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Wu L, Zhu X, Luo C, Zhao Y, Pan S, Shi K, Chen Y, Qiu J, Shen Z, Guo J, Jie W. Mechanistic role of RND3-regulated IL33/ST2 signaling on cardiomyocyte senescence. Life Sci 2024; 348:122701. [PMID: 38724005 DOI: 10.1016/j.lfs.2024.122701] [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: 03/20/2024] [Revised: 04/23/2024] [Accepted: 05/05/2024] [Indexed: 05/12/2024]
Abstract
Hyperinflammatory responses are pivotal in the cardiomyocyte senescence pathophysiology, with IL33 serving as a crucial pro-inflammatory mediator. Our previous findings highlighted RND3's suppressive effect on IL33 expression. This study aims to explore the role of RND3 in IL33/ST2 signaling activation and in cardiomyocyte senescence. Intramyocardial injection of exogenous IL33 reduces the ejection fraction and fractional shortening of rats, inducing the appearance of senescence-associated secretory phenotype (SASP) in myocardial tissues. Recombinant IL33 treatment of AC16 cardiomyocytes significantly upregulated expression of SASP factors like IL1α, IL6, and MCP1, and increased the p-p65/p65 ratio and proportions of SA-β-gal and γH2AX-positive cells. NF-κB inhibitor pyrrolidinedithiocarbamate ammonium (PDTC) and ST2 antibody astegolimab treatments mitigated above effects. RND3 gene knockout H9C2 cardiomyocytes using CRISPR/Cas9 technology upregulated IL33, ST2L, IL1α, IL6, and MCP1 levels, decreased sST2 levels, and increased SA-β-gal and γH2AX-positive cells. A highly possibility of binding between RND3 and IL33 proteins was showed by molecular docking and co-immunoprecipitation, and loss of RND3 attenuated ubiquitination mediated degradation of IL33; what's more, a panel of ubiquitination regulatory genes closely related to RND3 were screened using qPCR array. In contrast, RND3 overexpression in rats by injection of AAV9-CMV-RND3 particles inhibited IL33, ST2L, IL1α, IL6, and MCP1 expression in cardiac tissues, decreased serum IL33 levels, and increased sST2 levels. These results suggest that RND3 expression in cardiomyocytes modulates cell senescence by inhibiting the IL33/ST2/NF-κB signaling pathway, underscoring its potential as a therapeutic target in cardiovascular senescence.
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Affiliation(s)
- Linxu Wu
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, the First Affiliated Hospital, Hainan Medical University, Haikou 571199, P.R. China; Public Research Center of Hainan Medical University, Haikou 571199, P.R. China
| | - Xinglin Zhu
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, the First Affiliated Hospital, Hainan Medical University, Haikou 571199, P.R. China
| | - Cai Luo
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, the First Affiliated Hospital, Hainan Medical University, Haikou 571199, P.R. China
| | - Yangyang Zhao
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, the First Affiliated Hospital, Hainan Medical University, Haikou 571199, P.R. China
| | - Shanshan Pan
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, the First Affiliated Hospital, Hainan Medical University, Haikou 571199, P.R. China
| | - Kaijia Shi
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, the First Affiliated Hospital, Hainan Medical University, Haikou 571199, P.R. China
| | - Yan Chen
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, the First Affiliated Hospital, Hainan Medical University, Haikou 571199, P.R. China
| | - Jianmin Qiu
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, the First Affiliated Hospital, Hainan Medical University, Haikou 571199, P.R. China
| | - Zhihua Shen
- Department of Pathophysiology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang 524023, P.R. China.
| | - Junli Guo
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, the First Affiliated Hospital, Hainan Medical University, Haikou 571199, P.R. China.
| | - Wei Jie
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, the First Affiliated Hospital, Hainan Medical University, Haikou 571199, P.R. China.
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Zhang C, Meng Y, Han J. Emerging roles of mitochondrial functions and epigenetic changes in the modulation of stem cell fate. Cell Mol Life Sci 2024; 81:26. [PMID: 38212548 PMCID: PMC11072137 DOI: 10.1007/s00018-023-05070-6] [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: 11/01/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
Mitochondria serve as essential organelles that play a key role in regulating stem cell fate. Mitochondrial dysfunction and stem cell exhaustion are two of the nine distinct hallmarks of aging. Emerging research suggests that epigenetic modification of mitochondria-encoded genes and the regulation of epigenetics by mitochondrial metabolites have an impact on stem cell aging or differentiation. Here, we review how key mitochondrial metabolites and behaviors regulate stem cell fate through an epigenetic approach. Gaining insight into how mitochondria regulate stem cell fate will help us manufacture and preserve clinical-grade stem cells under strict quality control standards, contributing to the development of aging-associated organ dysfunction and disease.
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Affiliation(s)
- Chensong Zhang
- State Key Laboratory of Biotherapy and Cancer Center, Frontiers Science Center for Disease-Related Molecular Network, and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yang Meng
- State Key Laboratory of Biotherapy and Cancer Center, Frontiers Science Center for Disease-Related Molecular Network, and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, Frontiers Science Center for Disease-Related Molecular Network, and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Govender P, Ghai M, Okpeku M. Sex-specific DNA methylation: impact on human health and development. Mol Genet Genomics 2022; 297:1451-1466. [PMID: 35969270 DOI: 10.1007/s00438-022-01935-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022]
Abstract
Human evolution has shaped gender differences between males and females. Over the years, scientific studies have proposed that epigenetic modifications significantly influence sex-specific differences. The evolution of sex chromosomes with epigenetics as the driving force may have led to one sex being more adaptable than the other when exposed to various factors over time. Identifying and understanding sex-specific differences, particularly in DNA methylation, will help determine how each gender responds to factors, such as disease susceptibility, environmental exposure, brain development and neurodegeneration. From a medicine and health standpoint, sex-specific methylation studies have shed light on human disease severity, progression, and response to therapeutic intervention. Interesting findings in gender incongruent individuals highlight the role of genetic makeup in influencing DNA methylation differences. Sex-specific DNA methylation studies will empower the biotechnology and pharmaceutical industry with more knowledge to identify biomarkers, design and develop sex bias drugs leading to better treatment in men and women based on their response to different diseases.
