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Klughammer J, Romanovskaia D, Nemc A, Posautz A, Seid CA, Schuster LC, Keinath MC, Lugo Ramos JS, Kosack L, Evankow A, Printz D, Kirchberger S, Ergüner B, Datlinger P, Fortelny N, Schmidl C, Farlik M, Skjærven K, Bergthaler A, Liedvogel M, Thaller D, Burger PA, Hermann M, Distel M, Distel DL, Kübber-Heiss A, Bock C. Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species. Nat Commun 2023; 14:232. [PMID: 36646694 PMCID: PMC9842680 DOI: 10.1038/s41467-022-34828-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 11/08/2022] [Indexed: 01/18/2023] Open
Abstract
Methylation of cytosines is a prototypic epigenetic modification of the DNA. It has been implicated in various regulatory mechanisms across the animal kingdom and particularly in vertebrates. We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale DNA methylation profiles of multiple organs. Bioinformatic analysis of this large dataset quantified the association of DNA methylation with the underlying genomic DNA sequence throughout vertebrate evolution. We observed a broadly conserved link with two major transitions-once in the first vertebrates and again with the emergence of reptiles. Cross-species comparisons focusing on individual organs supported a deeply conserved association of DNA methylation with tissue type, and cross-mapping analysis of DNA methylation at gene promoters revealed evolutionary changes for orthologous genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution.
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Affiliation(s)
- Johanna Klughammer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. .,Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Daria Romanovskaia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Amelie Nemc
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Annika Posautz
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Charlotte A Seid
- Ocean Genome Legacy Center, Northeastern University Marine Science Center, Nahant, USA
| | - Linda C Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Juan Sebastian Lugo Ramos
- Max Planck Research Group Behavioral Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Lindsay Kosack
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ann Evankow
- Ocean Genome Legacy Center, Northeastern University Marine Science Center, Nahant, USA
| | - Dieter Printz
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Stefanie Kirchberger
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Bekir Ergüner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Nikolaus Fortelny
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christian Schmidl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Medical University of Vienna, Center for Pathophysiology Infectiology and Immunology, Institute of Hygiene and Applied Immunology, Vienna, Austria
| | - Miriam Liedvogel
- Max Planck Research Group Behavioral Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Institute of Avian Research, An der Vogelwarte, Wilhelmshaven, Germany
| | - Denise Thaller
- Department for Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Marcela Hermann
- Medical University of Vienna, Department of Medical Biochemistry, Vienna, Austria
| | - Martin Distel
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Daniel L Distel
- Ocean Genome Legacy Center, Northeastern University Marine Science Center, Nahant, USA
| | - Anna Kübber-Heiss
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. .,Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria.
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102
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Long-term impact of paediatric critical illness on the difference between epigenetic and chronological age in relation to physical growth. Clin Epigenetics 2023; 15:8. [PMID: 36639798 PMCID: PMC9840263 DOI: 10.1186/s13148-023-01424-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/07/2023] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Altered DNA-methylation affects biological ageing in adults and developmental processes in children. DNA-methylation is altered by environmental factors, trauma and illnesses. We hypothesised that paediatric critical illness, and the nutritional management in the paediatric intensive care unit (PICU), affects DNA-methylation changes that underly the developmental processes of childhood ageing. RESULTS We studied the impact of critical illness, and of the early use of parenteral nutrition (early-PN) versus late-PN, on "epigenetic age-deviation" in buccal mucosa of 818 former PICU-patients (406 early-PN, 412 late-PN) who participated in the 2-year follow-up of the multicentre PEPaNIC-RCT (ClinicalTrials.gov-NCT01536275), as compared with 392 matched healthy children, and assessed whether this relates to their impaired growth. The epigenetic age-deviation (difference between PedBE clock-estimated epigenetic age and chronological age) was calculated. Using bootstrapped multivariable linear regression models, we assessed the impact hereon of critical illness, and of early-PN versus late-PN. As compared with healthy children, epigenetic age of patients assessed 2 years after PICU-admission deviated negatively from chronological age (p < 0.05 in 51% of bootstrapped replicates), similarly in early-PN and late-PN groups. Next, we identified vulnerable subgroups for epigenetic age-deviation using interaction analysis. We revealed that DNA-methylation age-deceleration in former PICU-patients was dependent on age at time of illness (p < 0.05 for 83% of bootstrapped replicates), with vulnerability starting from 6 years onwards. Finally, we assessed whether vulnerability to epigenetic age-deviation could be related to impaired growth from PICU-admission to follow-up at 2 and 4 years. Multivariable repeated measures ANOVA showed that former PICU-patients, as compared with healthy children, grew less in height (p = 0.0002) and transiently gained weight (p = 0.0003) over the 4-year time course. Growth in height was more stunted in former PICU-patients aged ≥ 6-years at time of critical illness (p = 0.002) than in the younger patients. CONCLUSIONS As compared with healthy children, former PICU-patients, in particular those aged ≥ 6-years at time of illness, revealed epigenetic age-deceleration, with a physical correlate revealing stunted growth in height. Whether this vulnerability around the age of 6 years for epigenetic age-deceleration and stunted growth years later relates to altered endocrine pathways activated at the time of adrenarche requires further investigation.
