute of Biosciences, Botucatu 18618-689, São Paulo, Brazil
| | - Vinícius Augusto Simão
- Department of Structural and Functional Biology, UNESP-São Paulo State University, Institute of Biosciences, Botucatu 18618-689, São Paulo, Brazil
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, UT Health, San Antonio, TX, USA
| | - Walter Manucha
- Laboratorio de Farmacología Experimental Básica y Traslacional. Área de Farmacología, Departamento de Patología, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina; Instituto de Medicina y Biología Experimental de Cuyo, Consejo Nacional de Investigación Científica y Tecnológica (IMBECU-CONICET), Argentina.
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16
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El-Osta A. Editing the cardiac epigenome in broken heart syndrome. Eur Heart J 2021:ehab632. [PMID: 34491337 DOI: 10.1093/eurheartj/ehab632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Assam El-Osta
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
- Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, The Alfred Medical Research and Education Precinct, Monash University, Melbourne, VIC 3004, Australia
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, 3/F Lui Che Woo Clinical Sciences Building, 30-32 Ngan Shing Street, Sha Tin, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- University College Copenhagen, Faculty of Health, Department of Technology, Biomedical Laboratory Science, Copenhagen, Denmark
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17
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Sheffer M, Lowry E, Beelen N, Borah M, Amara SNA, Mader CC, Roth JA, Tsherniak A, Freeman SS, Dashevsky O, Gandolfi S, Bender S, Bryan JG, Zhu C, Wang L, Tariq I, Kamath GM, Simoes RDM, Dhimolea E, Yu C, Hu Y, Dufva O, Giannakis M, Syrgkanis V, Fraenkel E, Golub T, Romee R, Mustjoki S, Culhane AC, Wieten L, Mitsiades CS. Genome-scale screens identify factors regulating tumor cell responses to natural killer cells. Nat Genet 2021; 53:1196-1206. [PMID: 34253920 DOI: 10.1038/s41588-021-00889-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/18/2021] [Indexed: 12/26/2022]
Abstract
To systematically define molecular features in human tumor cells that determine their degree of sensitivity to human allogeneic natural killer (NK) cells, we quantified the NK cell responsiveness of hundreds of molecularly annotated 'DNA-barcoded' solid tumor cell lines in multiplexed format and applied genome-scale CRISPR-based gene-editing screens in several solid tumor cell lines, to functionally interrogate which genes in tumor cells regulate the response to NK cells. In these orthogonal studies, NK cell-sensitive tumor cells tend to exhibit 'mesenchymal-like' transcriptional programs; high transcriptional signature for chromatin remodeling complexes; high levels of B7-H6 (NCR3LG1); and low levels of HLA-E/antigen presentation genes. Importantly, transcriptional signatures of NK cell-sensitive tumor cells correlate with immune checkpoint inhibitor (ICI) resistance in clinical samples. This study provides a comprehensive map of mechanisms regulating tumor cell responses to NK cells, with implications for future biomarker-driven applications of NK cell immunotherapies.
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MESH Headings
- Allogeneic Cells/physiology
- Animals
- B7 Antigens/genetics
- Cell Line, Tumor
- Chromatin Assembly and Disassembly/physiology
- Cytotoxicity Tests, Immunologic/methods
- Cytotoxicity, Immunologic/genetics
- Cytotoxicity, Immunologic/physiology
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Genome, Human
- Histocompatibility Antigens Class I/genetics
- Histocompatibility Antigens Class I/immunology
- Humans
- Immune Checkpoint Inhibitors/pharmacology
- Killer Cells, Natural/physiology
- Mice, Inbred NOD
- Xenograft Model Antitumor Assays
- HLA-E Antigens
- Mice
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Affiliation(s)
- Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Ludwig Center, Harvard Medical School, Boston, MA, USA.
| | - Emily Lowry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicky Beelen
- Department of Transplantation Immunology, Maastricht University Medical Center+, Maastricht, the Netherlands
- School for Oncology and Developmental Biology, Maastricht University Medical Center+ GROW, Maastricht, the Netherlands
| | - Minasri Borah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Chris C Mader
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jennifer A Roth
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Aviad Tsherniak
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Samuel S Freeman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Sara Gandolfi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Samantha Bender
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jordan G Bryan
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Cong Zhu
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Li Wang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Ifrah Tariq
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Ricardo De Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Eugen Dhimolea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Channing Yu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Yiguo Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Sichuan University, Chengdu, China
| | - Olli Dufva
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | - Ernest Fraenkel
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Todd Golub
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Rizwan Romee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Aedin C Culhane
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Lotte Wieten
- Department of Transplantation Immunology, Maastricht University Medical Center+, Maastricht, the Netherlands
- School for Oncology and Developmental Biology, Maastricht University Medical Center+ GROW, Maastricht, the Netherlands
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Ludwig Center, Harvard Medical School, Boston, MA, USA.
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18
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Masi S, Ambrosini S, Mohammed SA, Sciarretta S, Lüscher TF, Paneni F, Costantino S. Epigenetic Remodeling in Obesity-Related Vascular Disease. Antioxid Redox Signal 2021; 34:1165-1199. [PMID: 32808539 DOI: 10.1089/ars.2020.8040] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Significance: The prevalence of obesity and cardiometabolic phenotypes is alarmingly increasing across the globe and is associated with atherosclerotic vascular complications and high mortality. In spite of multifactorial interventions, vascular residual risk remains high in this patient population, suggesting the need for breakthrough therapies. The mechanisms underpinning obesity-related vascular disease remain elusive and represent an intense area of investigation. Recent Advances: Epigenetic modifications-defined as environmentally induced chemical changes of DNA and histones that do not affect DNA sequence-are emerging as a potent modulator of gene transcription in the vasculature and might significantly contribute to the development of obesity-induced endothelial dysfunction. DNA methylation and histone post-translational modifications cooperate to build complex epigenetic signals, altering transcriptional networks that are implicated in redox homeostasis, mitochondrial function, vascular inflammation, and perivascular fat homeostasis in patients with cardiometabolic disturbances. Critical Issues: Deciphering the epigenetic landscape in the vasculature is extremely challenging due to the complexity of epigenetic signals and their function in regulating transcription. An overview of the most important epigenetic pathways is required to identify potential molecular targets to treat or prevent obesity-related endothelial dysfunction and atherosclerotic disease. This would enable the employment of precision medicine approaches in this setting. Future Directions: Current and future research efforts in this field entail a better definition of the vascular epigenome in obese patients as well as the unveiling of novel, cell-specific chromatin-modifying drugs that are able to erase specific epigenetic signals that are responsible for maladaptive transcriptional alterations and vascular dysfunction in obese patients. Antioxid. Redox Signal. 34, 1165-1199.
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Affiliation(s)
- Stefano Masi
- Dipartimento di Medicina Clinica e Sperimentale, Università di Pisa, Pisa, Italy
| | - Samuele Ambrosini
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
| | - Shafeeq A Mohammed
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
| | - Sebastiano Sciarretta
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy.,Department of AngioCardioNeurology, IRCCS Neuromed, Pozzilli, Italy
| | - Thomas F Lüscher
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland.,Heart Division, Royal Brompton and Harefield Hospital Trust, National Heart & Lung Institute, Imperial College, London, United Kingdom
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland.,Department of Cardiology, University Heart Center, University Hospital Zurich, Switzerland.,Department of Research and Education, University Hospital Zurich, Zurich, Switzerland
| | - Sarah Costantino
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
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19
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Khurana I, Maxwell S, Royce S, Mathiyalagan P, Karagiannis T, Mazarakis N, Vongsvivut J, K N H, Okabe J, Al-Hasani K, Samuel C, El-Osta A. SAHA attenuates Takotsubo-like myocardial injury by targeting an epigenetic Ac/Dc axis. Signal Transduct Target Ther 2021; 6:159. [PMID: 33875635 PMCID: PMC8055670 DOI: 10.1038/s41392-021-00546-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/10/2021] [Accepted: 02/25/2021] [Indexed: 12/27/2022] Open
Affiliation(s)
- Ishant Khurana
- Human Epigenetics Program, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Scott Maxwell
- Human Epigenetics Program, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Simon Royce
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute and Department of Pharmacology, Monash University, Clayton, VIC, Australia
| | - Prabhu Mathiyalagan
- Human Epigenetics Program, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Tom Karagiannis
- Human Epigenetics Program, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Nadia Mazarakis
- Human Epigenetics Program, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Jitraporn Vongsvivut
- Infrared Microspectroscopy Beamline, ANSTO - Australian Synchrotron, Clayton, VIC, Australia
| | - Harikrishnan K N
- Human Epigenetics Program, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Jun Okabe
- Human Epigenetics Program, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Keith Al-Hasani
- Human Epigenetics Program, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Chrishan Samuel
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute and Department of Pharmacology, Monash University, Clayton, VIC, Australia
| | - Assam El-Osta
- Human Epigenetics Program, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia. .,Department of Medicine and Therapeutics, The Chinese University of Hong Kong (CUHK), Hong Kong SAR; Hong Kong Institute of Diabetes and Obesity, CUHK, Hong Kong SAR; Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, CUHK, Shatin, Hong Kong, China. .,University College Copenhagen, Faculty of Health, Department of Technology, Biomedical Laboratory Science, Copenhagen, Denmark.