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Affiliation(s)
- Priyanka Govender
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
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4
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Accelerated epigenetic aging and inflammatory/immunological profile (ipAGE) in patients with chronic kidney disease. GeroScience 2022; 44:817-834. [PMID: 35237926 DOI: 10.1007/s11357-022-00540-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/23/2022] [Indexed: 12/13/2022] Open
Abstract
Chronic kidney disease (CKD) is defined by a reduced estimated glomerular filtration rate (eGFR). This failure can be related to a phenotype of accelerated aging. In this work, we considered 76 patients with end-stage renal disease (ESRD) and 83 healthy controls. We concomitantly evaluated for the first time two measures that can be informative of the rate of aging, i.e., whole blood DNA methylation using the Illumina Infinium EPIC array and plasma levels of a selection of inflammatory/immunological proteins using multiplex immunoassays. First of all, we demonstrated accelerated aging in terms of the most common epigenetic age estimators in CKD patients. Moreover, we developed a new clock/predictor of age based on the inflammatory/immunological profile (ipAGE) and identified the inflammatory/immunological biomarkers differentially expressed between cases and controls. IpAGE appeared to be more sensitive than epigenetic clocks in quantifying the accelerated aging phenotype of ESRD patients. Interestingly, we did not find any correlation between the age acceleration evaluated according to the epigenetic clocks and ipAGE in either the ESRD group or the control group. On the whole, our data show a consistent accelerated aging phenotype in ESRD patients, which is better appreciated by quantifying the underlying inflammatory processes (inflammaging) by ipAGE than by using epigenetic clocks.
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Inflammation, Aging, and Cardiovascular Disease: JACC Review Topic of the Week. J Am Coll Cardiol 2022; 79:837-847. [PMID: 35210039 PMCID: PMC8881676 DOI: 10.1016/j.jacc.2021.12.017] [Citation(s) in RCA: 116] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/08/2021] [Indexed: 01/19/2023]
Abstract
Aging and inflammation both contribute pivotally to cardiovascular (CV) and cerebrovascular disease, the leading causes of death and disability worldwide. The concept of inflamm-aging recognizes that low-grade inflammatory pathways observed in the elderly contribute to CV risk. Understanding the mechanisms that link inflammation and aging could reveal new therapeutic targets and offer options to cope with the growing aging population worldwide. This review reports recent scientific advances in the pathways through which inflamm-aging mediates age-dependent decline in CV function and disease onset and considers critically the translational potential of such concepts into everyday clinical practice.
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Ghanemi A, Yoshioka M, St-Amand J. Exercise, Diet and Sleeping as Regenerative Medicine Adjuvants: Obesity and Ageing as Illustrations. MEDICINES (BASEL, SWITZERLAND) 2022; 9:medicines9010007. [PMID: 35049940 PMCID: PMC8778846 DOI: 10.3390/medicines9010007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/21/2022]
Abstract
Regenerative medicine uses the biological and medical knowledge on how the cells and tissue regenerate and evolve in order to develop novel therapies. Health conditions such as ageing, obesity and cancer lead to an impaired regeneration ability. Exercise, diet choices and sleeping pattern have significant impacts on regeneration biology via diverse pathways including reducing the inflammatory and oxidative components. Thus, exercise, diet and sleeping management can be optimized towards therapeutic applications in regenerative medicine. It could allow to prevent degeneration, optimize the biological regeneration and also provide adjuvants for regenerative medicine.
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Affiliation(s)
- Abdelaziz Ghanemi
- Functional Genomics Laboratory, Endocrinology and Nephrology Axis, CHU de Québec-Université Laval Research Center, Québec, QC G1V 4G2, Canada; (A.G.); (M.Y.)
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec, QC G1V 0A6, Canada
| | - Mayumi Yoshioka
- Functional Genomics Laboratory, Endocrinology and Nephrology Axis, CHU de Québec-Université Laval Research Center, Québec, QC G1V 4G2, Canada; (A.G.); (M.Y.)
| | - Jonny St-Amand
- Functional Genomics Laboratory, Endocrinology and Nephrology Axis, CHU de Québec-Université Laval Research Center, Québec, QC G1V 4G2, Canada; (A.G.); (M.Y.)
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec, QC G1V 0A6, Canada
- Correspondence: ; Tel.: +1-418-654-2296
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Graham LC, Kline RA, Lamont DJ, Gillingwater TH, Mabbott NA, Skehel PA, Wishart TM. Temporal Profiling of the Cortical Synaptic Mitochondrial Proteome Identifies Ageing Associated Regulators of Stability. Cells 2021; 10:cells10123403. [PMID: 34943911 PMCID: PMC8700124 DOI: 10.3390/cells10123403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/15/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
Synapses are particularly susceptible to the effects of advancing age, and mitochondria have long been implicated as organelles contributing to this compartmental vulnerability. Despite this, the mitochondrial molecular cascades promoting age-dependent synaptic demise remain to be elucidated. Here, we sought to examine how the synaptic mitochondrial proteome (including strongly mitochondrial associated proteins) was dynamically and temporally regulated throughout ageing to determine whether alterations in the expression of individual candidates can influence synaptic stability/morphology. Proteomic profiling of wild-type mouse cortical synaptic and non-synaptic mitochondria across the lifespan revealed significant age-dependent heterogeneity between mitochondrial subpopulations, with aged organelles exhibiting unique protein expression profiles. Recapitulation of aged synaptic mitochondrial protein expression at the Drosophila neuromuscular junction has the propensity to perturb the synaptic architecture, demonstrating that temporal regulation of the mitochondrial proteome may directly modulate the stability of the synapse in vivo.
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Affiliation(s)
- Laura C. Graham
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK; (L.C.G.); (R.A.K.); (N.A.M.)
- Euan MacDonald Centre, Chancellor’s Building, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, UK; (T.H.G.); (P.A.S.)
| | - Rachel A. Kline
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK; (L.C.G.); (R.A.K.); (N.A.M.)
- Euan MacDonald Centre, Chancellor’s Building, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, UK; (T.H.G.); (P.A.S.)
| | - Douglas J. Lamont
- FingerPrints Proteomic Facility, College of Life Sciences, University of Dundee, Dow Street DD1 5EH, UK;
| | - Thomas H. Gillingwater
- Euan MacDonald Centre, Chancellor’s Building, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, UK; (T.H.G.); (P.A.S.)
- Centre for Discovery Brain Sciences, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Neil A. Mabbott
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK; (L.C.G.); (R.A.K.); (N.A.M.)
| | - Paul A. Skehel
- Euan MacDonald Centre, Chancellor’s Building, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, UK; (T.H.G.); (P.A.S.)
- Centre for Discovery Brain Sciences, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Thomas M. Wishart
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK; (L.C.G.); (R.A.K.); (N.A.M.)
- Euan MacDonald Centre, Chancellor’s Building, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, UK; (T.H.G.); (P.A.S.)
