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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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2
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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: 32] [Impact Index Per Article: 16.0] [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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3
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Daks A, Shuvalov O, Fedorova O, Petukhov A, Lezina L, Zharova A, Baidyuk E, Khudiakov A, Barlev NA. p53-Independent Effects of Set7/9 Lysine Methyltransferase on Metabolism of Non-Small Cell Lung Cancer Cells. Front Oncol 2021; 11:706668. [PMID: 34692483 PMCID: PMC8528242 DOI: 10.3389/fonc.2021.706668] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
Set7/9 is a lysine-specific methyltransferase, which regulates the functioning of both the histone and non-histone substrates, thereby significantly affecting the global gene expression landscape. Using microarray expression profiling, we have identified several key master regulators of metabolic networks, including c-Myc, that were affected by Set7/9 status. Consistent with this observation, c-Myc transcriptional targets-genes encoding the glycolytic enzymes hexokinase (HK2), aldolase (ALDOB), and lactate dehydrogenase (LDHA)-were upregulated upon Set7/9 knockdown (Set7/9KD). Importantly, we showed the short hairpin RNA (shRNA)-mediated attenuation of Set7/9 augmented c-Myc, GLUT1, HK2, ALDOA, and LDHA expression in non-small cell lung cancer (NSCLC) cell lines, not only at the transcriptional but also at the protein level. In line with this observation, Set7/9KD significantly augmented the membrane mitochondrial potential (MMP), glycolysis, respiration, and the proliferation rate of NSCLC cells. Importantly, all these effects of Set7/9 on cell metabolism were p53-independent. Bioinformatic analysis has shown a synergistic impact of Set7/9 together with either GLUT1, HIF1A, HK2, or LDHA on the survival of lung cancer patients. Based on these evidence, we hypothesize that Set7/9 can be an important regulator of energy metabolism in NSCLC.
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Affiliation(s)
- Alexandra Daks
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| | - Oleg Shuvalov
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| | - Olga Fedorova
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| | - Alexey Petukhov
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia.,Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, St Petersburg, Russia
| | - Larissa Lezina
- Regulation of Cell Signaling Laboratory, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Arsenia Zharova
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| | - Ekaterina Baidyuk
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| | - Alexander Khudiakov
- Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, St Petersburg, Russia
| | - Nickolai A Barlev
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia.,Regulation of Cell Signaling Laboratory, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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4
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Keating ST, Groh L, van der Heijden CDCC, Rodriguez H, Dos Santos JC, Fanucchi S, Okabe J, Kaipananickal H, van Puffelen JH, Helder L, Noz MP, Matzaraki V, Li Y, de Bree LCJ, Koeken VACM, Moorlag SJCFM, Mourits VP, Domínguez-Andrés J, Oosting M, Bulthuis EP, Koopman WJH, Mhlanga M, El-Osta A, Joosten LAB, Netea MG, Riksen NP. The Set7 Lysine Methyltransferase Regulates Plasticity in Oxidative Phosphorylation Necessary for Trained Immunity Induced by β-Glucan. Cell Rep 2021; 31:107548. [PMID: 32320649 PMCID: PMC7184679 DOI: 10.1016/j.celrep.2020.107548] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 01/31/2020] [Accepted: 03/31/2020] [Indexed: 12/25/2022] Open
Abstract
Trained immunity confers a sustained augmented response of innate immune cells to a secondary challenge, via a process dependent on metabolic and transcriptional reprogramming. Because of its previous associations with metabolic and transcriptional memory, as well as the importance of H3 histone lysine 4 monomethylation (H3K4me1) to innate immune memory, we hypothesize that the Set7 methyltransferase has an important role in trained immunity induced by β-glucan. Using pharmacological studies of human primary monocytes, we identify trained immunity-specific immunometabolic pathways regulated by Set7, including a previously unreported H3K4me1-dependent plasticity in the induction of oxidative phosphorylation. Recapitulation of β-glucan training in vivo additionally identifies Set7-dependent changes in gene expression previously associated with the modulation of myelopoiesis progenitors in trained immunity. By revealing Set7 as a key regulator of trained immunity, these findings provide mechanistic insight into sustained metabolic changes and underscore the importance of characterizing regulatory circuits of innate immune memory. Set7 regulates enhanced cytokine production in trained immunity in vitro Set7 knockout mice are unable to mount trained immunity against endotoxin challenge Set7 modulates cellular respiration in β-glucan-trained macrophages Set7-dependent histone methylation regulates MDH2 and SDHB in trained cells