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103
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Yazar V, Dawson VL, Dawson TM, Kang SU. DNA Methylation Signature of Aging: Potential Impact on the Pathogenesis of Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2023; 13:145-164. [PMID: 36710687 PMCID: PMC10041453 DOI: 10.3233/jpd-223517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Regulation of gene expression by epigenetic modifications means lasting and heritable changes in the function of genes without alterations in the DNA sequence. Of all epigenetic mechanisms identified thus far, DNA methylation has been of particular interest in both aging and age-related disease research over the last decade given the consistency of site-specific DNA methylation changes during aging that can predict future health and lifespan. An increasing line of evidence has implied the dynamic nature of DNA (de)methylation events that occur throughout the lifespan has a role in the pathophysiology of aging and age-associated neurodegenerative conditions, including Parkinson's disease (PD). In this regard, PD methylome shows, to some extent, similar genome-wide changes observed in the methylome of healthy individuals of matching age. In this review, we start by providing a brief overview of studies outlining global patterns of DNA methylation, then its mechanisms and regulation, within the context of aging and PD. Considering diverging lines of evidence from different experimental and animal models of neurodegeneration and how they combine to shape our current understanding of tissue-specific changes in DNA methylome in health and disease, we report a high-level comparison of the genomic methylation landscapes of brain, with an emphasis on dopaminergic neurons in PD and in natural aging. We believe this will be particularly useful for systematically dissecting overlapping genome-wide alterations in DNA methylation during PD and healthy aging, and for improving our knowledge of PD-specific changes in methylation patterns independent of aging process.
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Affiliation(s)
- Volkan Yazar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pharmacology and and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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104
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Takahashi Y, Asari M, Isozaki S, Hoshina C, Okuda K, Mori K, Namba R, Ochiai W, Shimizu K. Age prediction by methylation analysis of small amounts of DNA using locked nucleic acids. J Forensic Sci 2023; 68:267-274. [PMID: 36151731 DOI: 10.1111/1556-4029.15144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 12/31/2022]
Abstract
Age prediction based on methylation analysis has been reported in many populations, with 10 ng or more of DNA usually required for each determination. In this study, we designed thermostable locked nucleic acid (LNA) primers by replacing a small number of DNA bases in standard DNA primers with LNAs. We evaluated these primer sets by single-base extension analysis using 10, 5, or 2 ng of DNA that would be less than template DNA used in standard methylation testing, and determined sensitivity and accuracy. We analyzed EDARADD, SST, and KLF14 genes, targeting one CpG site in each gene. Melting temperature values of most LNA primers were 4°C higher than those of DNA primers. The intensities of signals from the EDARADD and SST genes were significantly improved by the LNA primers, by 3.3 times and 1.4 times, respectively, compared with the DNA primers using 2 ng of DNA. Coefficient of variation (CV) analysis was used to assess the accuracy of the determined methylation levels. CVs were increased using small amounts of DNA, but lower CVs were detected using LNA primers. We also showed high accuracy of age prediction for 51 individuals using LNA primers. The lowest mean absolute deviation was obtained using 10 ng of DNA and was 3.88 years with the LNA primers. Thermostable PCR primers were simply designed, and the LNAs improved the sensitivity and accuracy of methylation analysis for 10 ng or less of DNA.