- Centre for Dementia Prevention, The University of Edinburgh, 9A Bioquarter, 9 Little France Road, Edinburgh EH16 4UX, UK
- Correspondence:
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Mc Auley MT. DNA methylation in genes associated with the evolution of ageing and disease: A critical review. Ageing Res Rev 2021; 72:101488. [PMID: 34662746 DOI: 10.1016/j.arr.2021.101488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/30/2021] [Accepted: 10/12/2021] [Indexed: 12/28/2022]
Abstract
Ageing is characterised by a physical decline in biological functioning which results in a progressive risk of mortality with time. As a biological phenomenon, it is underpinned by the dysregulation of a myriad of complex processes. Recently, however, ever-increasing evidence has associated epigenetic mechanisms, such as DNA methylation (DNAm) with age-onset pathologies, including cancer, cardiovascular disease, and Alzheimer's disease. These diseases compromise healthspan. Consequently, there is a medical imperative to understand the link between epigenetic ageing, and healthspan. Evolutionary theory provides a unique way to gain new insights into epigenetic ageing and health. This review will: (1) provide a brief overview of the main evolutionary theories of ageing; (2) discuss recent genetic evidence which has revealed alleles that have pleiotropic effects on fitness at different ages in humans; (3) consider the effects of DNAm on pleiotropic alleles, which are associated with age related disease; (4) discuss how age related DNAm changes resonate with the mutation accumulation, disposable soma and programmed theories of ageing; (5) discuss how DNAm changes associated with caloric restriction intersect with the evolution of ageing; and (6) conclude by discussing how evolutionary theory can be used to inform investigations which quantify age-related DNAm changes which are linked to age onset pathology.
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Affiliation(s)
- Mark Tomás Mc Auley
- Faculty of Science and Engineering, University of Chester, Exton Park, Chester CH1 4BJ, UK.
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Szymczak S, Dose J, Torres GG, Heinsen FA, Venkatesh G, Datlinger P, Nygaard M, Mengel-From J, Flachsbart F, Klapper W, Christensen K, Lieb W, Schreiber S, Häsler R, Bock C, Franke A, Nebel A. DNA methylation QTL analysis identifies new regulators of human longevity. Hum Mol Genet 2021; 29:1154-1167. [PMID: 32160291 PMCID: PMC7206852 DOI: 10.1093/hmg/ddaa033] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 01/01/2020] [Accepted: 02/11/2020] [Indexed: 12/14/2022] Open
Abstract
Human longevity is a complex trait influenced by both genetic and environmental factors, whose interaction is mediated by epigenetic mechanisms like DNA methylation. Here, we generated genome-wide whole-blood methylome data from 267 individuals, of which 71 were long-lived (90–104 years), by applying reduced representation bisulfite sequencing. We followed a stringent two-stage analysis procedure using discovery and replication samples to detect differentially methylated sites (DMSs) between young and long-lived study participants. Additionally, we performed a DNA methylation quantitative trait loci analysis to identify DMSs that underlie the longevity phenotype. We combined the DMSs results with gene expression data as an indicator of functional relevance. This approach yielded 21 new candidate genes, the majority of which are involved in neurophysiological processes or cancer. Notably, two candidates (PVRL2, ERCC1) are located on chromosome 19q, in close proximity to the well-known longevity- and Alzheimer’s disease-associated loci APOE and TOMM40. We propose this region as a longevity hub, operating on both a genetic (APOE, TOMM40) and an epigenetic (PVRL2, ERCC1) level. We hypothesize that the heritable methylation and associated gene expression changes reported here are overall advantageous for the LLI and may prevent/postpone age-related diseases and facilitate survival into very old age.
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Affiliation(s)
- Silke Szymczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Janina Dose
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Guillermo G Torres
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Femke-Anouska Heinsen
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Geetha Venkatesh
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria
| | - Marianne Nygaard
- Research Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, DK-5000 Odense C, Denmark.,Department of Clinical Genetics, Odense University Hospital, DK-5000 Odense C, Denmark
| | - Jonas Mengel-From
- Research Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, DK-5000 Odense C, Denmark.,Department of Clinical Genetics, Odense University Hospital, DK-5000 Odense C, Denmark
| | - Friederike Flachsbart
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Wolfram Klapper
- Institute of Pathology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Kaare Christensen
- Research Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, DK-5000 Odense C, Denmark.,Department of Clinical Genetics, Odense University Hospital, DK-5000 Odense C, Denmark.,Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, DK-5000 Odense C, Denmark
| | - Wolfgang Lieb
- Institute of Epidemiology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, A-1090 Vienna, Austria.,Max Planck Institute for Informatics, Saarland Informatics Campus, D-66123 Saarbrücken, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, D-24105 Kiel, Germany
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Park SH, Lee SY, Kim SA. Mitochondrial DNA Methylation Is Higher in Acute Coronary Syndrome Than in Stable Coronary Artery Disease. In Vivo 2021; 35:181-189. [PMID: 33402465 DOI: 10.21873/invivo.12247] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND/AIM Decreased mitochondrial DNA copy number (mtDNA-CN) has been associated with coronary artery disease (CAD). We aimed to clarify the difference between stable CAD (SCAD) and acute coronary syndrome (ACS) regarding mtDNA-CN and the DNA methylation ratio in regions influencing the regulation of mitochondrial biogenesis. MATERIALS AND METHODS Using quantitative real-time polymerase chain reaction, mtDNA-CN was measured in peripheral blood leukocytes sampled from 50 patients with SCAD and 50 with ACS. We then conducted bisulfite modification of DNA followed by methylation-specific polymerase chain reaction to quantify mtDNA methylation in the mitochondrial D-loop region (mtDLR) and nuclear DNA methylation in the promoter region of nuclear peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A) gene. RESULTS Compared to patients with SCAD, those with ACS had significantly lower relative mtDNA-CN (0.89±0.24 vs. 1.00±0.28, p=0.013) and higher DNA methylation ratio of the mtDLR (1.11±0.24 vs. 1.00±0.25, p=0.027) Conclusion: Our findings suggest that increased DNA methylation in the mtDLR, which translates into reduced mtDNA content, may affect the clinical phenotype of CAD.
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Affiliation(s)
- Sang Hyun Park
- Department of Internal Medicine, School of Medicine, Eulji University, Daejeon, Republic of Korea
| | - Soo Young Lee
- Department of Pharmacology, School of Medicine, Eulji University, Daejeon, Republic of Korea
| | - Soon Ae Kim
- Department of Pharmacology, School of Medicine, Eulji University, Daejeon, Republic of Korea
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11
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Mitochondrial DNA Methylation and Human Diseases. Int J Mol Sci 2021; 22:ijms22094594. [PMID: 33925624 PMCID: PMC8123858 DOI: 10.3390/ijms22094594] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.