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20
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Lunke S, Maxwell S, Khurana I, K N H, Okabe J, Al-Hasani K, El-Osta A. Epigenetic evidence of an Ac/Dc axis by VPA and SAHA. Clin Epigenetics 2021; 13:58. [PMID: 33743782 PMCID: PMC7981901 DOI: 10.1186/s13148-021-01050-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Valproic acid (VPA) is one of the most commonly used anti-epileptic drugs with pharmacological actions on GABA and blocking voltage-gated ion channels. VPA also inhibits histone deacetylase (HDAC) activity. Suberoylanilide hydroxamic acid is also a member of a larger class of compounds that inhibit HDACs. At the time of this article, there are 123 active international clinical trials for VPA (also known as valproate, convulex, divalproex, and depakote) and SAHA (vorinostat, zolinza). While it is well known that VPA and SAHA influence the accumulation of acetylated lysine residues on histones, their true epigenetic complexity remains poorly understood. RESULTS Primary human cells were exposed to VPA and SAHA to understand the extent of histone acetylation (H3K9/14ac) using chromatin immunoprecipitation followed by sequencing (ChIP-seq). Because histone acetylation is often associated with modification of lysine methylation, we also examined H3K4me3 and H3K9me3. To assess the influence of the HDAC inhibitors on gene expression, we used RNA sequencing (RNA-seq). ChIP-seq reveals a distribution of histone modifications that is robust and more broadly regulated than previously anticipated by VPA and SAHA. Histone acetylation is a characteristic of the pharmacological inhibitors that influenced gene expression. Surprisingly, we observed histone deacetylation by VPA stimulation is a predominant signature following SAHA exposure and thus defines an acetylation/deacetylation (Ac/Dc) axis. ChIP-seq reveals regionalisation of histone acetylation by VPA and broader deacetylation by SAHA. Independent experiments confirm H3K9/14 deacetylation of NFκB target genes by SAHA. CONCLUSIONS The results provide an important framework for understanding the Ac/Dc axis by highlighting a broader complexity of histone modifications by the most established and efficacious anti-epileptic medication in this class, VPA and comparison with the broad spectrum HDAC inhibitor, SAHA.
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Affiliation(s)
- Sebastian Lunke
- Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - Scott Maxwell
- Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Ishant Khurana
- Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Harikrishnan K N
- Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jun Okabe
- Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Keith Al-Hasani
- Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Assam El-Osta
- Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia. .,Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia. .,Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia. .,Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia. .,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR. .,Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, 3/F Lui Che Woo Clinical Sciences Building, 30-32 Ngan Shing Street, Sha Tin, Hong Kong SAR. .,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR. .,Biomedical Laboratory Science, Department of Technology, Faculty of Health, University College Copenhagen, Copenhagen, Denmark.
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21
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Snelson M, Tan SM, Clarke RE, de Pasquale C, Thallas-Bonke V, Nguyen TV, Penfold SA, Harcourt BE, Sourris KC, Lindblom RS, Ziemann M, Steer D, El-Osta A, Davies MJ, Donnellan L, Deo P, Kellow NJ, Cooper ME, Woodruff TM, Mackay CR, Forbes JM, Coughlan MT. Processed foods drive intestinal barrier permeability and microvascular diseases. SCIENCE ADVANCES 2021; 7:7/14/eabe4841. [PMID: 33789895 PMCID: PMC8011970 DOI: 10.1126/sciadv.abe4841] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/12/2021] [Indexed: 05/04/2023]
Abstract
Intake of processed foods has increased markedly over the past decades, coinciding with increased microvascular diseases such as chronic kidney disease (CKD) and diabetes. Here, we show in rodent models that long-term consumption of a processed diet drives intestinal barrier permeability and an increased risk of CKD. Inhibition of the advanced glycation pathway, which generates Maillard reaction products within foods upon thermal processing, reversed kidney injury. Consequently, a processed diet leads to innate immune complement activation and local kidney inflammation and injury via the potent proinflammatory effector molecule complement 5a (C5a). In a mouse model of diabetes, a high resistant starch fiber diet maintained gut barrier integrity and decreased severity of kidney injury via suppression of complement. These results demonstrate mechanisms by which processed foods cause inflammation that leads to chronic disease.
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Affiliation(s)
- Matthew Snelson
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Victoria, Australia
| | - Sih Min Tan
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Victoria, Australia
| | - Rachel E Clarke
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Cassandra de Pasquale
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Victoria, Australia
| | - Vicki Thallas-Bonke
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Victoria, Australia
| | - Tuong-Vi Nguyen
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Victoria, Australia
| | - Sally A Penfold
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Victoria, Australia
| | - Brooke E Harcourt
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Karly C Sourris
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Victoria, Australia
| | - Runa S Lindblom
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Victoria, Australia
| | - Mark Ziemann
- Deakin University, School of Life and Environmental Sciences, Geelong, Victoria, Australia
| | - David Steer
- Monash Proteomics and Metabolomics Facility, Monash University, Melbourne, Victoria, Australia
| | - Assam El-Osta
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Victoria, Australia
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leigh Donnellan
- Health and Biomedical Innovation, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Permal Deo
- Health and Biomedical Innovation, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Nicole J Kellow
- Department of Nutrition, Dietetics and Food, Monash University, Melbourne, Victoria, Australia
| | - Mark E Cooper
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Victoria, Australia
| | - Trent M Woodruff
- School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Charles R Mackay
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Josephine M Forbes
- Glycation and Diabetes Group, Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Melinda T Coughlan
- Department of Diabetes, Central Clinical School, Alfred Medical Research and Education Precinct, Monash University, Melbourne, Victoria, Australia.
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
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22
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Valproic acid influences the expression of genes implicated with hyperglycaemia-induced complement and coagulation pathways. Sci Rep 2021; 11:2163. [PMID: 33495488 PMCID: PMC7835211 DOI: 10.1038/s41598-021-81794-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 01/11/2021] [Indexed: 01/04/2023] Open
Abstract
Because the liver plays a major role in metabolic homeostasis and secretion of clotting factors and inflammatory innate immune proteins, there is interest in understanding the mechanisms of hepatic cell activation under hyperglycaemia and whether this can be attenuated pharmacologically. We have previously shown that hyperglycaemia stimulates major changes in chromatin organization and metabolism in hepatocytes, and that the histone deacetylase inhibitor valproic acid (VPA) is able to reverse some of these metabolic changes. In this study, we have used RNA-sequencing (RNA-seq) to investigate how VPA influences gene expression in hepatocytes. Interesting, we observed that VPA attenuates hyperglycaemia-induced activation of complement and coagulation cascade genes. We also observe that many of the gene activation events coincide with changes to histone acetylation at the promoter of these genes indicating that epigenetic regulation is involved in VPA action.
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23
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Nasser S, Vialichka V, Biesiekierska M, Balcerczyk A, Pirola L. Effects of ketogenic diet and ketone bodies on the cardiovascular system: Concentration matters. World J Diabetes 2020; 11:584-595. [PMID: 33384766 PMCID: PMC7754168 DOI: 10.4239/wjd.v11.i12.584] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/29/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023] Open
Abstract
Ketone bodies have emerged as central mediators of metabolic health, and multiple beneficial effects of a ketogenic diet, impacting metabolism, neuronal pathologies and, to a certain extent, tumorigenesis, have been reported both in animal models and clinical research. Ketone bodies, endogenously produced by the liver, act pleiotropically as metabolic intermediates, signaling molecules, and epigenetic modifiers. The endothelium and the vascular system are central regulators of the organism’s metabolic state and become dysfunctional in cardiovascular disease, atherosclerosis, and diabetic micro- and macrovascular complications. As physiological circulating ketone bodies can attain millimolar concentrations, the endothelium is the first-line cell lineage exposed to them. While in diabetic ketoacidosis high ketone body concentrations are detrimental to the vasculature, recent research revealed that ketone bodies in the low millimolar range may exert beneficial effects on endothelial cell (EC) functioning by modulating the EC inflammatory status, senescence, and metabolism. Here, we review the long-held evidence of detrimental cardiovascular effects of ketoacidosis as well as the more recent evidence for a positive impact of ketone bodies—at lower concentrations—on the ECs metabolism and vascular physiology and the subjacent cellular and molecular mechanisms. We also explore arising controversies in the field and discuss the importance of ketone body concentrations in relation to their effects. At low concentration, endogenously produced ketone bodies upon uptake of a ketogenic diet or supplemented ketone bodies (or their precursors) may prove beneficial to ameliorate endothelial function and, consequently, pathologies in which endothelial damage occurs.
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Affiliation(s)
- Souad Nasser
- Carmen Laboratory, INSERM Unit 1060—Lyon 1 University, Pierre Benite 69310, France
| | - Varvara Vialichka
- Faculty of Biology and Environmental Protection, Department of Molecular Biophysics, University of Lodz, Lodz 90-236, Poland
- The University of Lodz Doctoral School of Exact and Natural Sciences, Lodz 90-237, Poland
| | - Marta Biesiekierska
- Faculty of Biology and Environmental Protection, Department of Molecular Biophysics, University of Lodz, Lodz 90-236, Poland
| | - Aneta Balcerczyk
- Faculty of Biology and Environmental Protection, Department of Molecular Biophysics, University of Lodz, Lodz 90-236, Poland
| | - Luciano Pirola
- Carmen Laboratory, INSERM Unit 1060—Lyon 1 University, Pierre Benite 69310, France
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24
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Lopez Sanchez MIG, Ziemann M, Bachem A, Makam R, Crowston JG, Pinkert CA, McKenzie M, Bedoui S, Trounce IA. Nuclear response to divergent mitochondrial DNA genotypes modulates the interferon immune response. PLoS One 2020; 15:e0239804. [PMID: 33031404 PMCID: PMC7544115 DOI: 10.1371/journal.pone.0239804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/14/2020] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial OXPHOS generates most of the energy required for cellular function. OXPHOS biogenesis requires the coordinated expression of the nuclear and mitochondrial genomes. This represents a unique challenge that highlights the importance of nuclear-mitochondrial genetic communication to cellular function. Here we investigated the transcriptomic and functional consequences of nuclear-mitochondrial genetic divergence in vitro and in vivo. We utilized xenomitochondrial cybrid cell lines containing nuclear DNA from the common laboratory mouse Mus musculus domesticus and mitochondrial DNA (mtDNA) from Mus musculus domesticus, or exogenous mtDNA from progressively divergent mouse species Mus spretus, Mus terricolor, Mus caroli and Mus pahari. These cybrids model a wide range of nuclear-mitochondrial genetic divergence that cannot be achieved with other research models. Furthermore, we used a xenomitochondrial mouse model generated in our laboratory that harbors wild-type, C57BL/6J Mus musculus domesticus nuclear DNA and homoplasmic mtDNA from Mus terricolor. RNA sequencing analysis of xenomitochondrial cybrids revealed an activation of interferon signaling pathways even in the absence of OXPHOS dysfunction or immune challenge. In contrast, xenomitochondrial mice displayed lower baseline interferon gene expression and an impairment in the interferon-dependent innate immune response upon immune challenge with herpes simplex virus, which resulted in decreased viral control. Our work demonstrates that nuclear-mitochondrial genetic divergence caused by the introduction of exogenous mtDNA can modulate the interferon immune response both in vitro and in vivo, even when OXPHOS function is not compromised. This work may lead to future insights into the role of mitochondrial genetic variation and the immune function in humans, as patients affected by mitochondrial disease are known to be more susceptible to immune challenges.