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Affiliation(s)
- Samuel T Keating
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Laszlo Groh
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Charlotte D C C van der Heijden
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hanah Rodriguez
- Epigenetics in Human Health and Disease, Department of Diabetes, Monash University, Melbourne, VIC, Australia
| | - Jéssica C Dos Santos
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Stephanie Fanucchi
- Division of Chemical, Systems and Synthetic Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Gene Expression and Biophysics Group, CSIR Biosciences, Pretoria, South Africa
| | - Jun Okabe
- Epigenetics in Human Health and Disease, Department of Diabetes, Monash University, Melbourne, VIC, Australia
| | - Harikrishnan Kaipananickal
- Epigenetics in Human Health and Disease, Department of Diabetes, Monash University, Melbourne, VIC, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Jelmer H van Puffelen
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands; Department for Health Evidence, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leonie Helder
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marlies P Noz
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Vasiliki Matzaraki
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yang Li
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands; Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine, Helmholtz Centre for Infection Research, Hannover Medical School, 30625 Hannover, Germany
| | - L Charlotte J de Bree
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands; Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark; Odense Patient Data Explorative Network, University of Southern Denmark/Odense University Hospital, Odense, Denmark
| | - Valerie A C M Koeken
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Simone J C F M Moorlag
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Vera P Mourits
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jorge Domínguez-Andrés
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elianne P Bulthuis
- Department of Biochemistry, Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Werner J H Koopman
- Department of Biochemistry, Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Musa Mhlanga
- Division of Chemical, Systems and Synthetic Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Assam El-Osta
- Epigenetics in Human Health and Disease, Department of Diabetes, Monash University, Melbourne, VIC, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia; Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong City, Hong Kong SAR
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute of 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
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands; Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Niels P Riksen
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands.
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5
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Kaspi A, Ziemann M. mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data. BMC Genomics 2020; 21:447. [PMID: 32600408 PMCID: PMC7325150 DOI: 10.1186/s12864-020-06856-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 06/19/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Inference of biological pathway activity via gene set enrichment analysis is frequently used in the interpretation of clinical and other omics data. With the proliferation of new omics profiling approaches and ever-growing size of data sets generated, there is a lack of tools available to perform and visualise gene set enrichments in analyses involving multiple contrasts. RESULTS To address this, we developed mitch, an R package for multi-contrast gene set enrichment analysis. It uses a rank-MANOVA statistical approach to identify sets of genes that exhibit joint enrichment across multiple contrasts. Its unique visualisation features enable the exploration of enrichments in up to 20 contrasts. We demonstrate the utility of mitch with case studies spanning multi-contrast RNA expression profiling, integrative multi-omics, tool benchmarking and single-cell RNA sequencing. Using simulated data we show that mitch has similar accuracy to state of the art tools for single-contrast enrichment analysis, and superior accuracy in identifying multi-contrast enrichments. CONCLUSION mitch is a versatile tool for rapidly and accurately identifying and visualising gene set enrichments in multi-contrast omics data. Mitch is available from Bioconductor ( https://bioconductor.org/packages/mitch ).
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Affiliation(s)
- Antony Kaspi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Mark Ziemann
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia.