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12
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Wang Y, Gao J, Wu F, Lai C, Li Y, Zhang G, Peng X, Yu S, Yang J, Wang W, Zhang W, Yang X. Biological and epigenetic alterations of mitochondria involved in cellular replicative and hydrogen peroxide-induced premature senescence of human embryonic lung fibroblasts. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 216:112204. [PMID: 33845364 DOI: 10.1016/j.ecoenv.2021.112204] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
The mitoepigenetic modifications may be closely related to cellular fate. Both the replicative and hydrogen peroxide (H2O2)-induced premature senescence models were used to detect the mitochondrial biological characteristics and the epigenetic factors during senescence of human embryonic lung fibroblasts. The mitochondrial quantity was decreased in two senescence stages, while the mitochondrial DNA (mtDNA) copy number was increased significantly and the methyltransferases activity likewise. And the acute mtROS accumulation could launch premature senescence. Later, the persistent premature senescence owned the higher level of adenosine triphosphate (ATP) and mitochondrial 5-methylcytosine (mt-5-mC), and the less level of 8-hydroxydeoxyguanosine (8-OHdG) than those of replicative senescence. The mtDNA methylation-related enzymes, binding protein and the mitochondrial transcription regulators presented the differentially expressed profiles in both senescent states. Interestingly, the hypermethylation in the CpG region of mitochondrial transcription factor B2 (TFB2M) contributed to its downregulation of mRNA level in replicative senescence. The alterations of the mitochondrial biological functions and mtDNA features would be novel candidate biomarkers involved in cellular senescence. The specific methylation status of mtDNA may also have a crosstalk with oxidative stress to the mitochondrial function, contributing to cellular senescence.
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Affiliation(s)
- Yan Wang
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Jianji Gao
- Department of Medical Quality Management, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, PR China
| | - Fan Wu
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Caiyun Lai
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Yueqi Li
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Gaoqiang Zhang
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Xinyue Peng
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Susu Yu
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Jiani Yang
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China
| | - Wei Wang
- Department of Occupational Health and Occupational Diseases, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, PR China
| | - Wenjuan Zhang
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, PR China.
| | - Xingfen Yang
- Key Laboratory of Tropical Disease Research of Guangdong Province, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, PR China.
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13
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Yusipov I, Bacalini MG, Kalyakulina A, Krivonosov M, Pirazzini C, Gensous N, Ravaioli F, Milazzo M, Giuliani C, Vedunova M, Fiorito G, Gagliardi A, Polidoro S, Garagnani P, Ivanchenko M, Franceschi C. Age-related DNA methylation changes are sex-specific: a comprehensive assessment. Aging (Albany NY) 2020; 12:24057-24080. [PMID: 33276343 PMCID: PMC7762479 DOI: 10.18632/aging.202251] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/19/2020] [Indexed: 12/18/2022]
Abstract
The existence of a sex gap in human health and longevity has been widely documented. Autosomal DNA methylation differences between males and females have been reported, but so far few studies have investigated if DNA methylation is differently affected by aging in males and females. We performed a meta-analysis of 4 large whole blood datasets, comparing 4 aspects of epigenetic age-dependent remodeling between the two sexes: differential methylation, variability, epimutations and entropy. We reported that a large fraction (43%) of sex-associated probes undergoes age-associated DNA methylation changes, and that a limited number of probes show age-by-sex interaction. We experimentally validated 2 regions mapping in FIGN and PRR4 genes and showed sex-specific deviations of their methylation patterns in models of decelerated (centenarians) and accelerated (Down syndrome) aging. While we did not find sex differences in the age-associated increase in epimutations and entropy, we showed that the number of probes having an age-related increase in methylation variability is 15 times higher in males compared to females. Our results can offer new epigenetic tools to study the interaction between aging and sex and can pave the way to the identification of molecular triggers of sex differences in longevity and age-related diseases prevalence.
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Affiliation(s)
- Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia.,Mathematics of Future Technologies Center, Lobachevsky University, Nizhniy Novgorod, Russia
| | | | - Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Mikhail Krivonosov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Noémie Gensous
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum – University of Bologna, Bologna, Italy
| | - Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum – University of Bologna, Bologna, Italy
| | - Maddalena Milazzo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum – University of Bologna, Bologna, Italy
| | - Cristina Giuliani
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy.,School of Anthropology and Museum Ethnography, University of Oxford, Oxford, UK
| | - Maria Vedunova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhni Novgorod, Nizhni Novgorod, Russia
| | - Giovanni Fiorito
- Department of Biomedical Sciences, University of Sassari, Italy.,Department of Epidemiology and Public Health, MRC/HPA Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - Amedeo Gagliardi
- Italian Institute for Genomic Medicine (IIGM), Candiolo 10060, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo 10060, Italy
| | - Silvia Polidoro
- Department of Epidemiology and Public Health, MRC/HPA Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK.,Italian Institute for Genomic Medicine (IIGM), Candiolo 10060, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo 10060, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum – University of Bologna, Bologna, Italy.,Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Applied Biomedical Research Center (CRBA), Policlinico S.Orsola-Malpighi Polyclinic, Bologna, Italy.,CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia.,Mathematics of Future Technologies Center, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia
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14
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Whitwell HJ, Bacalini MG, Blyuss O, Chen S, Garagnani P, Gordleeva SY, Jalan S, Ivanchenko M, Kanakov O, Kustikova V, Mariño IP, Meyerov I, Ullner E, Franceschi C, Zaikin A. The Human Body as a Super Network: Digital Methods to Analyze the Propagation of Aging. Front Aging Neurosci 2020; 12:136. [PMID: 32523526 PMCID: PMC7261843 DOI: 10.3389/fnagi.2020.00136] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
Biological aging is a complex process involving multiple biological processes. These can be understood theoretically though considering them as individual networks-e.g., epigenetic networks, cell-cell networks (such as astroglial networks), and population genetics. Mathematical modeling allows the combination of such networks so that they may be studied in unison, to better understand how the so-called "seven pillars of aging" combine and to generate hypothesis for treating aging as a condition at relatively early biological ages. In this review, we consider how recent progression in mathematical modeling can be utilized to investigate aging, particularly in, but not exclusive to, the context of degenerative neuronal disease. We also consider how the latest techniques for generating biomarker models for disease prediction, such as longitudinal analysis and parenclitic analysis can be applied to as both biomarker platforms for aging, as well as to better understand the inescapable condition. This review is written by a highly diverse and multi-disciplinary team of scientists from across the globe and calls for greater collaboration between diverse fields of research.