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Affiliation(s)
- M. Isabel G. Lopez Sanchez
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail: (MIGLS); (IAT)
| | - Mark Ziemann
- Department of Diabetes, Monash University Central Clinical School, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
- School of Life and Environmental Sciences, Deakin University, Victoria, Australia
| | - Annabell Bachem
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Rahul Makam
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Jonathan G. Crowston
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Carl A. Pinkert
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, United States of America
| | - Matthew McKenzie
- School of Life and Environmental Sciences, Deakin University, Victoria, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Sammy Bedoui
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ian A. Trounce
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail: (MIGLS); (IAT)
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25
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Histone Deacetylase Inhibitor Suberoylanilide Hydroxamic Acid Improves Energetic Status and Cardiomyogenic Differentiation of Human Dilated Myocardium-Derived Primary Mesenchymal Cells. Int J Mol Sci 2020; 21:ijms21144845. [PMID: 32650632 PMCID: PMC7402340 DOI: 10.3390/ijms21144845] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 02/08/2023] Open
Abstract
Background. In this study the effect of histone deacetylase (HDAC) inhibitor suberoylanilide hydroxamic acid (SAHA) on the energetic status and cardiomyogenic differentiation of human healthy and dilated myocardium-derived mesenchymal stromal cells (hmMSC) have been investigated. Methods. The hmMSC were isolated from the healthy and dilated post-operation heart biopsies by explant outgrowth method. Cell proliferation, HDAC activity, mitochondrial membrane potential, and level of adenosine triphosphate (ATP) were evaluated. The effect of SAHA on mitochondrial parameters has been investigated also by Seahorse XF analyzer and cardiomyogenic differentiation was confirmed by the expression of transcription factor NK2 Homeobox 5 (Nkx2.5), cardiac troponin T and alpha cardiac actin at gene and protein levels. Results. Dilated myocardium-derived hmMSC had almost 1.5 folds higher HDAC activity compared to the healthy cells and significantly lower mitochondrial membrane potential and ATP level. HDAC class I and II inhibitor SAHA improved energetic status of mitochondria in dilated myocardium-isolated hmMSC and increased expression of cardiac specific proteins during 14 days of exposure of cells to SAHA. Conclusions. HDAC inhibitor SAHA can be a promising therapeutic for dilated cardiomyopathy (DCM). Dilated hmMSC exposed to SAHA improved energetic status and, subsequently, cardiomyogenic differentiation. Data suggest that human dilated myocardium-derived MSC still have cardio tissue regenerative potential, which might be stimulated by HDAC inhibitors.
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26
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Stowers RS, Shcherbina A, Israeli J, Gruber JJ, Chang J, Nam S, Rabiee A, Teruel MN, Snyder MP, Kundaje A, Chaudhuri O. Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility. Nat Biomed Eng 2019; 3:1009-1019. [PMID: 31285581 PMCID: PMC6899165 DOI: 10.1038/s41551-019-0420-5] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/31/2019] [Indexed: 11/10/2022]
Abstract
In breast cancer, the increased stiffness of the extracellular matrix is a key driver of malignancy. Yet little is known about the epigenomic changes that underlie the tumorigenic impact of extracellular matrix mechanics. Here, we show in a three-dimensional culture model of breast cancer that stiff extracellular matrix induces a tumorigenic phenotype through changes in chromatin state. We found that increased stiffness yielded cells with more wrinkled nuclei and with increased lamina-associated chromatin, that cells cultured in stiff matrices displayed more accessible chromatin sites, which exhibited footprints of Sp1 binding, and that this transcription factor acts along with the histone deacetylases 3 and 8 to regulate the induction of stiffness-mediated tumorigenicity. Just as cell culture on soft environments or in them rather than on tissue-culture plastic better recapitulates the acinar morphology observed in mammary epithelium in vivo, mammary epithelial cells cultured on soft microenvironments or in them also more closely replicate the in vivo chromatin state. Our results emphasize the importance of culture conditions for epigenomic studies, and reveal that chromatin state is a critical mediator of mechanotransduction.
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Affiliation(s)
- Ryan S Stowers
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
| | - Anna Shcherbina
- Department of Biological Data Science, Stanford University, Stanford, CA, USA
| | - Johnny Israeli
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Physics, Stanford University, Stanford, CA, USA
| | - Joshua J Gruber
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine, Oncology Division, Stanford University, Stanford, CA, USA
| | - Julie Chang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sungmin Nam
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
| | - Atefeh Rabiee
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Mary N Teruel
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ovijit Chaudhuri
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA.
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27
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Sanchez GJ, Richmond PA, Bunker EN, Karman SS, Azofeifa J, Garnett AT, Xu Q, Wheeler GE, Toomey CM, Zhang Q, Dowell RD, Liu X. Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers. Nucleic Acids Res 2019; 46:1756-1776. [PMID: 29240919 PMCID: PMC5829637 DOI: 10.1093/nar/gkx1225] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/08/2017] [Indexed: 12/22/2022] Open
Abstract
Histone deacetylase inhibitors (HDACIs) are known to alter gene expression by both up- and down-regulation of protein-coding genes in normal and cancer cells. However, the exact regulatory mechanisms of action remain uncharacterized. Here we investigated genome wide dose-dependent epigenetic and transcriptome changes in response to HDACI largazole in a transformed and a non-transformed cell line. Exposure to low nanomolar largazole concentrations (<GI50) predominantly resulted in upregulation of gene transcripts whereas higher largazole doses (≥GI50) triggered a general decrease in mRNA accumulation. Largazole induces elevation of histone H3 acetylation at Lys-9 and Lys-27 along many gene bodies but does not correlate with up- or down-regulation of the associated transcripts. A higher dose of largazole results in more RNA polymerase II pausing at the promoters of actively transcribed genes and cell death. The most prevalent changes associated with transcriptional regulation occur at distal enhancer elements. Largazole promotes H3K27 acetylation at a subset of poised enhancers and unexpectedly, we also found active enhancers that become decommissioned in a dose and cell type-dependent manner. In particular, largazole decreases RNA polymerase II accumulation at super-enhancers (SEs) and preferentially suppresses SE-driven transcripts that are associated with oncogenic activities in transformed cells.
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Affiliation(s)
- Gilson J Sanchez
- Department of Chemistry and Biochemistry, University of Colorado-Boulder, Boulder, CO 80309, USA
| | - Phillip A Richmond
- BioFrontiers Institute and IQ Biology Program, University of Colorado-Boulder, Boulder, CO 80303, USA.,Molecular, Cellular, and Developmental Biology, University of Colorado-Boulder, Boulder, CO 80309, USA
| | - Eric N Bunker
- Department of Chemistry and Biochemistry, University of Colorado-Boulder, Boulder, CO 80309, USA
| | - Samuel S Karman
- Department of Chemistry and Biochemistry, University of Colorado-Boulder, Boulder, CO 80309, USA
| | - Joseph Azofeifa
- BioFrontiers Institute and IQ Biology Program, University of Colorado-Boulder, Boulder, CO 80303, USA
| | - Aaron T Garnett
- Ecology and Evolutionary Biology, University of Colorado-Boulder, Boulder, CO 80309, USA
| | - Quanbin Xu
- Department of Chemistry and Biochemistry, University of Colorado-Boulder, Boulder, CO 80309, USA
| | - Graycen E Wheeler
- Department of Chemistry and Biochemistry, University of Colorado-Boulder, Boulder, CO 80309, USA
| | - Cathryn M Toomey
- Department of Chemistry and Biochemistry, University of Colorado-Boulder, Boulder, CO 80309, USA
| | - Qinghong Zhang
- Department of Dermatology, University of Colorado Denver, Aurora, CO 80045, USA
| | - Robin D Dowell
- BioFrontiers Institute and IQ Biology Program, University of Colorado-Boulder, Boulder, CO 80303, USA.,Molecular, Cellular, and Developmental Biology, University of Colorado-Boulder, Boulder, CO 80309, USA
| | - Xuedong Liu
- Department of Chemistry and Biochemistry, University of Colorado-Boulder, Boulder, CO 80309, USA
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28
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Mechanism of Action for HDAC Inhibitors-Insights from Omics Approaches. Int J Mol Sci 2019; 20:ijms20071616. [PMID: 30939743 PMCID: PMC6480157 DOI: 10.3390/ijms20071616] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 01/01/2023] Open
Abstract
Histone deacetylase inhibitors (HDIs) are a class of prominent epigenetic drugs that are currently being tested in hundreds of clinical trials against a variety of diseases. A few compounds have already been approved for treating lymphoma or myeloma. HDIs bind to the zinc-containing catalytic domain of the histone deacetylase (HDACs) and they repress the deacetylase enzymatic activity. The broad therapeutic effect of HDIs with seemingly low toxicity is somewhat puzzling when considering that most HDIs lack strict specificity toward any individual HDAC and, even if they do, each individual HDAC has diverse functions under different physiology scenarios. Here, we review recent mechanistic studies using omics approaches, including epigenomics, transcriptomics, proteomics, metabolomics, and chemoproteomics, methods. These omics studies provide non-biased insights into the mechanism of action for HDIs.