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Silencing Lysine-Specific Histone Demethylase 1 (LSD1) Causes Increased HP1-Positive Chromatin, Stimulation of DNA Repair Processes, and Dysregulation of Proliferation by Chk1 Phosphorylation in Human Endothelial Cells. Cells 2019; 8:cells8101212. [PMID: 31591366 PMCID: PMC6829479 DOI: 10.3390/cells8101212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/21/2019] [Accepted: 09/30/2019] [Indexed: 12/13/2022] Open
Abstract
The methylation of histone lysine residues modifies chromatin conformation and regulates the expression of genes implicated in cell metabolism. Lysine-specific demethylase 1 (LSD1) is a flavin-dependent monoamine oxidase that can demethylate mono- and dimethylated histone lysines 4 and 9 (H3K4 and H3K9). The removal of methyl groups from the lysine residues of histone and non-histone proteins was found to be an important regulatory factor of cell proliferation. However, its role has not been fully elucidated. In this study, we assessed LSD1-mediated cell cycle progression using a human endothelial cell model. The short hairpin RNA knockdown of LSD1 inhibits the G2/M phase of cell cycle progression by checkpoint kinase 1 (Chk1) phosphorylation (S137). We observed elevated DNA damage, which was consistent with the increased detection of double-strand breaks as well as purines and pyrimidines oxidation, which accompanied the activation of ATR/ATRIP signaling by H2AXS139 phosphorylation. The irreversible pharmacological inhibition of LSD1 by 2-phenylcyclopropylamine (2-PCPA) inactivated its enzymatic activity, causing significant changes in heterochromatin and euchromatin conformation assessed by chromatin assembly factor 1 subunit A (CAF1A) and heterochromatin protein 1 isoform α and γ (HP1α/γ) immunofluorescence analysis. We conclude that the knockdown of LSD1 in endothelial cells leads to increased HP1-positive chromatin, the stimulation of DNA repair processes, and the dysregulation of proliferation machinery.
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Xu S, Kamato D, Little PJ, Nakagawa S, Pelisek J, Jin ZG. Targeting epigenetics and non-coding RNAs in atherosclerosis: from mechanisms to therapeutics. Pharmacol Ther 2019; 196:15-43. [PMID: 30439455 PMCID: PMC6450782 DOI: 10.1016/j.pharmthera.2018.11.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Atherosclerosis, the principal cause of cardiovascular death worldwide, is a pathological disease characterized by fibro-proliferation, chronic inflammation, lipid accumulation, and immune disorder in the vessel wall. As the atheromatous plaques develop into advanced stage, the vulnerable plaques are prone to rupture, which causes acute cardiovascular events, including ischemic stroke and myocardial infarction. Emerging evidence has suggested that atherosclerosis is also an epigenetic disease with the interplay of multiple epigenetic mechanisms. The epigenetic basis of atherosclerosis has transformed our knowledge of epigenetics from an important biological phenomenon to a burgeoning field in cardiovascular research. Here, we provide a systematic and up-to-date overview of the current knowledge of three distinct but interrelated epigenetic processes (including DNA methylation, histone methylation/acetylation, and non-coding RNAs), in atherosclerotic plaque development and instability. Mechanistic and conceptual advances in understanding the biological roles of various epigenetic modifiers in regulating gene expression and functions of endothelial cells (vascular homeostasis, leukocyte adhesion, endothelial-mesenchymal transition, angiogenesis, and mechanotransduction), smooth muscle cells (proliferation, migration, inflammation, hypertrophy, and phenotypic switch), and macrophages (differentiation, inflammation, foam cell formation, and polarization) are discussed. The inherently dynamic nature and reversibility of epigenetic regulation, enables the possibility of epigenetic therapy by targeting epigenetic "writers", "readers", and "erasers". Several Food Drug Administration-approved small-molecule epigenetic drugs show promise in pre-clinical studies for the treatment of atherosclerosis. Finally, we discuss potential therapeutic implications and challenges for future research involving cardiovascular epigenetics, with an aim to provide a translational perspective for identifying novel biomarkers of atherosclerosis, and transforming precision cardiovascular research and disease therapy in modern era of epigenetics.