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Affiliation(s)
- Harry J Whitwell
- Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | | | - Oleg Blyuss
- School of Physics, Astronomy and Mathematics, University of Hertfordshire, Harfield, United Kingdom.,Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Shangbin Chen
- Britton Chance Centre for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, China
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Susan Yu Gordleeva
- Laboratory of Systems Medicine of Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Sarika Jalan
- Complex Systems Laboratory, Discipline of Physics, Indian Institute of Technology Indore, Indore, India.,Centre for Bio-Science and Bio-Medical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Oleg Kanakov
- Laboratory of Systems Medicine of Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Valentina Kustikova
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Ines P Mariño
- Department of Biology and Geology, Physics and Inorganic Chemistry, Universidad Rey Juan Carlos, Madrid, Spain
| | - Iosif Meyerov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Ekkehard Ullner
- Department of Physics (SUPA), Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Alexey Zaikin
- Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Department of Mathematics, Institute for Women's Health, University College London, London, United Kingdom
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15
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Borkowska J, Domaszewska-Szostek A, Kołodziej P, Wicik Z, Połosak J, Buyanovskaya O, Charzewski L, Stańczyk M, Noszczyk B, Puzianowska-Kuznicka M. Alterations in 5hmC level and genomic distribution in aging-related epigenetic drift in human adipose stem cells. Epigenomics 2020; 12:423-437. [PMID: 32031421 DOI: 10.2217/epi-2019-0131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim: To clarify mechanisms affecting the level and distribution of 5-hydroxymethylcytosine (5hmC) during aging. Materials & methods: We examined levels and genomic distribution of 5hmC along with the expression of ten-eleven translocation methylcytosine dioxygenases (TETs) in adipose stem cells in young and age-advanced individuals. Results: 5hmC levels were higher in adipose stem cells of age-advanced than young individuals (p = 0.0003), but were not associated with age-related changes in expression of TETs. 5hmC levels correlated with population doubling time (r = 0.62; p = 0.01). We identified 58 differentially hydroxymethylated regions. Hypo-hydroxymethylated differentially hydroxymethylated regions were approximately twofold enriched in CCCTC-binding factor binding sites. Conclusion: Accumulation of 5hmC in aged cells can result from inefficient active demethylation due to altered TETs activity and reduced passive demethylation due to slower proliferation.
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Affiliation(s)
- Joanna Borkowska
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Anna Domaszewska-Szostek
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Paulina Kołodziej
- Department of Geriatrics & Gerontology, Medical Centre of Postgraduate Education, 61/63 Kleczewska Street, 01-826 Warsaw, Poland
| | - Zofia Wicik
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Jacek Połosak
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Olga Buyanovskaya
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Lukasz Charzewski
- Faculty of Physics, University of Warsaw, 5 Pasteur Street, 02-093 Warsaw, Poland
| | - Marek Stańczyk
- Department of General Surgery, Wolski Hospital, 17 Kasprzaka Street, 01-211 Warsaw, Poland
| | - Bartłomiej Noszczyk
- Department of Plastic Surgery, Medical Centre of Postgraduate Education, 99/103 Marymoncka Street, 01-813 Warsaw, Poland
| | - Monika Puzianowska-Kuznicka
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland.,Department of Geriatrics & Gerontology, Medical Centre of Postgraduate Education, 61/63 Kleczewska Street, 01-826 Warsaw, Poland
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16
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Aging and Caloric Restriction Modulate the DNA Methylation Profile of the Ribosomal RNA Locus in Human and Rat Liver. Nutrients 2020; 12:nu12020277. [PMID: 31973116 PMCID: PMC7070571 DOI: 10.3390/nu12020277] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/13/2020] [Accepted: 01/17/2020] [Indexed: 12/21/2022] Open
Abstract
A growing amount of evidence suggests that the downregulation of protein synthesis is an adaptive response during physiological aging, which positively contributes to longevity and can be modulated by nutritional interventions like caloric restriction (CR). The expression of ribosomal RNA (rRNA) is one of the main determinants of translational rate, and epigenetic modifications finely contribute to its regulation. Previous reports suggest that hypermethylation of ribosomal DNA (rDNA) locus occurs with aging, although with some species- and tissue- specificity. In the present study, we experimentally measured DNA methylation of three regions (the promoter, the 5′ of the 18S and the 5′ of 28S sequences) in the rDNA locus in liver tissues from rats at two, four, 10, and 18 months. We confirm previous findings, showing age-related hypermethylation, and describe, for the first time, that this gain in methylation also occurs in human hepatocytes. Furthermore, we show that age-related hypermethylation is enhanced in livers of rat upon CR at two and 10 months, and that at two months a trend towards the reduction of rRNA expression occurs. Collectively, our results suggest that CR modulates age-related regulation of methylation at the rDNA locus, thus providing an epigenetic readout of the pro-longevity effects of CR.
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17
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Scarpato R, Testi S, Colosimo V, Garcia Crespo C, Micheli C, Azzarà A, Tozzi MG, Ghirri P. Role of oxidative stress, genome damage and DNA methylation as determinants of pathological conditions in the newborn: an overview from conception to early neonatal stage. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 783:108295. [DOI: 10.1016/j.mrrev.2019.108295] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 11/25/2019] [Accepted: 12/24/2019] [Indexed: 12/15/2022]
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18
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Guarasci F, D'Aquila P, Montesanto A, Corsonello A, Bellizzi D, Passarino G. Individual DNA Methylation Profile is Correlated with Age and can be Targeted to Modulate Healthy Aging and Longevity. Curr Pharm Des 2019; 25:4139-4149. [DOI: 10.2174/1381612825666191112095655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023]
Abstract
:Patterns of DNA methylation, the best characterized epigenetic modification, are modulated by aging. In humans, different studies at both site-specific and genome-wide levels have reported that modifications of DNA methylation are associated with the chronological aging process but also with the quality of aging (or biological aging), providing new perspectives for establishing powerful biomarkers of aging.:In this article, the role of DNA methylation in aging and longevity has been reviewed by analysing literature data about DNA methylation variations occurring during the lifetime in response to environmental factors and genetic background, and their association with the aging process and, in particular, with the quality of aging. Special attention has been devoted to the relationship between nuclear DNA methylation patterns, mitochondrial DNA epigenetic modifications, and longevity. Mitochondrial DNA has recently been reported to modulate global DNA methylation levels of the nuclear genome during the lifetime, and, in spite of the previous belief, it has been found to be the target of methylation modifications.:Analysis of DNA methylation profiles across lifetime shows that a remodeling of the methylome occurs with age and/or with age-related decline. Thus, it can be an excellent biomarker of aging and of the individual decline and frailty status. The knowledge about the mechanisms underlying these modifications is crucial since it might allow the opportunity for targeted treatment to modulate the rate of aging and longevity.
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Affiliation(s)
- Francesco Guarasci
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Patrizia D'Aquila
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Andrea Corsonello
- Unit of Geriatric Pharmacoepidemiology, Scientific Research Institute - Italian National Research Center on Aging (IRCCS INRCA), Cosenza, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
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19
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Bacalini MG, Franceschi C, Gentilini D, Ravaioli F, Zhou X, Remondini D, Pirazzini C, Giuliani C, Marasco E, Gensous N, Di Blasio AM, Ellis E, Gramignoli R, Castellani G, Capri M, Strom S, Nardini C, Cescon M, Grazi GL, Garagnani P. Molecular Aging of Human Liver: An Epigenetic/Transcriptomic Signature. J Gerontol A Biol Sci Med Sci 2019; 74:1-8. [PMID: 29554203 DOI: 10.1093/gerona/gly048] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Indexed: 12/12/2022] Open
Abstract
The feasibility of liver transplantation from old healthy donors suggests that this organ is able to preserve its functionality during aging. To explore the biological basis of this phenomenon, we characterized the epigenetic profile of liver biopsies collected from 45 healthy liver donors ranging from 13 to 90 years old using the Infinium HumanMethylation450 BeadChip. The analysis indicates that a large remodeling in DNA methylation patterns occurs, with 8,823 age-associated differentially methylated CpG probes. Notably, these age-associated changes tended to level off after the age of 60, as confirmed by Horvath's clock. Using stringent selection criteria, we further identified a DNA methylation signature of aging liver including 75 genomic regions. We demonstrated that this signature is specific for liver compared to other tissues and that it is able to detect biological age-acceleration effects associated with obesity. Finally, we combined DNA methylation measurements with available expression data. Although the intersection between the two omic characterizations was low, both approaches suggested a previously unappreciated role of epithelial-mesenchymal transition and Wnt-signaling pathways in the aging of human liver.