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29
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Cleophas MCP, Crişan TO, Klück V, Hoogerbrugge N, Netea-Maier RT, Dinarello CA, Netea MG, Joosten LAB. Romidepsin suppresses monosodium urate crystal-induced cytokine production through upregulation of suppressor of cytokine signaling 1 expression. Arthritis Res Ther 2019; 21:50. [PMID: 30728075 PMCID: PMC6366029 DOI: 10.1186/s13075-019-1834-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/22/2019] [Indexed: 02/01/2023] Open
Abstract
Background Acute gouty arthritis currently is the most common form of inflammatory arthritis in developed countries. Treatment is still suboptimal. Dosage of urate-lowering therapy is often too low to reach target urate levels, and adherence to therapy is poor. In this study, we therefore explore a new treatment option to limit inflammation in acute gout: specific histone deacetylase (HDAC) inhibition. Methods Peripheral blood mononuclear cells (PBMCs) were cultured with a combination of monosodium urate crystals (MSU) and palmitic acid (C16.0) in order to activate the NLRP3 inflammasome and induce IL-1β production. HDAC inhibitors and other compounds were added beforehand with a 1-h pre-incubation period. Results The HDAC1/2 inhibitor romidepsin was most potent in lowering C16.0+MSU-induced IL-1β production compared to other specific class I HDAC inhibitors. At 10 nM, romidepsin decreased IL-1β, IL-1Ra, IL-6, and IL-8 production. IL-1β mRNA was significantly decreased at 25 nM. Although romidepsin increased PTEN expression, PBMCs from patients with germline mutations in PTEN still responded well to romidepsin. Romidepsin also increased SOCS1 expression and blocked STAT1 and STAT3 activation. Furthermore, experiments with bortezomib showed that blocking the proteasome reverses the cytokine suppression by romidepsin. Conclusions Our results show that romidepsin is a very potent inhibitor of C16.0+MSU-induced cytokines in vitro. Romidepsin upregulated transcription of SOCS1, which was shown to directly target inflammatory signaling molecules for proteasomal degradation. Inhibiting the proteasome therefore reversed the cytokine-suppressive effects of romidepsin. HDAC1/2 dual inhibition could therefore be a highly potent new treatment option for acute gout, although safety has to be determined in vivo. Electronic supplementary material The online version of this article (10.1186/s13075-019-1834-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M C P Cleophas
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - T O Crişan
- Department of Medical Genetics, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - V Klück
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - N Hoogerbrugge
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - R T Netea-Maier
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - C A Dinarello
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Division of Infectious Diseases, Department of Medicine, University of Colorado, Denver, Aurora, CO, 80045, USA
| | - M G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115, Bonn, Germany
| | - L A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands. .,Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands. .,Department of Medical Genetics, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.
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30
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Epigenetics, cardiovascular disease, and cellular reprogramming. J Mol Cell Cardiol 2019; 128:129-133. [PMID: 30690032 DOI: 10.1016/j.yjmcc.2019.01.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 01/22/2019] [Indexed: 12/29/2022]
Abstract
Under the seeming disorder of "junk" sequences the last decade has seen developments in our understanding of non-coding RNA's (ncRNAs). It's a complex revised order and nowhere is this more relevant than in the developing heart whereby old rules have been set aside to make room for new ones. The development of the mammalian heart has been studied at the genetic and cellular level for several decades because these areas were considered ideal control points. As such, detailed mechanisms governing cell lineages are well described. Emerging evidence suggests a complex new order regulated by epigenetic mechanisms mark cardiac cell lineage. Indeed, molecular cardiologists are in the process of shedding light on the roles played by ncRNAs, nucleic acid methylation and histone/chromatin modifications in specific pathologies of the heart. The aim of this article is to discuss some of the recent advances in the field of cardiovascular epigenetics that are related to direct cell reprogramming and repair. As such, we explore ncRNAs as nodes regulating signaling networks and attempt to make sense of regulatory disorder by reinforcing the importance of epigenetic components in the developmental program.
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31
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Khan AW, Ziemann M, Rafehi H, Maxwell S, Ciccotosto GD, El-Osta A. MeCP2 interacts with chromosomal microRNAs in brain. Epigenetics 2018; 12:1028-1037. [PMID: 29412786 DOI: 10.1080/15592294.2017.1391429] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Although methyl CpG binding domain protein-2 (MeCP2) is commonly understood to function as a silencing factor at methylated DNA sequences, recent studies also show that MeCP2 can bind unmethylated sequences and coordinate gene activation. MeCP2 displays broad binding patterns throughout the genome, with high expression levels similar to histone H1 in neurons. Despite its significant presence in the brain, only subtle gene expression changes occur in the absence of MeCP2. This may reflect a more complex regulatory mechanism of MeCP2 to complement chromatin binding. Using an RNA immunoprecipitation of native chromatin technique, we identify MeCP2 interacting microRNAs in mouse primary cortical neurons. In addition, comparison with mRNA sequencing data from Mecp2-null mice suggests that differentially expressed genes may indeed be targeted by MeCP2-interacting microRNAs. These findings highlight the MeCP2 interaction with microRNAs that may modulate its binding with chromatin and regulate gene expression.
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Affiliation(s)
- Abdul Waheed Khan
- a Central Clinical School, Faculty of Medicine , Monash University , Victoria , Australia.,b Baker IDI Heart and Diabetes Institute , The Alfred Medical Research and Education Precinct , Melbourne , Victoria 3004 , Australia.,c Department of Pathology , The University of Melbourne , Parkville , Victoria , Australia
| | - Mark Ziemann
- a Central Clinical School, Faculty of Medicine , Monash University , Victoria , Australia.,b Baker IDI Heart and Diabetes Institute , The Alfred Medical Research and Education Precinct , Melbourne , Victoria 3004 , Australia
| | - Haloom Rafehi
- a Central Clinical School, Faculty of Medicine , Monash University , Victoria , Australia.,b Baker IDI Heart and Diabetes Institute , The Alfred Medical Research and Education Precinct , Melbourne , Victoria 3004 , Australia
| | - Scott Maxwell
- a Central Clinical School, Faculty of Medicine , Monash University , Victoria , Australia.,b Baker IDI Heart and Diabetes Institute , The Alfred Medical Research and Education Precinct , Melbourne , Victoria 3004 , Australia
| | - Giuseppe D Ciccotosto
- c Department of Pathology , The University of Melbourne , Parkville , Victoria , Australia.,d Bio21 Molecular science and Biotechnology Institute , Victoria , Australia
| | - Assam El-Osta
- a Central Clinical School, Faculty of Medicine , Monash University , Victoria , Australia.,b Baker IDI Heart and Diabetes Institute , The Alfred Medical Research and Education Precinct , Melbourne , Victoria 3004 , Australia.,c Department of Pathology , The University of Melbourne , Parkville , Victoria , Australia.,e Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital , The Chinese University of Hong Kong , Hong Kong SAR
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32
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Rafehi H, Kaspi A, Ziemann M, Okabe J, Karagiannis TC, El-Osta A. Systems approach to the pharmacological actions of HDAC inhibitors reveals EP300 activities and convergent mechanisms of regulation in diabetes. Epigenetics 2018; 12:991-1003. [PMID: 28886276 DOI: 10.1080/15592294.2017.1371892] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Given the skyrocketing costs to develop new drugs, repositioning of approved drugs, such as histone deacetylase (HDAC) inhibitors, may be a promising strategy to develop novel therapies. However, a gap exists in the understanding and advancement of these agents to meaningful translation for which new indications may emerge. To address this, we performed systems-level analyses of 33 independent HDAC inhibitor microarray studies. Based on network analysis, we identified enrichment for pathways implicated in metabolic syndrome and diabetes (insulin receptor signaling, lipid metabolism, immunity and trafficking). Integration with ENCODE ChIP-seq datasets identified suppression of EP300 target genes implicated in diabetes. Experimental validation indicates reversal of diabetes-associated EP300 target genes in primary vascular endothelial cells derived from a diabetic individual following inhibition of HDACs (by SAHA), EP300, or EP300 knockdown. Our computational systems biology approach provides an adaptable framework for the prediction of novel therapeutics for existing disease.