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Affiliation(s)
- Yuta Takahashi
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa, Japan.,Department of Pharmacokinetics, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Shinagawa, Japan
| | - Masaru Asari
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Shotaro Isozaki
- Department of Forensic Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Chisato Hoshina
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Katsuhiro Okuda
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Kanae Mori
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Ryo Namba
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Wataru Ochiai
- Department of Pharmacokinetics, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Shinagawa, Japan
| | - Keiko Shimizu
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa, Japan
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105
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Benincasa G, Maron BA, Affinito O, D’Alto M, Franzese M, Argiento P, Schiano C, Romeo E, Bontempo P, Golino P, Berrino L, Loscalzo J, Napoli C. Association Between Circulating CD4 + T Cell Methylation Signatures of Network-Oriented SOCS3 Gene and Hemodynamics in Patients Suffering Pulmonary Arterial Hypertension. J Cardiovasc Transl Res 2023; 16:17-30. [PMID: 35960497 PMCID: PMC9944731 DOI: 10.1007/s12265-022-10294-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023]
Abstract
Pathogenic DNA methylation changes may be involved in pulmonary arterial hypertension (PAH) onset and its progression, but there is no data on potential associations with patient-derived hemodynamic parameters. The reduced representation bisulfite sequencing (RRBS) platform identified N = 631 differentially methylated CpG sites which annotated to N = 408 genes (DMGs) in circulating CD4+ T cells isolated from PAH patients vs. healthy controls (CTRLs). A promoter-restricted network analysis established the PAH subnetwork that included 5 hub DMGs (SOCS3, GNAS, ITGAL, NCOR2, NFIC) and 5 non-hub DMGs (NR4A2, GRM2, PGK1, STMN1, LIMS2). The functional analysis revealed that the SOCS3 gene was the most recurrent among the top ten significant pathways enriching the PAH subnetwork, including the growth hormone receptor and the interleukin-6 signaling. Correlation analysis showed that the promoter methylation levels of each network-oriented DMG were associated individually with hemodynamic parameters. In particular, SOCS3 hypomethylation was negatively associated with right atrial pressure (RAP) and positively associated with cardiac index (CI) (|r|≥ 0.6). A significant upregulation of the SOCS3, ITGAL, NFIC, NCOR2, and PGK1 mRNA levels (qRT-PCR) in peripheral blood mononuclear cells from PAH patients vs. CTRLs was found (P ≤ 0.05). By immunoblotting, a significant upregulation of the SOCS3 protein was confirmed in PAH patients vs. CTRLs (P < 0.01). This is the first network-oriented study which integrates circulating CD4+ T cell DNA methylation signatures, hemodynamic parameters, and validation experiments in PAH patients at first diagnosis or early follow-up. Our data suggests that SOCS3 gene might be involved in PAH pathogenesis and serve as potential prognostic biomarker.
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Affiliation(s)
- Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.
| | - Bradley A. Maron
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, MB Boston, USA ,Harvard Medical School, Boston, MA USA
| | | | - Michele D’Alto
- Department of Cardiology, Monaldi Hospital, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | | | - Paola Argiento
- Department of Cardiology, Monaldi Hospital, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Concetta Schiano
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Emanuele Romeo
- Department of Cardiology, Monaldi Hospital, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Paola Bontempo
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Paolo Golino
- Department of Cardiology, Monaldi Hospital, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Liberato Berrino
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, MB Boston, USA
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy ,IRCCS SDN, Naples, Italy
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106
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Dapas M, Thompson EE, Wentworth-Sheilds W, Clay S, Visness CM, Calatroni A, Sordillo JE, Gold DR, Wood RA, Makhija M, Khurana Hershey GK, Sherenian MG, Gruchalla RS, Gill MA, Liu AH, Kim H, Kattan M, Bacharier LB, Rastogi D, Altman MC, Busse WW, Becker PM, Nicolae D, O’Connor GT, Gern JE, Jackson DJ, Ober C. Multi-omic association study identifies DNA methylation-mediated genotype and smoking exposure effects on lung function in children living in urban settings. PLoS Genet 2023; 19:e1010594. [PMID: 36638096 PMCID: PMC9879483 DOI: 10.1371/journal.pgen.1010594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 01/26/2023] [Accepted: 12/23/2022] [Indexed: 01/14/2023] Open
Abstract
Impaired lung function in early life is associated with the subsequent development of chronic respiratory disease. Most genetic associations with lung function have been identified in adults of European descent and therefore may not represent those most relevant to pediatric populations and populations of different ancestries. In this study, we performed genome-wide association analyses of lung function in a multiethnic cohort of children (n = 1,035) living in low-income urban neighborhoods. We identified one novel locus at the TDRD9 gene in chromosome 14q32.33 associated with percent predicted forced expiratory volume in one second (FEV1) (p = 2.4x10-9; βz = -0.31, 95% CI = -0.41- -0.21). Mendelian randomization and mediation analyses revealed that this genetic effect on FEV1 was partially mediated by DNA methylation levels at this locus in airway epithelial cells, which were also associated with environmental tobacco smoke exposure (p = 0.015). Promoter-enhancer interactions in airway epithelial cells revealed chromatin interaction loops between FEV1-associated variants in TDRD9 and the promoter region of the PPP1R13B gene, a stimulator of p53-mediated apoptosis. Expression of PPP1R13B in airway epithelial cells was significantly associated the FEV1 risk alleles (p = 1.3x10-5; β = 0.12, 95% CI = 0.06-0.17). These combined results highlight a potential novel mechanism for reduced lung function in urban youth resulting from both genetics and smoking exposure.