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Affiliation(s)
| | - Claudio Franceschi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Italy.,DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy.,CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Italy
| | - Francesco Ravaioli
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy
| | - Xiaoyuan Zhou
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, PR China.,University of Chinese Academy of Sciences, Beijing, PR China.,Department of Neurology, University of San Francisco, California
| | - Daniel Remondini
- Department of Physics and Astronomy (DIFA) and INFN Sez. Bologna, Alma Mater Studiorum, Italy
| | | | - Cristina Giuliani
- Department of Biological Geological and Environmental Sciences, Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Italy
| | - Elena Marasco
- CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy
| | - Noémie Gensous
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy
| | | | - Ewa Ellis
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Roberto Gramignoli
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Gastone Castellani
- CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy.,Department of Biological Geological and Environmental Sciences, Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Italy
| | - Miriam Capri
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy.,CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy
| | - Stephen Strom
- Department of Laboratory Medicine, Karolinska Institute and Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Christine Nardini
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,CNR IAC "Mauro Picone", Roma, Italy.,Personal Genomics S.r.l., Verona, Italy
| | - Matteo Cescon
- General Surgery and Transplant Unit, Department of Medical and Surgical Sciences, Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | | | - Paolo Garagnani
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Bologna, Italy.,CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Bologna, Italy.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna, Italy.,Institute of Molecular Genetics (IGM)-CNR, Unit of Bologna, Italy.,Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopaedic Institute, Bologna, Italy
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20
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Çevik B, Mançe-Çalışır Ö, Atbaşoğlu EC, Saka MC, Alptekin K, Üçok A, Sırmatel B, Gülöksüz S, Tükün A, van Os J, Gümüş-Akay G. Psychometric liability to psychosis and childhood adversities are associated with shorter telomere length: A study on schizophrenia patients, unaffected siblings, and non-clinical controls. J Psychiatr Res 2019; 111:169-185. [PMID: 30776705 DOI: 10.1016/j.jpsychires.2019.01.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/20/2018] [Accepted: 01/27/2019] [Indexed: 02/06/2023]
Abstract
Compared to the general population, individuals diagnosed with Schizophrenia (SCZ) experience a higher frequency and an earlier onset of chronic medical disorders, resulting in a reduction in life expectancy by an average of 15-25 years. Recently, it has been hypothesized that SCZ is a syndrome of accelerated aging. Childhood adversity was also associated with the pathogenesis and course of SCZ. Our hypothesis was that both SCZ patients and their unaffected siblings would have shorter telomere length (TL) compared to of non-clinical controls. Our additional goals were to determine (1) whether shorter TL correlates with intermediate phenotypes of SCZ (i.e. Psychosis-like symptoms and schizotypal traits); and (2) whether childhood adversities have a moderating role in TL shortening among SCZ and their unaffected siblings. To this end, SCZ patients (n = 100), their unaffected siblings (n = 100) and non-clinical controls (n = 100) were enrolled. The main variables were TL, measured by aTL-qPCR; psychotic-like and schizotypal symptoms, assessed by The Community Assessment of Psychic Experience (CAPE) and the Structured Interview for Schizotypy-Revised (SIS-R), respectively; and childhood adversities evaluated by the Childhood Experience of Care and Abuse (CECA)-Interview. Potentially relevant variables also included in the analyses were: Global Assessment of Functioning (GAF) scores, cognitive performance, and socio-demographic features. In contrast to our hypothesis patients had similar TL when compared to the non-clinical controls. Interestingly, unaffected siblings had longer TL compared to both patients and controls (p < 0.001). Independent from group status a negative correlation was observed between TL and psychotic-like symptoms as rated by the CAPE (p < 0.01). Childhood adversities, especially loneliness between ages 0 and 11 were also negatively associated with TL (p < 0.05). Our findings suggest that psychometric liability to psychosis and childhood adversities may be associated with shorter TL. Unaffected siblings had longer TL, suggesting the potential role of resilience on both the TL and the clinical presentation. These findings must be considered preliminary, calling for larger-scale replication efforts.
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Affiliation(s)
- Burcu Çevik
- Brain Research Center, Ankara University, Ankara, Turkey; Biotechnology Institute, Ankara University, Ankara, Turkey
| | | | - Eşref Cem Atbaşoğlu
- Department of Psychiatry, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Meram Can Saka
- Department of Psychiatry, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Köksal Alptekin
- Department of Psychiatry, Dokuz Eylül University Faculty of Medicine, Izmir, Turkey
| | - Alp Üçok
- Department of Psychiatry, Istanbul University Faculty of Medicine, Istanbul, Turkey
| | - Burcu Sırmatel
- Department of Physiology, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Sinan Gülöksüz
- Department of Psychiatry and Neuropsychology Maastricht University Medical Center, Maastricht, the Netherlands; Department of Psychiatry, Yale School of Medicine, New Haven, USA
| | - Ajlan Tükün
- Center of Genetic Diagnosis, Duzen Laboratories Group, Ankara, Turkey
| | - Jim van Os
- Maastricht University Medical Centre, Maastricht, the Netherlands; Brain Centre Rudolf Magnus, Utrecht University Medical Centre, Utrecht, the Netherlands; King's College London, Department of Psychosis Studies, Institute of Psychiatry, London, UK
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21
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Montesanto A, D'Aquila P, Rossano V, Passarino G, Bellizzi D. Mini Nutritional Assessment Scores Indicate Higher Risk for Prospective Mortality and Contrasting Correlation With Age-Related Epigenetic Biomarkers. Front Endocrinol (Lausanne) 2019; 10:672. [PMID: 31632350 PMCID: PMC6779723 DOI: 10.3389/fendo.2019.00672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 09/16/2019] [Indexed: 02/03/2023] Open
Abstract
The plasticity of the individual epigenetic landscape that goes to countless rearrangements throughout life is closely the reflection of environmental factors such as chemical exposure, socio-economic status and nutrient intakes both early and late in life. The Mini Nutritional Assessment (MNA) is a well-validated tool for assessing malnutrition in old people. It includes 6 (MNA-SF) or 18 (MNA-LF) self-reported questions derived from general, anthropometric, dietary, and self- assessment. We evaluated the association between the nutritional status, as measured by MNA, and methylation biomarkers we previously demonstrated to be associated with chronological and biological age in human. We found that malnutrition is positively correlated with DNA methylation status at the global level, in line with our previous reports. On the contrary, most of the sites located within specific genes, which were previously reported to be correlated with chronological and biological aging, showed to be not affected by malnutrition, or even to have correlations with malnutrition opposite to those previously reported with frailty. These results may suggest that malnutrition is among the first effects of disability and other age- related problems and a generalized non-specific epigenetic remodeling may be the initial response of the organism. By contrast, the fine remodeling of specific genomic sites is scarcely affected by malnutrition and may respond to a more complex interaction of different factors. Therefore, although malnutrition in the elderly is certainly a risk factor for survival, this is partially independent of the aging process of the organism which leads to the methylation remodeling previously described to measure chronological and biological aging.