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Affiliation(s)
- Haloom Rafehi
- a Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Monash University , Melbourne , Victoria , Australia
| | - Antony Kaspi
- a Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Monash University , Melbourne , Victoria , Australia
| | - Mark Ziemann
- a Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Monash University , Melbourne , Victoria , Australia
| | - Jun Okabe
- a Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Monash University , Melbourne , Victoria , Australia
| | - Tom C Karagiannis
- a Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Monash University , Melbourne , Victoria , Australia.,b Department of Pathology, The University of Melbourne , Parkville , Victoria , Australia
| | - Assam El-Osta
- a Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Monash University , Melbourne , Victoria , Australia.,b Department of Pathology, The University of Melbourne , Parkville , Victoria , Australia.,c Faculty of Medicine, Nursing and Health Sciences, Department of Diabetes, Monash University , Melbourne , Victoria , Australia.,d Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong , Hong Kong SAR
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33
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Nguyen MN, Ziemann M, Kiriazis H, Su Y, Thomas Z, Lu Q, Donner DG, Zhao WB, Rafehi H, Sadoshima J, McMullen JR, El-Osta A, Du XJ. Galectin-3 deficiency ameliorates fibrosis and remodeling in dilated cardiomyopathy mice with enhanced Mst1 signaling. Am J Physiol Heart Circ Physiol 2018; 316:H45-H60. [PMID: 30387702 DOI: 10.1152/ajpheart.00609.2018] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Dilated cardiomyopathy (DCM) is a major cause of heart failure without effective therapy. Fibrogenesis plays a key role in the development of DCM, but little is known of the expression of the profibrotic factor galectin-3 (Gal-3) and its role in DCM pathophysiology. In a mouse DCM model with transgenic (TG) overexpression of mammalian sterile 20-like kinase 1 (Mst1), we studied Gal-3 expression and effects of the Gal-3 inhibitor modified citrus pectin (MCP) or Gal-3 gene knockout (KO). Gal-3 deletion in TG mice (TG/KO) was achieved by crossbreeding Mst1-TG mice with Gal-3 KO mice. The DCM phenotype was assessed by echocardiography and micromanometry. Cardiac expression of Gal-3 and fibrosis were determined. The cardiac transcriptome was profiled by RNA sequencing. Mst1-TG mice at 3-8 mo of age exhibited upregulated expression of Gal-3 by ~40-fold. TG mice had dilatation of cardiac chambers, suppressed left ventricular (LV) ejection fraction, poor LV contractility and relaxation, a threefold increase in LV collagen content, and upregulated fibrotic genes. Four-month treatment with MCP showed no beneficial effects. Gal-3 deletion in Mst1-TG mice attenuated chamber dilatation, organ congestion, and fibrogenesis. RNA sequencing identified profound disturbances by Mst1 overexpression in the cardiac transcriptome, which largely remained in TG/KO hearts. Gal-3 deletion in Mst1-TG mice, however, partially reversed the dysregulated transcriptional signaling involving extracellular matrix remodeling and collagen formation. We conclude that cardiac Mst1 activation leads to marked Gal-3 upregulation and transcriptome disturbances in the heart. Gal-3 deficiency attenuated cardiac remodeling and fibrotic signaling. NEW & NOTEWORTHY We found in a transgenic mouse dilated cardiomyopathy (DCM) model a pronounced upregulation of galectin-3 in cardiomyocytes. Galectin-3 gene deletion reduced cardiac fibrosis and fibrotic gene profiles and ameliorated cardiac remodeling and dysfunction. These benefits of galectin-3 deletion were in contrast to the lack of effect of treatment with the galectin-3 inhibitor modified citrus pectin. Our study suggests that suppression of galectin-3 mRNA expression could be used to treat DCM with high cardiac galectin-3 content.
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Affiliation(s)
- My-Nhan Nguyen
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia.,Central Clinical School, Monash University , Melbourne, Victoria , Australia
| | - Mark Ziemann
- Department of Diabetes, Monash University , Melbourne, Victoria , Australia
| | - Helen Kiriazis
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia
| | - Yidan Su
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia
| | - Zara Thomas
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia
| | - Qun Lu
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia.,Health Science Center, Xian Jiaotong University , Xian , People's Republic of China
| | - Daniel G Donner
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia
| | - Wei-Bo Zhao
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia
| | - Haloom Rafehi
- Department of Diabetes, Monash University , Melbourne, Victoria , Australia
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School , Newark, New Jersey
| | - Julie R McMullen
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia.,Central Clinical School, Monash University , Melbourne, Victoria , Australia
| | - Assam El-Osta
- Department of Diabetes, Monash University , Melbourne, Victoria , Australia.,Prince of Wales Hospital, The Chinese University of Hong Kong , Shatin, Hong Kong Special Administrative Region , People's Republic of China
| | - Xiao-Jun Du
- Baker Heart and Diabetes Institute , Melbourne, Victoria , Australia.,Central Clinical School, Monash University , Melbourne, Victoria , Australia.,Health Science Center, Xian Jiaotong University , Xian , People's Republic of China
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34
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Rösler B, Wang X, Keating ST, Joosten LAB, Netea MG, van de Veerdonk FL. HDAC inhibitors modulate innate immune responses to micro-organisms relevant to chronic mucocutaneous candidiasis. Clin Exp Immunol 2018; 194:205-219. [PMID: 30069986 PMCID: PMC6194342 DOI: 10.1111/cei.13192] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2018] [Indexed: 12/11/2022] Open
Abstract
Signal transducer and activator of transcription 1 (STAT-1) gain-of-function (GOF) mutations cause chronic mucocutaneous candidiasis (CMC), a disease associated with Candida albicans and Staphylococcus aureus infection. Patients suffer from dysegulated immune responses due to aberrant cell programming and function. We investigated the effect of inhibitory molecules targeting histone deacetylases (HDACi) on the immune responses of peripheral blood mononuclear cells (PBMCs) of healthy controls and patients with CMC towards microbes relevant for CMC. PBMCs cells were pretreated with HDACi and challenged with C. albicans or S. aureus. Innate and adaptive cytokines were measured in cell culture supernatants by enzyme-linked immunosorbent assay (ELISA). We assessed the effect of HDAC inhibitors on T helper type 1 (Th1) and Th17 cells and measured STAT-1 and STAT-3 phosphorylation using flow cytometry. Panobinostat, a pan-HDAC inhibitor, strongly inhibits innate and adaptive cytokines upon challenge with C. albicans or S. aureus. Specific inhibitors (entinostat or RGFP966) also had a tendency to lower production of most innate cytokines in CMC patient cells. Entinostat and RGFP966 increased the production of interleukin (IL)-22 specifically after S. aureus challenge in patient cells. In healthy and control cells, entinostat and RGFP966 treatment down-regulated STAT-1 phosphorylation while pSTAT-3 levels remained stable. HDACi modulate cytokine production in response to C. albicans and S. aureus. Pan-inhibitors lower overall cytokine production, whereas specific inhibitors confer a selective effect. Entinostat and RGFP966 are promising therapeutic candidates to treat STAT-1 GOF due to their capacity to restore IL-22 production and decrease STAT-1 phosphorylation; however, their inhibition of innate cytokines poses a possible risk to secondary infections.
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Affiliation(s)
- B. Rösler
- Department of Internal Medicine, Radboud Center for Infectious diseases (RCI)Radboud UMCNijmegenthe Netherlands
| | - X. Wang
- Department of Internal Medicine, Radboud Center for Infectious diseases (RCI)Radboud UMCNijmegenthe Netherlands
- Department of DermatologyPeking University First HospitalBeijingChina
| | - S. T. Keating
- Department of Internal Medicine, Radboud Center for Infectious diseases (RCI)Radboud UMCNijmegenthe Netherlands
| | - L. A. B. Joosten
- Department of Internal Medicine, Radboud Center for Infectious diseases (RCI)Radboud UMCNijmegenthe Netherlands
| | - M. G. Netea
- Department of Internal Medicine, Radboud Center for Infectious diseases (RCI)Radboud UMCNijmegenthe Netherlands
- Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES)University of BonnBonnGermany
| | - F. L. van de Veerdonk
- Department of Internal Medicine, Radboud Center for Infectious diseases (RCI)Radboud UMCNijmegenthe Netherlands
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35
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Rodriguez H, El-Osta A. Epigenetic Contribution to the Development and Progression of Vascular Diabetic Complications. Antioxid Redox Signal 2018; 29:1074-1091. [PMID: 29304555 DOI: 10.1089/ars.2017.7347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SIGNIFICANCE The number of people suffering from diabetes worldwide is steadily rising. Complications from diabetes, including cardiovascular and renal disease, contribute to the high morbidity and mortality associated with this disease. Recent Advances: Hyperglycemia promotes tissue damage through diverse mechanisms involving increased production of reactive oxygen species. Increased oxidative stress drives changes in chromatin structure that mediate gene expression changes leading to the upregulation of proinflammatory and profibrotic mediators. The epigenetic contribution to diabetes-induced changes in gene expression is increasingly recognized as a key factor in the development and progression of vascular diabetic complications. CRITICAL ISSUES The mechanisms through which stimuli from the diabetic milieu promote epigenetic changes remain poorly understood. In addition, glycemic control constitutes an important factor influencing epigenetic states in diabetes, and the phenomenon of hyperglycemic memory warrants further research. FUTURE DIRECTIONS Knowledge of the molecular mechanisms underlying epigenetic changes in diabetes may allow the design of novel therapeutic strategies to reduce the burden of diabetic complications. Furthermore, certain epigenetic markers are detected early during the onset of diabetes and its complications and may prove useful as biomarkers for disease risk prediction.