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Affiliation(s)
- Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | - Emma E. Thompson
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | | | - Selene Clay
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | | | | | - Joanne E. Sordillo
- Department of Population Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Diane R. Gold
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert A. Wood
- Department of Pediatrics, Johns Hopkins University Medical Center, Baltimore, Maryland, United States of America
| | - Melanie Makhija
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children’s Hospital, Chicago, Illinois, United States of America
| | - Gurjit K. Khurana Hershey
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Michael G. Sherenian
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Rebecca S. Gruchalla
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michelle A. Gill
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Andrew H. Liu
- Department of Allergy and Immunology, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Haejin Kim
- Department of Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Meyer Kattan
- Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Leonard B. Bacharier
- Monroe Carell Jr. Children’s Hospital at Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Deepa Rastogi
- Children’s National Health System, Washington, District of Columbia, United States of America
| | - Matthew C. Altman
- Department of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - William W. Busse
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Dan Nicolae
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - George T. O’Connor
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - James E. Gern
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Daniel J. Jackson
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
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107
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Harris CS, Miaskowski CA, Conley YP, Hammer MJ, Dhruva AA, Levine JD, Olshen AB, Kober KM. Gastrointestinal Symptom Cluster is Associated With Epigenetic Regulation of Lymphotoxin Beta in Oncology Patients Receiving Chemotherapy. Biol Res Nurs 2023; 25:51-64. [PMID: 35929442 PMCID: PMC9900252 DOI: 10.1177/10998004221115863] [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] [Indexed: 12/14/2022]
Abstract
OBJECTIVES While the gastrointestinal symptom cluster (GISC) is common in patients receiving chemotherapy, limited information is available on its underlying mechanism(s). Emerging evidence suggests a role for inflammatory processes through the actions of the nuclear factor kappa B (NF-κB) signaling pathway. This study evaluated for associations between a GISC and levels of DNA methylation for genes within this pathway. METHODS Prior to their second or third cycle of chemotherapy, 1071 outpatients reported symptom occurrence using the Memorial Symptom Assessment Scale. A GISC was identified using exploratory factor analysis. Differential methylation analyses were performed in two independent samples using EPIC (n = 925) and 450K (n = 146) microarrays. Trans expression-associated CpG (eCpG) loci for 56 NF-κB signaling pathway genes were evaluated. Loci significance were assessed using an exploratory false discovery rate (FDR) of 25% for the EPIC sample. For the validation assessment using the 450K sample, significance was assessed at an unadjusted p-value of 0.05. RESULTS For the EPIC sample, the GISC was associated with increased expression of lymphotoxin beta (LTB) at one differentially methylated trans eCpG locus (cg03171795; FDR = 0.168). This association was not validated in the 450K sample. CONCLUSIONS This study is the first to identify an association between a GISC and epigenetic regulation of a gene that is involved in the initiation of gastrointestinal immune responses. Findings suggest that increased LTB expression by hypermethylation of a trans eCpG locus is involved in the occurrence of this cluster in patients receiving chemotherapy. LTB may be a potential therapeutic target for this common cluster.