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22
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Nardini C, Moreau JF, Gensous N, Ravaioli F, Garagnani P, Bacalini MG. The epigenetics of inflammaging: The contribution of age-related heterochromatin loss and locus-specific remodelling and the modulation by environmental stimuli. Semin Immunol 2018; 40:49-60. [PMID: 30396810 DOI: 10.1016/j.smim.2018.10.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 12/12/2022]
Abstract
A growing amount of evidences indicates that inflammaging - the chronic, low grade inflammation state characteristic of the elderly - is the result of genetic as well as environmental or stochastic factors. Some of these, such as the accumulation of senescent cells that are persistent during aging or accompany its progression, seem to be sufficient to initiate the aging process and to fuel it. Others, like exposure to environmental compounds or infections, are temporary and resolve within a (relatively) short time. In both cases, however, a cellular memory of the event can be established by means of epigenetic modulation of the genome. In this review we will specifically discuss the relationship between epigenetics and inflammaging. In particular, we will show how age-associated epigenetic modifications concerned with heterochromatin loss and gene-specific remodelling, can promote inflammaging. Furthermore, we will recall how the exposure to specific nutritional, environmental and microbial stimuli can affect the rate of inflammaging through epigenetic mechanisms, touching also on the recent insight given by the concept of trained immunity.
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Affiliation(s)
- Christine Nardini
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; CNR IAC "Mauro Picone", Roma, Italy; Personal Genomics S.r.l., Verona, Italy
| | - Jean-Francois Moreau
- University of Bordeaux, CNRS-UMR5164, 146 rue Léo Saignat, 33076 Bordeaux, France; CHU Bordeaux, Place Amélie Raba-Léon, Bordeaux, France
| | - Noémie Gensous
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden; Laboratory of Cell Biology, Rizzoli Orthopaedic Institute, Bologna, Italy; CNR Institute of Molecular Genetics, Unit of Bologna, Bologna, Italy; Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy.
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23
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Wolters JEJ, van Breda SGJ, Grossmann J, Fortes C, Caiment F, Kleinjans JCS. Integrated 'omics analysis reveals new drug-induced mitochondrial perturbations in human hepatocytes. Toxicol Lett 2018; 289:1-13. [PMID: 29501571 DOI: 10.1016/j.toxlet.2018.02.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/02/2018] [Accepted: 02/23/2018] [Indexed: 12/11/2022]
Abstract
We performed a multiple 'omics study by integrating data on epigenomic, transcriptomic, and proteomic perturbations associated with mitochondrial dysfunction in primary human hepatocytes caused by the liver toxicant valproic acid (VPA), to deeper understand downstream events following epigenetic alterations in the mitochondrial genome. Furthermore, we investigated persistence of cross-omics changes after terminating drug treatment. Upon transient methylation changes of mitochondrial genes during VPA-treatment, increasing complexities of gene-interaction networks across time were demonstrated, which normalized during washout. Furthermore, co-expression between genes and their corresponding proteins increased across time. Additionally, in relation to persistently decreased ATP production, we observed decreased expression of mitochondrial complex I and III-V genes. Persistent transcripts and proteins were related to citric acid cycle and β-oxidation. In particular, we identified a potential novel mitochondrial-nuclear signaling axis, MT-CO2-FN1-MYC-CPT1. In summary, this cross-omics study revealed dynamic responses of the mitochondrial epigenome to an impulse toxicant challenge resulting in persistent mitochondrial dysfunctioning. Moreover, this approach allowed for discriminating between the toxic effect of VPA and adaptation.
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Affiliation(s)
- Jarno E J Wolters
- Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
| | - Simone G J van Breda
- Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
| | - Jonas Grossmann
- Functional Genomics Center Zurich, Functional Genomics Center Zurich, University Zurich/ETH Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Claudia Fortes
- Functional Genomics Center Zurich, Functional Genomics Center Zurich, University Zurich/ETH Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Florian Caiment
- Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
| | - Jos C S Kleinjans
- Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
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24
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Evaluation of Lymphocyte Response to the Induced Oxidative Stress in a Cohort of Ageing Subjects, including Semisupercentenarians and Their Offspring. Mediators Inflamm 2018; 2018:7109312. [PMID: 29681767 PMCID: PMC5842690 DOI: 10.1155/2018/7109312] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/16/2017] [Accepted: 11/27/2017] [Indexed: 12/22/2022] Open
Abstract
The production of reactive oxygen species (ROS) may promote immunosenescence if not counterbalanced by the antioxidant systems. Cell membranes, proteins, and nucleic acids become the target of ROS and progressively lose their structure and functions. This process could lead to an impairment of the immune response. However, little is known about the capability of the immune cells of elderly individuals to dynamically counteract the oxidative stress. Here, the response of the main lymphocyte subsets to the induced oxidative stress in semisupercentenarians (CENT), their offspring (OFF), elderly controls (CTRL), and young individuals (YO) was analyzed using flow cytometry. The results showed that the ratio of the ROS levels between the induced and noninduced (I/NI) oxidative stress conditions was higher in CTRL and OFF than in CENT and YO, in almost all T, B, and NK subsets. Moreover, the ratio of reduced glutathione levels between I/NI conditions was higher in OFF and CENT compared to the other groups in almost all the subsets. Finally, we observed significant correlations between the response to the induced oxidative stress and the degree of methylation in specific genes on the oxidative stress pathway. Globally, these data suggest that the capability to buffer dynamic changes in the oxidative environment could be a hallmark of longevity in humans.