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Affiliation(s)
- Suowen Xu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
| | - Danielle Kamato
- School of Pharmacy, The University of Queensland, Wooloongabba, QLD 4102, Australia; Department of Pharmacy, Xinhua College of Sun Yat-sen University, Guangzhou 510520, China
| | - Peter J Little
- School of Pharmacy, The University of Queensland, Wooloongabba, QLD 4102, Australia; Department of Pharmacy, Xinhua College of Sun Yat-sen University, Guangzhou 510520, China
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Jaroslav Pelisek
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Germany
| | - Zheng Gen Jin
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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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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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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10
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Keating ST, van Diepen JA, Riksen NP, El-Osta A. Epigenetics in diabetic nephropathy, immunity and metabolism. Diabetologia 2018; 61:6-20. [PMID: 29128937 PMCID: PMC6448927 DOI: 10.1007/s00125-017-4490-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/22/2017] [Indexed: 01/01/2023]
Abstract
When it comes to the epigenome, there is a fine line between clarity and confusion-walk that line and you will discover another fascinating level of transcription control. With the genetic code representing the cornerstone of rules for information that is encoded to proteins somewhere above the genome level there is a set of rules by which chemical information is also read. These epigenetic modifications show a different side of the genetic code that is diverse and regulated, hence modifying genetic transcription transiently, ranging from short- to long-term alterations. While this complexity brings exquisite control it also poses a formidable challenge to efforts to decode mechanisms underlying complex disease. Recent technological and computational advances have improved unbiased acquisition of epigenomic patterns to improve our understanding of the complex chromatin landscape. Key to resolving distinct chromatin signatures of diabetic complications is the identification of the true physiological targets of regulatory proteins, such as reader proteins that recognise, writer proteins that deposit and eraser proteins that remove specific chemical moieties. But how might a diverse group of proteins regulate the diabetic landscape from an epigenomic perspective? Drawing from an ever-expanding compendium of experimental and clinical studies, this review details the current state-of-play and provides a perspective of chromatin-dependent mechanisms implicated in diabetic complications, with a special focus on diabetic nephropathy. We hypothesise a codified signature of the diabetic epigenome and provide examples of prime candidates for chemical modification. As for the pharmacological control of epigenetic marks, we explore future strategies to expedite and refine the search for clinically relevant discoveries. We also consider the challenges associated with therapeutic strategies targeting epigenetic pathways.
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Affiliation(s)
- Samuel T Keating
- Department of Internal Medicine, Department of Internal Medicine (463), Radboud University Medical Center, Nijmegen, PO Box 9101, 6500 HB, Nijmegen, the Netherlands.
| | - Janna A van Diepen
- Department of Internal Medicine, Department of Internal Medicine (463), Radboud University Medical Center, Nijmegen, PO Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Niels P Riksen
- Department of Internal Medicine, Department of Internal Medicine (463), Radboud University Medical Center, Nijmegen, PO Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Assam El-Osta
- Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC, 3004, Australia.
- Department of Pathology, The University of Melbourne, Parkville, VIC, Australia.
- 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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11
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Keating ST, Riksen NP, Netea MG. Planarians SET New Paths for Innate Immune Memory. EBioMedicine 2017; 20:7-8. [PMID: 28487051 PMCID: PMC5478199 DOI: 10.1016/j.ebiom.2017.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 05/04/2017] [Indexed: 12/31/2022] Open
Affiliation(s)
- Samuel T Keating
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Niels P Riksen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany.
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12
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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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13
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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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14
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15
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Current perspectives in Set7 mediated stem cell differentiation. Noncoding RNA 2016; 2:ncrna2040014. [PMID: 29657272 PMCID: PMC5831927 DOI: 10.3390/ncrna2040014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 11/18/2016] [Accepted: 11/23/2016] [Indexed: 12/14/2022] Open
Abstract
Set7 is a key regulatory enzyme involved in the methylation of lysine residues of histone and non-histone proteins. This lysine methyltransferase is induced during stem cell differentiation and regulates lineage specific gene transcription and cell fate. In this article we discuss recent experimental evidence identifying regulatory targets under the control of Set7 as well as emerging evidence of regulation in stem cell differentiation. Furthermore, we discuss the function of non-coding RNAs regulated by Set7 implicated in cell plasticity.
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16
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Tuano NK, Okabe J, Ziemann M, Cooper ME, El-Osta A. Set7 mediated interactions regulate transcriptional networks in embryonic stem cells. Nucleic Acids Res 2016; 44:9206-9217. [PMID: 27439711 PMCID: PMC5100561 DOI: 10.1093/nar/gkw621] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/01/2016] [Indexed: 12/17/2022] Open
Abstract
Histone methylation by lysine methyltransferase enzymes regulate the expression of genes implicated in lineage specificity and cellular differentiation. While it is known that Set7 catalyzes mono-methylation of histone and non-histone proteins, the functional importance of this enzyme in stem cell differentiation remains poorly understood. We show Set7 expression is increased during mouse embryonic stem cell (mESC) differentiation and is regulated by the pluripotency factors, Oct4 and Sox2. Transcriptional network analyses reveal smooth muscle (SM) associated genes are subject to Set7-mediated regulation. Furthermore, pharmacological inhibition of Set7 activity confirms this regulation. We observe Set7-mediated modification of serum response factor (SRF) and mono-methylation of histone H4 lysine 4 (H3K4me1) regulate gene expression. We conclude the broad substrate specificity of Set7 serves to control key transcriptional networks in embryonic stem cells.