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Affiliation(s)
| | - Christine A. Miaskowski
- School of Nursing, University of
California, San Francisco, CA, USA
- School of Medicine, University of
California, San Francisco, CA, USA
| | - Yvette P. Conley
- School of Nursing, University of
Pittsburgh, Pittsburgh, PA, USA
| | - Marilyn J. Hammer
- The Phyllis F. Cantor Center for
Research in Nursing and Patient Care Services, Dana-Farber Cancer
Institute, Boston, MA, USA
| | - Anand A. Dhruva
- School of Medicine, University of
California, San Francisco, CA, USA
| | - Jon D. Levine
- School of Medicine, University of
California, San Francisco, CA, USA
| | - Adam B. Olshen
- School of Medicine, University of
California, San Francisco, CA, USA
| | - Kord M. Kober
- School of Nursing, University of
California, San Francisco, CA, USA
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108
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Jamshidi A, Liu MC, Klein EA, Venn O, Hubbell E, Beausang JF, Gross S, Melton C, Fields AP, Liu Q, Zhang N, Fung ET, Kurtzman KN, Amini H, Betts C, Civello D, Freese P, Calef R, Davydov K, Fayzullina S, Hou C, Jiang R, Jung B, Tang S, Demas V, Newman J, Sakarya O, Scott E, Shenoy A, Shojaee S, Steffen KK, Nicula V, Chien TC, Bagaria S, Hunkapiller N, Desai M, Dong Z, Richards DA, Yeatman TJ, Cohn AL, Thiel DD, Berry DA, Tummala MK, McIntyre K, Sekeres MA, Bryce A, Aravanis AM, Seiden MV, Swanton C. Evaluation of cell-free DNA approaches for multi-cancer early detection. Cancer Cell 2022; 40:1537-1549.e12. [PMID: 36400018 DOI: 10.1016/j.ccell.2022.10.022] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 08/03/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022]
Abstract
In the Circulating Cell-free Genome Atlas (NCT02889978) substudy 1, we evaluate several approaches for a circulating cell-free DNA (cfDNA)-based multi-cancer early detection (MCED) test by defining clinical limit of detection (LOD) based on circulating tumor allele fraction (cTAF), enabling performance comparisons. Among 10 machine-learning classifiers trained on the same samples and independently validated, when evaluated at 98% specificity, those using whole-genome (WG) methylation, single nucleotide variants with paired white blood cell background removal, and combined scores from classifiers evaluated in this study show the highest cancer signal detection sensitivities. Compared with clinical stage and tumor type, cTAF is a more significant predictor of classifier performance and may more closely reflect tumor biology. Clinical LODs mirror relative sensitivities for all approaches. The WG methylation feature best predicts cancer signal origin. WG methylation is the most promising technology for MCED and informs development of a targeted methylation MCED test.
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Affiliation(s)
| | - Minetta C Liu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | | | | | | | | | | | - Nan Zhang
- GRAIL, LLC, Menlo Park, CA 94025, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Zhao Dong
- GRAIL, LLC, Menlo Park, CA 94025, USA
| | | | - Timothy J Yeatman
- Gibbs Cancer Center and Research Institute, Spartanburg, SC 29303, USA; Department of Surgery, University of Utah, Salt Lake City, UT 84112, USA
| | - Allen L Cohn
- Rocky Mountain Cancer Center, Denver, CO 80218, USA
| | - David D Thiel
- Department of Urology, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Donald A Berry
- Department of Biostatistics, MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | | | | | | | | | | | - Charles Swanton
- Francis Crick Institute, London, NW1 1AT, UK; UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, London, WC1E 6DD, UK
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Urban VS, Cegledi A, Mikala G. Multiple myeloma, a quintessential malignant disease of aging: a geroscience perspective on pathogenesis and treatment. GeroScience 2022; 45:727-746. [PMID: 36508077 PMCID: PMC9742673 DOI: 10.1007/s11357-022-00698-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/18/2022] [Indexed: 12/14/2022] Open
Abstract
Multiple myeloma (MM) is an incurable plasma cell malignancy, which is predominantly a disease of older adults (the median age at diagnosis is 70 years). The slow progression from asymptomatic stages and the late-onset of MM suggest fundamental differences compared to many other hematopoietic system-related malignancies. The concept discussed in this review is that age-related changes at the level of terminally differentiated plasma cells act as the main risk factors for the development of MM. Epigenetic and genetic changes that characterize both MM development and normal aging are highlighted. The relationships between cellular aging processes, genetic mosaicism in plasma cells, and risk for MM and the stochastic processes contributing to clonal selection and expansion of mutated plasma cells are investigated. In line with the DNA damage accumulation theory of aging, in this review, the evolution of monoclonal gammopathy to symptomatic MM is considered. Therapeutic consequences of age-dependent comorbidities that lead to frailty and have fundamental influence on treatment outcome are described. The importance of considering geriatric states when planning the life-long treatment course of an elderly MM patient in order to achieve maximal therapeutic benefit is emphasized.