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25
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Aging and nutrition induce tissue-specific changes on global DNA methylation status in rats. Mech Ageing Dev 2018; 174:47-54. [PMID: 29427568 DOI: 10.1016/j.mad.2018.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/31/2018] [Accepted: 02/06/2018] [Indexed: 01/12/2023]
Abstract
A number of epigenetic studies have demonstrated that DNA methylation patterns exhibit a tissue specificity, but not much has been done to highlight the extent of this phenomenon. Moreover, it is unknown how external factors modulate the plasticity of the tissue specific epigenetic profile. We examined global DNA methylation profiles in tissues from rats of different age, fed with standard or low-calorie diet, and evaluated their association with aging and nutrition. Tissue-specific variations occur during aging with hyper-methylation taking place in all tissues except for liver. The expression of enzymes involved in methylation reactions (DNMTs and TETs) was consistent with the methylation patterns. Nutrition affects global DNA methylation status throughout lifespan. Interestingly, the differences among different tissues are magnified in 96 weeks old rats fed with low calorie diet. Moreover, the low-calorie diet appears to affect the offspring's epigenetic status more strongly if administered during the maternal pre-gestational period than the gestational and lactation time. Therefore, we propose that changes in the global DNA methylation status may represent an epigenetic mechanism by which age and nutrition intersect each other and, in turn, influence the aging plasticity.
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26
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Wolters JEJ, van Breda SGJ, Caiment F, Claessen SM, de Kok TMCM, Kleinjans JCS. Nuclear and Mitochondrial DNA Methylation Patterns Induced by Valproic Acid in Human Hepatocytes. Chem Res Toxicol 2017; 30:1847-1854. [PMID: 28853863 PMCID: PMC5645762 DOI: 10.1021/acs.chemrestox.7b00171] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Valproic
acid (VPA) is one of the most widely prescribed antiepileptic
drugs in the world. Despite its pharmacological importance, it may
cause liver toxicity and steatosis through mitochondrial dysfunction.
The aim of this study is to further investigate VPA-induced mechanisms
of steatosis by analyzing changes in patterns of methylation in nuclear
DNA (nDNA) and mitochondrial DNA (mtDNA). Therefore, primary human
hepatocytes (PHHs) were exposed to an incubation concentration of
VPA that was shown to cause steatosis without inducing overt cytotoxicity.
VPA was administered daily for 5 days, and this was followed by a
3 day washout (WO). Methylated DNA regions (DMRs) were identified
by using the methylated DNA immunoprecipitation–sequencing
(MeDIP-seq) method. The nDNA DMRs after VPA treatment could indeed
be classified into oxidative stress- and steatosis-related pathways.
In particular, networks of the steatosis-related gene EP300 provided novel insight into the mechanisms of toxicity induced by
VPA treatment. Furthermore, we suggest that VPA induces a crosstalk
between nDNA hypermethylation and mtDNA hypomethylation that plays
a role in oxidative stress and steatosis development. Although most
VPA-induced methylation patterns appeared reversible upon terminating
VPA treatment, 31 nDNA DMRs (including 5 zinc finger protein genes)
remained persistent after the WO period. Overall, we have shown that
MeDIP-seq analysis is highly informative in disclosing novel mechanisms
of VPA-induced toxicity in PHHs. Our results thus provide a prototype
for the novel generation of interesting methylation biomarkers for
repeated dose liver toxicity in vitro.
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Affiliation(s)
- Jarno E J Wolters
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Simone G J van Breda
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Sandra M Claessen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
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27
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Guastafierro T, Bacalini MG, Marcoccia A, Gentilini D, Pisoni S, Di Blasio AM, Corsi A, Franceschi C, Raimondo D, Spanò A, Garagnani P, Bondanini F. Genome-wide DNA methylation analysis in blood cells from patients with Werner syndrome. Clin Epigenetics 2017; 9:92. [PMID: 28861129 PMCID: PMC5577832 DOI: 10.1186/s13148-017-0389-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/15/2017] [Indexed: 12/15/2022] Open
Abstract
Background Werner syndrome is a progeroid disorder characterized by premature age-related phenotypes. Although it is well established that autosomal recessive mutations in the WRN gene is responsible for Werner syndrome, the molecular alterations that lead to disease phenotype remain still unidentified. Results To address whether epigenetic changes can be associated with Werner syndrome phenotype, we analysed genome-wide DNA methylation profile using the Infinium MethylationEPIC BeadChip in the whole blood from three patients affected by Werner syndrome compared with three age- and sex-matched healthy controls. Hypermethylated probes were enriched in glycosphingolipid biosynthesis, FoxO signalling and insulin signalling pathways, while hypomethylated probes were enriched in PI3K-Akt signalling and focal adhesion pathways. Twenty-two out of 47 of the differentially methylated genes belonging to the enriched pathways resulted differentially expressed in a publicly available dataset on Werner syndrome fibroblasts. Interestingly, differentially methylated regions identified CERS1 and CERS3, two members of the ceramide synthase family. Moreover, we found differentially methylated probes within ITGA9 and ADAM12 genes, whose methylation is altered in systemic sclerosis, and within the PRDM8 gene, whose methylation is affected in dyskeratosis congenita and Down syndrome. Conclusions DNA methylation changes in the peripheral blood from Werner syndrome patients provide new insight in the pathogenesis of the disease, highlighting in some cases a functional correlation of gene expression and methylation status. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0389-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- T Guastafierro
- UOC of Clinical Biochemistry, Sandro Pertini Hospital, Rome, Italy.,CRIIS (Interdisciplinary, Interdepartmental and Specialistic Reference Center for Early Diagnosis of Scleroderma, Treatment of Sclerodermic Ulcers and Videocapillaroscopy), Sandro Pertini Hospital, Rome, Italy
| | - M G Bacalini
- IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - A Marcoccia
- CRIIS (Interdisciplinary, Interdepartmental and Specialistic Reference Center for Early Diagnosis of Scleroderma, Treatment of Sclerodermic Ulcers and Videocapillaroscopy), Sandro Pertini Hospital, Rome, Italy.,UOSD Ischemic Microangiopathy and Sclerodermic Ulcers, Sandro Pertini Hospital, Rome, Italy
| | - D Gentilini
- Centre for Biomedical Research and Technologies, Italian Auxologic Institute, IRCCS, Milan, Italy
| | - S Pisoni
- Centre for Biomedical Research and Technologies, Italian Auxologic Institute, IRCCS, Milan, Italy
| | - A M Di Blasio
- Centre for Biomedical Research and Technologies, Italian Auxologic Institute, IRCCS, Milan, Italy
| | - A Corsi
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - C Franceschi
- IRCCS Institute of Neurological Sciences, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna, Italy
| | - D Raimondo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - A Spanò
- UOC of Clinical Biochemistry, Sandro Pertini Hospital, Rome, Italy
| | - P Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna, Italy.,Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institute at Huddinge University Hospital, S-141 86 Stockholm, Sweden.,CNR Institute for Molecular Genetics, Unit of Bologna, Bologna, Italy.,Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopedic Institute, Bologna, Italy
| | - F Bondanini
- CRIIS (Interdisciplinary, Interdepartmental and Specialistic Reference Center for Early Diagnosis of Scleroderma, Treatment of Sclerodermic Ulcers and Videocapillaroscopy), Sandro Pertini Hospital, Rome, Italy.,UOC of Clinical Pathology, Saint' Eugenio Hospital, Rome, Italy
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