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Affiliation(s)
- Natasha K Tuano
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
| | - Jun Okabe
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia .,Faculty of Medicine, Nursing and Health Sciences, Monash University, Victoria, Australia
| | - Mark Ziemann
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia.,Epigenomic Profiling Facility, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
| | - Mark E Cooper
- Junvenile Diabetes Research Foundation (JDRF) Danielle Alberti Centre for Diabetic Complications, Diabetes Division, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia .,Faculty of Medicine, Nursing and Health Sciences, Monash University, Victoria, Australia.,Epigenomic Profiling Facility, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia.,Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
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17
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Mathiyalagan P, Keating ST, Al-Hasani K, El-Osta A. Epigenetic-mediated reprogramming of pancreatic endocrine cells. Antioxid Redox Signal 2015; 22:1483-95. [PMID: 25621632 DOI: 10.1089/ars.2014.6103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
SIGNIFICANCE Type 1 diabetes (T1D) results from cell-mediated autoimmune destruction of insulin-secreting pancreatic beta cells (β-cells). In the context of T1D, the scarcity of organ donors has driven research to alternate sources of functionally competent, insulin-secreting β-cells as substitute for donor islets to meet the clinical need for transplantation therapy. RECENT ADVANCES Experimental evidence of an inherent plasticity of pancreatic cells has fuelled interest in in vivo regeneration of β-cells. Transcriptional modulation and direct reprogramming of noninsulin secreting pancreatic α-cells to functionally mimic insulin-secreting β-cells is one of the promising avenues to the treatment of diabetes. Recent studies now show that adult progenitor and glucagon(+) α-cells can be converted into β-like cells in vivo, as a result of specific activation of the Pax4 gene in α-cells and curing diabetes in preclinical models. CRITICAL ISSUES The challenge now is to understand the precise developmental transitions mediated by endocrine transcription factors and co-regulatory determinants responsible for pancreatic function and repair. FUTURE DIRECTIONS Epigenetic-mediated regulation of transcription factor binding in pancreatic α-cells by specific drugs to direct reprogramming into functional insulin producing cells could be of potential innovative therapy for the treatment of T1D.
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Affiliation(s)
- Prabhu Mathiyalagan
- 1 Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct , Melbourne, Australia
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18
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ZHOU JUN, XIE MING, SHI YING, LUO BAIHUA, GONG GUANGHUI, LI JUANNI, WANG JUNPU, ZHAO WENJIAN, ZI YUAN, WU XIAOYING, WEN JIFANG. MicroRNA-153 functions as a tumor suppressor by targeting SET7 and ZEB2 in ovarian cancer cells. Oncol Rep 2015; 34:111-20. [DOI: 10.3892/or.2015.3952] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/31/2015] [Indexed: 11/05/2022] Open
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19
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Abstract
Despite the wealth of pre-clinical support for a role for reactive oxygen and nitrogen species (ROS/RNS) in the aetiology of diabetic complications, enthusiasm for antioxidant therapeutic approaches has been dampened by less favourable outcomes in large clinical trials. This has necessitated a re-evaluation of pre-clinical evidence and a more rational approach to antioxidant therapy. The present review considers current evidence, from both pre-clinical and clinical studies, to address the benefits of antioxidant therapy. The main focus of the present review is on the effects of direct targeting of ROS-producing enzymes, the bolstering of antioxidant defences and mechanisms to improve nitric oxide availability. Current evidence suggests that a more nuanced approach to antioxidant therapy is more likely to yield positive reductions in end-organ injury, with considerations required for the types of ROS/RNS involved, the timing and dosage of antioxidant therapy, and the selective targeting of cell populations. This is likely to influence future strategies to lessen the burden of diabetic complications such as diabetes-associated atherosclerosis, diabetic nephropathy and diabetic retinopathy.