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Affiliation(s)
- Veronika S. Urban
- Department of Morphology and Physiology, Faculty of Health Sciences, Semmelweis University, Budapest, Hungary
| | - Andrea Cegledi
- Department of Hematology and Stem Cell Transplantation, South Pest Central Hospital–National Institute for Hematology and Infectious Diseases, Budapest, Hungary
| | - Gabor Mikala
- Department of Hematology and Stem Cell Transplantation, South Pest Central Hospital-National Institute for Hematology and Infectious Diseases, Budapest, Hungary.
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Liu C, Wang Z, Hui Q, Goldberg J, Smith NL, Shah AJ, Murrah N, Shallenberger L, Diggers E, Bremner JD, Sun YV, Vaccarino V. Association between depression and epigenetic age acceleration: A co-twin control study. Depress Anxiety 2022; 39:741-750. [PMID: 35758529 PMCID: PMC9729366 DOI: 10.1002/da.23279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/26/2022] [Accepted: 06/18/2022] [Indexed: 01/27/2023] Open
Abstract
INTRODUCTION Prior studies have shown inconsistent findings of an association between depression and epigenetic aging. DNA methylation (DNAm) age acceleration can measure biological aging. We adopted a robust co-twin control study design to examine whether depression is associated with DNAm age acceleration after accounting for the potential confounding influences of genetics and family environment. METHODS We analyzed data on a sub-cohort of the Vietnam Era Twin Registry. A total of 291 twins participated at baseline and 177 at follow-up visit after a mean of 11.7 years, with 111 participants having DNA samples for both time points. Depression was measured using the Beck Depression Inventory II (BDI-II). Six measures of DNAm age acceleration were computed at each time point, including Horvath's DNAm age acceleration (HorvathAA), intrinsic epigenetic age acceleration (IEAA), Hannum's DNAm age acceleration (HannumAA), extrinsic epigenetic age acceleration (EEAA), GrimAge acceleration (GrimAA), and PhenoAge acceleration (PhenoAA). Mixed-effects modeling was used to assess the within-pair association between depression and DNAm age acceleration. RESULTS At baseline, a 10-unit higher BDI-II total score was associated with HannumAA (0.73 years, 95% confidence interval [CI] 0.13-1.33, p = .019) and EEAA (0.94 years, 95% CI 0.22-1.66, p = .012). At follow-up, 10-unit higher BDI-II score was associated with PhenoAA (1.32 years, 95% CI 0.18-2.47, p = .027). CONCLUSION We identified that depression is associated with higher levels of DNAm age acceleration. Further investigation is warranted to better understand the underlying mechanisms for the potential causal relationship between depression and accelerated aging.
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Affiliation(s)
- Chang Liu
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Zeyuan Wang
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Qin Hui
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Jack Goldberg
- Vietnam Era Twin Registry, Seattle Epidemiologic Research and Information Center, Cooperative Studies Program, Office of Research and Development, Department of Veterans Affairs, Seattle, WA, USA
| | - Nicholas L. Smith
- Vietnam Era Twin Registry, Seattle Epidemiologic Research and Information Center, Cooperative Studies Program, Office of Research and Development, Department of Veterans Affairs, Seattle, WA, USA
| | - Amit J. Shah
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA
- Atlanta VA Health Care System, 1670 Clairmont Road, Decatur, GA 30033, USA
| | - Nancy Murrah
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Lucy Shallenberger
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - Emily Diggers
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
| | - J. Douglas Bremner
- Atlanta VA Health Care System, 1670 Clairmont Road, Decatur, GA 30033, USA
- Departments of Psychiatry and Behavioral Sciences and Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA
| | - Yan V. Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
- Atlanta VA Health Care System, 1670 Clairmont Road, Decatur, GA 30033, USA
| | - Viola Vaccarino
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA
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Woodward AA, Urbanowicz RJ, Naj AC, Moore JH. Genetic heterogeneity: Challenges, impacts, and methods through an associative lens. Genet Epidemiol 2022; 46:555-571. [PMID: 35924480 PMCID: PMC9669229 DOI: 10.1002/gepi.22497] [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: 05/18/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 01/07/2023]
Abstract
Genetic heterogeneity describes the occurrence of the same or similar phenotypes through different genetic mechanisms in different individuals. Robustly characterizing and accounting for genetic heterogeneity is crucial to pursuing the goals of precision medicine, for discovering novel disease biomarkers, and for identifying targets for treatments. Failure to account for genetic heterogeneity may lead to missed associations and incorrect inferences. Thus, it is critical to review the impact of genetic heterogeneity on the design and analysis of population level genetic studies, aspects that are often overlooked in the literature. In this review, we first contextualize our approach to genetic heterogeneity by proposing a high-level categorization of heterogeneity into "feature," "outcome," and "associative" heterogeneity, drawing on perspectives from epidemiology and machine learning to illustrate distinctions between them. We highlight the unique nature of genetic heterogeneity as a heterogeneous pattern of association that warrants specific methodological considerations. We then focus on the challenges that preclude effective detection and characterization of genetic heterogeneity across a variety of epidemiological contexts. Finally, we discuss systems heterogeneity as an integrated approach to using genetic and other high-dimensional multi-omic data in complex disease research.