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Affiliation(s)
- Hanah Rodriguez
- 1 Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University , Melbourne, Australia
| | - Assam El-Osta
- 1 Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University , Melbourne, Australia .,2 Department of Pathology, University of Melbourne , Melbourne, Australia .,3 Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong , Hong Kong SAR, China
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36
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van der Heijden CDCC, Noz MP, Joosten LAB, Netea MG, Riksen NP, Keating ST. Epigenetics and Trained Immunity. Antioxid Redox Signal 2018; 29:1023-1040. [PMID: 28978221 PMCID: PMC6121175 DOI: 10.1089/ars.2017.7310] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SIGNIFICANCE A growing body of clinical and experimental evidence has challenged the traditional understanding that only the adaptive immune system can mount immunological memory. Recent findings describe the adaptive characteristics of the innate immune system, underscored by its ability to remember antecedent foreign encounters and respond in a nonspecific sensitized manner to reinfection. This has been termed trained innate immunity. Although beneficial in the context of recurrent infections, this might actually contribute to chronic immune-mediated diseases, such as atherosclerosis. Recent Advances: In line with its proposed role in sustaining cellular memories, epigenetic reprogramming has emerged as a critical determinant of trained immunity. Recent technological and computational advances that improve unbiased acquisition of epigenomic profiles have significantly enhanced our appreciation for the complexities of chromatin architecture in the contexts of diverse immunological challenges. CRITICAL ISSUES Key to resolving the distinct chromatin signatures of innate immune memory is a comprehensive understanding of the precise physiological targets of regulatory proteins that recognize, deposit, and remove chemical modifications from chromatin as well as other gene-regulating factors. Drawing from a rapidly expanding compendium of experimental and clinical studies, this review details a current perspective of the epigenetic pathways that support the adapted phenotypes of monocytes and macrophages. FUTURE DIRECTIONS We explore future strategies that are aimed at exploiting the mechanism of trained immunity to improve the prevention and treatment of infections and immune-mediated chronic disorders.
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Affiliation(s)
| | - Marlies P Noz
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Leo A B Joosten
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Mihai G Netea
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands .,2 Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn , Bonn, Germany
| | - Niels P Riksen
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Samuel T Keating
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands
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Narayanan S, Loganathan G, Mokshagundam S, Hughes MG, Williams SK, Balamurugan AN. Endothelial cell regulation through epigenetic mechanisms: Depicting parallels and its clinical application within an intra-islet microenvironment. Diabetes Res Clin Pract 2018; 143:120-133. [PMID: 29953914 DOI: 10.1016/j.diabres.2018.06.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/31/2018] [Accepted: 06/19/2018] [Indexed: 12/12/2022]
Abstract
The intra-islet endothelial cells (ECs), the building blocks of islet microvasculature, govern a number of cellular and pathophysiological processes associated with the pancreatic tissue. These cells are key to the angiogenic process and essential for islet revascularization after transplantation. Understanding fundamental mechanisms by which ECs regulate the angiogenic process is important as these cells maintain and regulate the intra-islet environment facilitated by a complex signaling crosstalk with the surrounding endocrine cells. In recent years, many studies have demonstrated the impact of epigenetic regulation on islet cell development and function. This review will present an overview of the reports involving endothelial epigenetic mechanisms particularly focusing on histone modifications which have been identified to play a critical role in governing EC functions by modifying the chromatin structure. A better understanding of epigenetic mechanisms by which these cells regulate gene expression and function to orchestrate cellular physiology and pathology is likely to offer improved insights on the functioning and regulation of an intra-islet endothelial microvascular environment.
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Affiliation(s)
- Siddharth Narayanan
- Clinical Islet Cell Laboratory, Center for Cellular Transplantation, Cardiovascular Innovation Institute, Department of Surgery, University of Louisville, Louisville, KY 40202, United States
| | - Gopalakrishnan Loganathan
- Clinical Islet Cell Laboratory, Center for Cellular Transplantation, Cardiovascular Innovation Institute, Department of Surgery, University of Louisville, Louisville, KY 40202, United States
| | | | - Michael G Hughes
- Clinical Islet Cell Laboratory, Center for Cellular Transplantation, Cardiovascular Innovation Institute, Department of Surgery, University of Louisville, Louisville, KY 40202, United States
| | - Stuart K Williams
- Department of Physiology, University of Louisville, Louisville, KY 40202, United States
| | - Appakalai N Balamurugan
- Clinical Islet Cell Laboratory, Center for Cellular Transplantation, Cardiovascular Innovation Institute, Department of Surgery, University of Louisville, Louisville, KY 40202, United States.
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Repression of human and mouse brain inflammaging transcriptome by broad gene-body histone hyperacetylation. Proc Natl Acad Sci U S A 2018; 115:7611-7616. [PMID: 29967166 DOI: 10.1073/pnas.1800656115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Brain "inflammaging," a low-grade and chronic inflammation, is a major hallmark for aging-related neurodegenerative diseases. Here, by profiling H3K27ac and gene expression patterns in human and mouse brains, we found that age-related up-regulated (Age-Up) and down-regulated (Age-Down) genes have distinct H3K27ac patterns. Although both groups show promoter H3K27ac, the Age-Up genes, enriched for inflammation-related functions, are additionally marked by broad H3K27ac distribution over their gene bodies, which is progressively reduced during aging. Age-related gene expression changes can be predicted by gene-body H3K27ac level. Contrary to the presumed transcription activation function of promoter H3K27ac, we found that broad gene-body hyper H3K27ac suppresses overexpression of inflammaging genes. Altogether, our findings revealed opposite regulations by H3K27ac of Age-Up and Age-Down genes and a mode of broad gene-body H3K27ac in repressing transcription.
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Cunningham CM, Eghbali M. An Introduction to Epigenetics in Cardiovascular Development, Disease, and Sexualization. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1065:31-47. [PMID: 30051375 DOI: 10.1007/978-3-319-77932-4_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Epigenetic regulation of gene expression is integral to cell differentiation, development, and disease. Modes of epigenetic regulation-including DNA methylation, histone modifications, and ncRNA-based regulation-alter chromatin structure, promotor accessibility, and contribute to posttranscriptional modifications. In the cardiovascular system, epigenetic regulation is necessary for proper cardiovascular development and homeostasis, while epigenetic dysfunction is associated with improper cardiac development and disease.Early sexualization of tissues, including X-inactivation in females and maternal and paternal imprinting, is also orchestrated through epigenetic mechanisms. Furthermore, sex chromosomes encode various sex-specific genes involved in epigenetic regulation, while sex hormones can act as regulatory cofactors that may predispose or protect males and females against developing diseases with a marked sex bias.The following book chapter summarizes the field of epigenetics in the context of cardiovascular development and disease while also highlighting the role of epigenetic regulation as a powerful source of sex differences within the cardiovascular system.
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Affiliation(s)
- Christine M Cunningham
- Department of Anesthesiology and Perioperative Medicine, Division of Molecular Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA
| | - Mansoureh Eghbali
- Department of Anesthesiology and Perioperative Medicine, Division of Molecular Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA.
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Mandoli A, Singh AA, Prange KHM, Tijchon E, Oerlemans M, Dirks R, Ter Huurne M, Wierenga ATJ, Janssen-Megens EM, Berentsen K, Sharifi N, Kim B, Matarese F, Nguyen LN, Hubner NC, Rao NA, van den Akker E, Altucci L, Vellenga E, Stunnenberg HG, Martens JHA. The Hematopoietic Transcription Factors RUNX1 and ERG Prevent AML1-ETO Oncogene Overexpression and Onset of the Apoptosis Program in t(8;21) AMLs. Cell Rep 2017; 17:2087-2100. [PMID: 27851970 DOI: 10.1016/j.celrep.2016.08.082] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 05/06/2016] [Accepted: 08/16/2016] [Indexed: 01/24/2023] Open
Abstract
The t(8;21) acute myeloid leukemia (AML)-associated oncoprotein AML1-ETO disrupts normal hematopoietic differentiation. Here, we have investigated its effects on the transcriptome and epigenome in t(8,21) patient cells. AML1-ETO binding was found at promoter regions of active genes with high levels of histone acetylation but also at distal elements characterized by low acetylation levels and binding of the hematopoietic transcription factors LYL1 and LMO2. In contrast, ERG, FLI1, TAL1, and RUNX1 bind at all AML1-ETO-occupied regulatory regions, including those of the AML1-ETO gene itself, suggesting their involvement in regulating AML1-ETO expression levels. While expression of AML1-ETO in myeloid differentiated induced pluripotent stem cells (iPSCs) induces leukemic characteristics, overexpression increases cell death. We find that expression of wild-type transcription factors RUNX1 and ERG in AML is required to prevent this oncogene overexpression. Together our results show that the interplay of the epigenome and transcription factors prevents apoptosis in t(8;21) AML cells.
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Affiliation(s)
- Amit Mandoli
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Abhishek A Singh
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Koen H M Prange
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Esther Tijchon
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Marjolein Oerlemans
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Rene Dirks
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Menno Ter Huurne
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Albertus T J Wierenga
- Department of Hematology, University of Groningen and University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, the Netherlands; Department of Laboratory Medicine, University of Groningen and University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Eva M Janssen-Megens
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Kim Berentsen
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Nilofar Sharifi
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Bowon Kim
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Filomena Matarese
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Luan N Nguyen
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Nina C Hubner
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Nagesha A Rao
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Emile van den Akker
- Sanquin Research Department of Hematopoiesis, P.O. Box 9190, 1006 AD Amsterdam, the Netherlands
| | - Lucia Altucci
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Vico Luigi de Crecchio 7, 80138 Napoli, Italy; Istituto di Genetica e Biofisica "Adriano Buzzati Traverso," Via P. Castellino 131, 80131 Napoli, Italy
| | - Edo Vellenga
- Department of Hematology, University of Groningen and University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Hendrik G Stunnenberg
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Joost H A Martens
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands; Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Vico Luigi de Crecchio 7, 80138 Napoli, Italy.