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20
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Maganti AV, Maier B, Tersey SA, Sampley ML, Mosley AL, Özcan S, Pachaiyappan B, Woster PM, Hunter CS, Stein R, Mirmira RG. Transcriptional activity of the islet β cell factor Pdx1 is augmented by lysine methylation catalyzed by the methyltransferase Set7/9. J Biol Chem 2015; 290:9812-22. [PMID: 25713082 DOI: 10.1074/jbc.m114.616219] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 12/21/2022] Open
Abstract
The transcription factor Pdx1 is crucial to islet β cell function and regulates target genes in part through interaction with coregulatory factors. Set7/9 is a Lys methyltransferase that interacts with Pdx1. Here we tested the hypothesis that Lys methylation of Pdx1 by Set7/9 augments Pdx1 transcriptional activity. Using mass spectrometry and mutational analysis of purified proteins, we found that Set7/9 methylates the N-terminal residues Lys-123 and Lys-131 of Pdx1. Methylation of these residues occurred only in the context of intact, full-length Pdx1, suggesting a specific requirement of secondary and/or tertiary structural elements for catalysis by Set7/9. Immunoprecipitation assays and mass spectrometric analysis using β cells verified Lys methylation of endogenous Pdx1. Cell-based luciferase reporter assays using wild-type and mutant transgenes revealed a requirement of Pdx1 residue Lys-131, but not Lys-123, for transcriptional augmentation by Set7/9. Lys-131 was not required for high-affinity interactions with DNA in vitro, suggesting that its methylation likely enhances post-DNA binding events. To define the role of Set7/9 in β cell function, we generated mutant mice in which the gene encoding Set7/9 was conditionally deleted in β cells (Set(Δ)β). Set(Δ)β mice exhibited glucose intolerance similar to Pdx1-deficient mice, and their isolated islets showed impaired glucose-stimulated insulin secretion with reductions in expression of Pdx1 target genes. Our results suggest a previously unappreciated role for Set7/9-mediated methylation in the maintenance of Pdx1 activity and β cell function.
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Affiliation(s)
| | - Bernhard Maier
- Department of Pediatrics and the Herman B. Wells Center for Pediatric Research
| | - Sarah A Tersey
- Department of Pediatrics and the Herman B. Wells Center for Pediatric Research
| | - Megan L Sampley
- the Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40536
| | | | - Sabire Özcan
- the Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40536
| | - Boobalan Pachaiyappan
- the Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, South Carolina 29425, and
| | - Patrick M Woster
- the Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, South Carolina 29425, and
| | - Chad S Hunter
- the Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Roland Stein
- the Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Raghavendra G Mirmira
- From the Department of Cellular and Integrative Physiology, Department of Pediatrics and the Herman B. Wells Center for Pediatric Research, Department of Biochemistry and Molecular Biology, and Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana 46202,
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21
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Abstract
The molecular signatures of epigenetic regulation and chromatin architectures are fundamental to genetically determined biological processes. Covalent and post-translational chemical modification of the chromatin template can sensitize the genome to changing environmental conditions to establish diverse functional states. Recent interest and research focus surrounds the direct connections between metabolism and chromatin dynamics, which now represents an important conceptual challenge to explain many aspects of metabolic dysfunction. Several components of the epigenetic machinery require intermediates of cellular metabolism for enzymatic function. Furthermore, changes to intracellular metabolism can alter the expression of specific histone methyltransferases and acetyltransferases conferring widespread variations in epigenetic modification patterns. Specific epigenetic influences of dietary glucose and lipid consumption, as well as undernutrition, are observed across numerous organs and pathways associated with metabolism. Studies have started to define the chromatin-dependent mechanisms underlying persistent and pathophysiological changes induced by altered metabolism. Importantly, numerous recent studies demonstrate that gene regulation underlying phenotypic determinants of adult metabolic health is influenced by maternal and early postnatal diet. These emerging concepts open new perspectives to combat the rising global epidemic of metabolic disorders.
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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 (S.T.K., A.E.-O.), Baker IDI Heart & Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia; Department of Pathology, The University of Melbourne, Victoria, Australia (A.E.-O.); and Central Clinical School, Department of Medicine, Monash University, Melbourne, 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 (S.T.K., A.E.-O.), Baker IDI Heart & Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia; Department of Pathology, The University of Melbourne, Victoria, Australia (A.E.-O.); and Central Clinical School, Department of Medicine, Monash University, Melbourne, Victoria, Australia (A.E.-O.)
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