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Affiliation(s)
- Alexa A. Woodward
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ryan J. Urbanowicz
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Adam C. Naj
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jason H. Moore
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
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Childhood Trauma and Epigenetics: State of the Science and Future. Curr Environ Health Rep 2022; 9:661-672. [PMID: 36242743 DOI: 10.1007/s40572-022-00381-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW There is a great deal of interest regarding the biological embedding of childhood trauma and social exposures through epigenetic mechanisms, including DNA methylation (DNAm), but a comprehensive understanding has been hindered by issues of limited reproducibility between studies. This review presents a summary of the literature on childhood trauma and DNAm, highlights issues in the field, and proposes some potential solutions. RECENT FINDINGS Investigations of the associations between DNAm and childhood trauma are commonly performed using candidate gene approaches, specifically involving genes related to neurological and stress pathways. Childhood trauma is defined in a wide range of ways in several societal contexts. However, although variations in DNAm are frequently found in stress-related genes, unsupervised epigenome-wide association studies (EWAS) have shown limited reproducibility both between studies and in relating these changes to exposures. The reproducibility of childhood trauma DNAm studies, and the field of social epigenetics in general, may be improved by increasing sample sizes, standardizing variables, making use of effect size thresholds, collecting longitudinal and intervention samples, appropriately accounting for known confounding factors, and applying causal analysis wherever possible, such as "two-step epigenetic Mendelian randomization."
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Ramini D, Latini S, Giuliani A, Matacchione G, Sabbatinelli J, Mensà E, Bacalini MG, Garagnani P, Rippo MR, Bronte G, Bonafè M, Cardelli M, Olivieri F. Replicative Senescence-Associated LINE1 Methylation and LINE1-Alu Expression Levels in Human Endothelial Cells. Cells 2022; 11:cells11233799. [PMID: 36497059 PMCID: PMC9739197 DOI: 10.3390/cells11233799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
One of the main challenges of current research on aging is to identify the complex epigenetic mechanisms involved in the acquisition of the cellular senescent phenotype. Despite some evidence suggested that epigenetic changes of DNA repetitive elements, including transposable elements (TE) sequences, are associated with replicative senescence of fibroblasts, data on different types of cells are scarce. We previously analysed genome-wide DNA methylation of young and replicative senescent human endothelial cells (HUVECs), highlighting increased levels of demethylated sequences in senescent cells. Here, we aligned the most significantly demethylated single CpG sites to the reference genome and annotated their localization inside TE sequences and found a significant hypomethylation of sequences belonging to the Long-Interspersed Element-1 (LINE-1 or L1) subfamilies L1M, L1P, and L1HS. To verify the hypothesis that L1 demethylation could be associated with increased transcription/activation of L1s and/or Alu elements (non-autonomous retroelements that usually depend on L1 sequences for reverse transcription and retrotransposition), we quantified the RNA expression levels of both L1 (generic L1 elements or site-specific L1PA2 on chromosome 14) and Alu elements in young and senescent HUVECs and human dermal fibroblasts (NHDFs). The RNA expression of Alu and L1 sequences was significantly increased in both senescent HUVECs and NHDFs, whereas the RNA transcript of L1PA2 on chromosome 14 was not significantly modulated in senescent cells. Moreover, we found an increased amount of TE DNA copies in the cytoplasm of senescent HUVECs and NHDFs. Our results support the hypothesis that TE, which are significantly increased in senescent cells, could be retrotranscribed to DNA sequences.