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Early transcriptional alteration of histone deacetylases in a murine model of doxorubicin-induced cardiomyopathy. PLoS One 2017; 12:e0180571. [PMID: 28662206 PMCID: PMC5491252 DOI: 10.1371/journal.pone.0180571] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 06/16/2017] [Indexed: 12/22/2022] Open
Abstract
Doxorubicin is a potent chemotherapeutic agent that is widely-used to treat a variety of cancers but causes acute and chronic cardiac injury, severely limiting its use. Clinically, the acute side effects of doxorubicin are mostly manageable, whereas the delayed consequences can lead to life-threatening heart failure, even decades after cancer treatment. The cardiotoxicity of doxorubicin is subject to a critical cumulative dose and so dosage limitation is considered to be the best way to reduce these effects. Hence, a number of studies have defined a "safe dose" of the drug, both in animal models and clinical settings, with the aim of avoiding long-term cardiac effects. Here we show that a dose generally considered as safe in a mouse model can induce harmful changes in the myocardium, as early as 2 weeks after infusion. The adverse changes include the development of fibrotic lesions, disarray of cardiomyocytes and a major transcription dysregulation. Importantly, low-dose doxorubicin caused specific changes in the transcriptional profile of several histone deacetylases (HDACs) which are epigenetic regulators of cardiac remodelling. This suggests that cardioprotective therapies, aimed at modulating HDACs during doxorubicin treatment, deserve further exploration.
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DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. Nat Genet 2017; 49:1052-1060. [PMID: 28604729 DOI: 10.1038/ng.3889] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 05/03/2017] [Indexed: 12/13/2022]
Abstract
Several mechanisms of action have been proposed for DNA methyltransferase and histone deacetylase inhibitors (DNMTi and HDACi), primarily based on candidate-gene approaches. However, less is known about their genome-wide transcriptional and epigenomic consequences. By mapping global transcription start site (TSS) and chromatin dynamics, we observed the cryptic transcription of thousands of treatment-induced non-annotated TSSs (TINATs) following DNMTi and HDACi treatment. The resulting transcripts frequently splice into protein-coding exons and encode truncated or chimeric ORFs translated into products with predicted abnormal or immunogenic functions. TINAT transcription after DNMTi treatment coincided with DNA hypomethylation and gain of classical promoter histone marks, while HDACi specifically induced a subset of TINATs in association with H2AK9ac, H3K14ac, and H3K23ac. Despite this mechanistic difference, both inhibitors convergently induced transcription from identical sites, as we found TINATs to be encoded in solitary long terminal repeats of the ERV9/LTR12 family, which are epigenetically repressed in virtually all normal cells.
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Venosa A, Gow JG, Hall L, Malaviya R, Gow AJ, Laskin JD, Laskin DL. Regulation of Nitrogen Mustard-Induced Lung Macrophage Activation by Valproic Acid, a Histone Deacetylase Inhibitor. Toxicol Sci 2017; 157:222-234. [PMID: 28184907 PMCID: PMC6075217 DOI: 10.1093/toxsci/kfx032] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Nitrogen mustard (NM)-induced lung injury is associated with an accumulation of proinflammatory/cytotoxic M1 and antiinflammatory/wound repair M2 macrophages, which have been implicated in tissue injury and repair. Herein, we analyzed the effects of valproic acid (VPA), a histone deacetylase (HDAC) inhibitor with antiinflammatory and antioxidant activity, on lung macrophages responding to NM. Treatment of rats with NM (0.125 mg/kg, i.t.) resulted in structural alterations in the lung and a macrophage-rich inflammatory cell infiltrate, at 3 d and 7 d. This was accompanied by expression of PCNA, a marker of proliferation, and CYPb5, HO-1, and MnSOD, markers of oxidative stress. Administration of VPA (300 mg/kg/day; i.p.), beginning 30 min after NM, reduced increases in PCNA, CYPb5, HO-1, and MnSOD. This was associated with increases in immature CD11b+CD43+ M1 macrophages in the lung, and decreases in mature CD11b+CD43- M2 macrophages 3 d post NM, suggesting delayed maturation and phenotypic switching. VPA also attenuated NM-induced increases in lung iNOS+ and CCR2+ M1 macrophages, a response correlated with downregulation of NOS2, IL12B, PTGS2, MMP-9, and CCR2 expression. Conversely, numbers of CD68+, CD163+ , and ATR-1α+ M2 macrophages increased after VPA, along with the expression of IL10, ApoE, and ATR-1A. NM exposure resulted in increased HDAC activity and upregulation of HDAC2 and acetylated H3K9 in the lung. Whereas VPA blunted the effects of NM on HDAC2 expression, histone H3K9 acetylation increased. These data suggest that alterations in the balance between histone acetylases and deacetylases contribute to lung macrophage maturation and activation following NM exposure.
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Affiliation(s)
- Alessandro Venosa
- Department of Pharmacology and Toxicology, Rutgers University, Ernest Mario School of Pharmacy, Piscataway, New Jersey 08854
| | - James G. Gow
- Department of Pharmacology and Toxicology, Rutgers University, Ernest Mario School of Pharmacy, Piscataway, New Jersey 08854
| | - LeRoy Hall
- Drug Safety Sciences, Johnson & Johnson, Raritan, New Jersey 08869
| | - Rama Malaviya
- Department of Pharmacology and Toxicology, Rutgers University, Ernest Mario School of Pharmacy, Piscataway, New Jersey 08854
| | - Andrew J. Gow
- Department of Pharmacology and Toxicology, Rutgers University, Ernest Mario School of Pharmacy, Piscataway, New Jersey 08854
| | - Jeffrey D. Laskin
- Department of Environmental and Occupational Health, School of Public Health, Rutgers University, Piscataway, New Jersey 08854
| | - Debra L. Laskin
- Department of Pharmacology and Toxicology, Rutgers University, Ernest Mario School of Pharmacy, Piscataway, New Jersey 08854
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Keating ST, Plutzky J, El-Osta A. Epigenetic Changes in Diabetes and Cardiovascular Risk. Circ Res 2017; 118:1706-22. [PMID: 27230637 DOI: 10.1161/circresaha.116.306819] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/30/2016] [Indexed: 01/03/2023]
Abstract
Cardiovascular complications remain the leading causes of morbidity and premature mortality in patients with diabetes mellitus. Studies in humans and preclinical models demonstrate lasting gene expression changes in the vasculopathies initiated by previous exposure to high glucose concentrations and the associated overproduction of reactive oxygen species. The molecular signatures of chromatin architectures that sensitize the genome to these and other cardiometabolic risk factors of the diabetic milieu are increasingly implicated in the biological memory underlying cardiovascular complications and now widely considered as promising therapeutic targets. Atherosclerosis is a complex heterocellular disease where the contributing cell types possess distinct epigenomes shaping diverse gene expression. Although the extent that pathological chromatin changes can be manipulated in human cardiovascular disease remains to be established, the clinical applicability of epigenetic interventions will be greatly advanced by a deeper understanding of the cell type-specific roles played by writers, erasers, and readers of chromatin modifications in the diabetic vasculature. This review details a current perspective of epigenetic mechanisms of macrovascular disease in diabetes mellitus and highlights recent key descriptions of chromatinized changes associated with persistent gene expression in endothelial, smooth muscle, and circulating immune cells relevant to atherosclerosis. Furthermore, we discuss the challenges associated with pharmacological targeting of epigenetic networks to correct abnormal or deregulated gene expression as a strategy to alleviate the clinical burden of diabetic cardiovascular disease.
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Affiliation(s)
- Samuel T Keating
- From the Epigenetics in Human Health and Disease Laboratory (S.T.K., A.E.-O.) and Epigenomics Profiling Facility (A.E.-O.), Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia; Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (J.P.); Department of Pathology, The University of Melbourne, Victoria, Australia (A.E.-O.); and Central Clinical School, Department of Medicine, Monash University, Victoria, Australia (A.E.-O.)
| | - Jorge Plutzky
- From the Epigenetics in Human Health and Disease Laboratory (S.T.K., A.E.-O.) and Epigenomics Profiling Facility (A.E.-O.), Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia; Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (J.P.); Department of Pathology, The University of Melbourne, Victoria, Australia (A.E.-O.); and Central Clinical School, Department of Medicine, Monash University, Victoria, Australia (A.E.-O.)
| | - Assam El-Osta
- From the Epigenetics in Human Health and Disease Laboratory (S.T.K., A.E.-O.) and Epigenomics Profiling Facility (A.E.-O.), Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia; Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (J.P.); Department of Pathology, The University of Melbourne, Victoria, Australia (A.E.-O.); and Central Clinical School, Department of Medicine, Monash University, Victoria, Australia (A.E.-O.).
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45
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Metabolism and chromatin dynamics in health and disease. Mol Aspects Med 2017; 54:1-15. [DOI: 10.1016/j.mam.2016.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 09/22/2016] [Accepted: 09/27/2016] [Indexed: 01/04/2023]
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46
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Khan AW, Ziemann M, Corcoran SJ, K N H, Okabe J, Rafehi H, Maxwell SS, Esler MD, El-Osta A. NET silencing by let-7i in postural tachycardia syndrome. JCI Insight 2017; 2:e90183. [PMID: 28352654 DOI: 10.1172/jci.insight.90183] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
While strongly implicated in postural tachycardia syndrome (POTS), considerable controversy exists regarding norepinephrine transporter (NET) loss of function. POTS is characterized by the clinical symptoms of orthostatic intolerance, lightheadedness, tachycardia, and syncope or near syncope with upright posture. Abnormal sympathetic nervous system activity is typical, of a type which suggests dysfunction of the NET, with evidence that the gene responsible is under tight epigenetic control. Using RNA of isolated chromatin combined with massive parallel sequencing (RICh-seq) we show that let-7i miRNA suppresses NET by methyl-CpG-binding protein 2 (MeCP2). Vorinostat restores epigenetic control and NET expression in leukocytes derived from POTS participants.
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Affiliation(s)
- Abdul Waheed Khan
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark Ziemann
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Susan J Corcoran
- Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Harikrishnan K N
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jun Okabe
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Haloom Rafehi
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Scott S Maxwell
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Murray D Esler
- Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
| | - Assam El-Osta
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia.,Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia.,Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
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47
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The pro-inflammatory signalling regulator Stat4 promotes vasculogenesis of great vessels derived from endothelial precursors. Nat Commun 2017; 8:14640. [PMID: 28256502 PMCID: PMC5338034 DOI: 10.1038/ncomms14640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 01/17/2017] [Indexed: 01/05/2023] Open
Abstract
Vasculogenic defects of great vessels (GVs) are a major cause of congenital cardiovascular diseases. However, genetic regulators of endothelial precursors in GV vasculogenesis remain largely unknown. Here we show that Stat4, a transcription factor known for its regulatory role of pro-inflammatory signalling, promotes GV vasculogenesis in zebrafish. We find stat4 transcripts highly enriched in nkx2.5+ endothelial precursors in the pharynx and demonstrate that genetic ablation of stat4 causes stenosis of pharyngeal arch arteries (PAAs) by suppressing PAAs 3–6 angioblast development. We further show that stat4 is a downstream target of nkx2.5 and that it autonomously promotes proliferation of endothelial precursors of the mesoderm. Mechanistically, stat4 regulates the emerging PAA angioblasts by inhibiting the expression of hdac3 and counteracting the effect of stat1a. Altogether, our study establishes a role for Stat4 in zebrafish great vessel development, and suggests that Stat4 may serve as a therapeutic target for GV defects. Stat4 is a transcription factor known to regulate pro-inflammatory signalling. Here, Meng et al. show that Stat4 is not only regulating inflammation but it is also crucial for great vessels development and endothelial precursor proliferation in zebrafish, by inhibiting the expression of hdac3 and counteracting the effect of Stat1a.
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48
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Hu L, Yu Y, Huang H, Fan H, Hu L, Yin C, Li K, Fulton DJR, Chen F. Epigenetic Regulation of Interleukin 6 by Histone Acetylation in Macrophages and Its Role in Paraquat-Induced Pulmonary Fibrosis. Front Immunol 2017; 7:696. [PMID: 28194150 PMCID: PMC5276821 DOI: 10.3389/fimmu.2016.00696] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 12/28/2016] [Indexed: 12/29/2022] Open
Abstract
Overexpression of interleukin 6 (IL-6) has been proposed to contribute to pulmonary fibrosis and other fibrotic diseases. However, the regulatory mechanisms and the role of IL-6 in fibrosis remain poorly understood. Epigenetics refers to alterations of gene expression without changes in the DNA sequence. Alternation of chromatin accessibility by histone acetylation acts as a critical epigenetic mechanism to regulate various gene transcriptions. The goal of this study was to determine the impact of IL-6 in paraquat (PQ)-induced pulmonary fibrosis and to explore whether the epigenetic regulations may play a role in transcriptional regulation of IL-6. In PQ-treated lungs and macrophages, we found that the mRNA and protein expression of IL-6 was robustly increased in a time-dependent and a dose-dependent manner. Our data demonstrated that PQ-induced IL-6 expression in macrophages plays a central role in pulmonary fibrosis through enhanced epithelial-to-mesenchymal transition (EMT). IL-6 expression and its role to enhance PQ-induced pulmonary fibrosis were increased by histone deacetylase (HDAC) inhibition and prevented by histone acetyltransferase (HAT) inhibition. In addition, the ability of CRISPR-ON transcription activation system (CRISPR-ON) to promote transcription of IL-6 was enhanced by HDAC inhibitor and blocked by HAT inhibitor. Chromatin immunoprecipitation experiments revealed that HDAC inhibitor increased histones activation marks H3K4me3 and H3K9ac at IL-6 promoter regions. In conclusion, IL-6 functioning through EMT in PQ-induced pulmonary fibrosis was regulated dynamically by HDAC and HAT both in vitro and in vivo via epigenetically regulating chromatin accessibility.
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Affiliation(s)
- Lingli Hu
- Department of Forensic Medicine, Nanjing Medical University , Nanjing , China
| | - Yanfang Yu
- Department of Forensic Medicine, Nanjing Medical University , Nanjing , China
| | - Huijie Huang
- Department of Forensic Medicine, Nanjing Medical University , Nanjing , China
| | - Hanting Fan
- Department of Forensic Medicine, Nanjing Medical University , Nanjing , China
| | - Li Hu
- Department of Forensic Medicine, Nanjing Medical University , Nanjing , China
| | - Caiyong Yin
- Department of Forensic Medicine, Nanjing Medical University , Nanjing , China
| | - Kai Li
- Department of Forensic Medicine, Nanjing Medical University , Nanjing , China
| | - David J R Fulton
- Vascular Biology Center, Augusta University, Augusta, GA, USA; Department of Pharmacology, Augusta University, Augusta, GA, USA
| | - Feng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, China; Vascular Biology Center, Augusta University, Augusta, GA, USA
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Wu Y, Leng Y, Meng Q, Xue R, Zhao B, Zhan L, Xia Z. Suppression of Excessive Histone Deacetylases Activity in Diabetic Hearts Attenuates Myocardial Ischemia/Reperfusion Injury via Mitochondria Apoptosis Pathway. J Diabetes Res 2017; 2017:8208065. [PMID: 28191472 PMCID: PMC5278197 DOI: 10.1155/2017/8208065] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 11/11/2016] [Accepted: 11/22/2016] [Indexed: 02/06/2023] Open
Abstract
Background. Histone deacetylases (HDACs) play a pivotal role in signaling modification and gene transcriptional regulation that are essential for cardiovascular pathophysiology. Diabetic hearts with higher HDACs activity were more vulnerable to myocardial ischemia/reperfusion (MI/R) injury compared with nondiabetic hearts. We are curious about whether suppression of excessive HDACs activity in diabetic heart protects against MI/R injury. Methods. Diabetic rats were subjected to 45 min of ischemia, followed by 3 h of reperfusion. H9C2 cardiomyocytes were exposed to high glucose for 24 h, followed by 4 h of hypoxia and 2 h of reoxygenation (H/R). Results. Both MI/R injury and diabetes mellitus elevated myocardium HDACs activity. MI/R induced apoptotic cell death was significantly decreased in diabetic rats treated with HDACs inhibitor trichostatin A (TSA). TSA administration markedly moderated dissipation of mitochondrial membrane potential, protected the integrity of mitochondrial permeability transition pore (mPTP), and decreased cell apoptosis. Notably, cotreatment with Akt inhibitor partly or absolutely inhibited the protective effect of TSA in vivo and in vitro. Furthermore, TSA administration activated Akt/Foxo3a pathway, leading to Foxo3a cytoplasm translocation and attenuation proapoptosis protein Bim expression. Conclusions. Both diabetes mellitus and MI/R injury increased cardiac HDACs activity. Suppression of HDACs activity triggered protective effects against MI/R and H/R injury under hyperglycemia conditions through Akt-modulated mitochondrial apoptotic pathways via Foxo3a/Bim.
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Affiliation(s)
- Yang Wu
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province 430060, China
| | - Yan Leng
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province 430060, China
| | - Qingtao Meng
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province 430060, China
| | - Rui Xue
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province 430060, China
| | - Bo Zhao
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province 430060, China
| | - Liying Zhan
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province 430060, China
| | - Zhongyuan Xia
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province 430060, China
- *Zhongyuan Xia:
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Qi Y, Wang D, Wang D, Jin T, Yang L, Wu H, Li Y, Zhao J, Du F, Song M, Wang R. HEDD: the human epigenetic drug database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw159. [PMID: 28025347 PMCID: PMC5199199 DOI: 10.1093/database/baw159] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/06/2016] [Accepted: 11/06/2016] [Indexed: 01/08/2023]
Abstract
Epigenetic drugs are chemical compounds that target disordered post-translational modification of histone proteins and DNA through enzymes, and the recognition of these changes by adaptor proteins. Epigenetic drug-related experimental data such as gene expression probed by high-throughput sequencing, co-crystal structure probed by X-RAY diffraction and binding constants probed by bio-assay have become widely available. The mining and integration of multiple kinds of data can be beneficial to drug discovery and drug repurposing. HEMD and other epigenetic databases store comprehensively epigenetic data where users can acquire segmental information of epigenetic drugs. However, some data types such as high-throughput datasets are not provide by these databases and they do not support flexible queries for epigenetic drug-related experimental data. Therefore, in reference to HEMD and other epigenetic databases, we developed a relatively comprehensive database for human epigenetic drugs. The human epigenetic drug database (HEDD) focuses on the storage and integration of epigenetic drug datasets obtained from laboratory experiments and manually curated information. The latest release of HEDD incorporates five kinds of datasets: (i) drug, (ii) target, (iii) disease, (vi) high-throughput and (v) complex. In order to facilitate data extraction, flexible search options were built in HEDD, which allowed an unlimited condition query for specific kinds of datasets using drug names, diseases and experiment types. Database URL:http://hedds.org/
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Affiliation(s)
- Yunfeng Qi
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Dadong Wang
- Department of Computer Science and Technology, Computer College, Jilin Normal University, Siping, China
| | - Daying Wang
- Department of Social Physical Education, Physical Education College, Jilin Normal University, Siping, China
| | - Taicheng Jin
- Department of Biotechnology, School of Life Science, Jilin Normal University, Siping, China
| | - Liping Yang
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Hui Wu
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Yaoyao Li
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Jing Zhao
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Fengping Du
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Mingxia Song
- Department of Bioscience, School of Life Science, Jilin Normal University, Siping, China
| | - Renjun Wang
- Department of Biotechnology, School of Life Science, Jilin Normal University, Siping, China
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