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Affiliation(s)
- Deborah Ramini
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy
| | - Silvia Latini
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Angelica Giuliani
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
- Correspondence: ; Tel.: +39-071-220-6243
| | - Giulia Matacchione
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Jacopo Sabbatinelli
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
- Laboratory Medicine Unit, Azienda Ospedaliero Universitaria delle Marche, 60126 Ancona, Italy
| | - Emanuela Mensà
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, 40126 Bologna, Italy
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”-Unit of Bologna, 40126 Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, 141 86 Huddinge, Sweden
| | - Maria Rita Rippo
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Giuseppe Bronte
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Massimiliano Bonafè
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
| | - Maurizio Cardelli
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121 Ancona, Italy
| | - Fabiola Olivieri
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
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Engelbrecht HR, Merrill SM, Gladish N, MacIsaac JL, Lin DTS, Ecker S, Chrysohoou CA, Pes GM, Kobor MS, Rehkopf DH. Sex differences in epigenetic age in Mediterranean high longevity regions. FRONTIERS IN AGING 2022; 3:1007098. [PMID: 36506464 PMCID: PMC9726738 DOI: 10.3389/fragi.2022.1007098] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/21/2022] [Indexed: 11/24/2022]
Abstract
Sex differences in aging manifest in disparities in disease prevalence, physical health, and lifespan, where women tend to have greater longevity relative to men. However, in the Mediterranean Blue Zones of Sardinia (Italy) and Ikaria (Greece) are regions of centenarian abundance, male-female centenarian ratios are approximately one, diverging from the typical trend and making these useful regions in which to study sex differences of the oldest old. Additionally, these regions can be investigated as examples of healthy aging relative to other populations. DNA methylation (DNAm)-based predictors have been developed to assess various health biomarkers, including biological age, Pace of Aging, serum interleukin-6 (IL-6), and telomere length. Epigenetic clocks are biological age predictors whose deviation from chronological age has been indicative of relative health differences between individuals, making these useful tools for interrogating these differences in aging. We assessed sex differences between the Horvath, Hannum, GrimAge, PhenoAge, Skin and Blood, and Pace of Aging predictors from individuals in two Mediterranean Blue Zones and found that men displayed positive epigenetic age acceleration (EAA) compared to women according to all clocks, with significantly greater rates according to GrimAge (β = 3.55; p = 1.22 × 10-12), Horvath (β = 1.07; p = 0.00378) and the Pace of Aging (β = 0.0344; p = 1.77 × 10-08). Other DNAm-based biomarkers findings indicated that men had lower DNAm-predicted serum IL-6 scores (β = -0.00301, p = 2.84 × 10-12), while women displayed higher DNAm-predicted proportions of regulatory T cells than men from the Blue Zone (p = 0.0150, 95% Confidence Interval [0.00131, 0.0117], Cohen's d = 0.517). All clocks showed better correlations with chronological age in women from the Blue Zones than men, but all clocks showed large mean absolute errors (MAE >30 years) in both sexes, except for PhenoAge (MAE <5 years). Thus, despite their equal survival to older ages in these Mediterranean Blue Zones, men in these regions remain biologically older by most measured DNAm-derived metrics than women, with the exception of the IL-6 score and proportion of regulatory T cells.
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Affiliation(s)
- Hannah-Ruth Engelbrecht
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Sarah M. Merrill
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Nicole Gladish
- Department of Epidemiology and Population Health, School of Medicine, Stanford University, Palo Alto, CA, United States
| | - Julie L. MacIsaac
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - David T. S. Lin
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Simone Ecker
- UCL Cancer Institute, University College London, London, United Kingdom
| | | | - Giovanni M. Pes
- Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Michael S. Kobor
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,*Correspondence: Michael S. Kobor, ; David H. Rehkopf,
| | - David H. Rehkopf
- Department of Epidemiology and Population Health, School of Medicine, Stanford University, Palo Alto, CA, United States,*Correspondence: Michael S. Kobor, ; David H. Rehkopf,
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Ferilli M, Ciolfi A, Pedace L, Niceta M, Radio FC, Pizzi S, Miele E, Cappelletti C, Mancini C, Galluccio T, Andreani M, Iascone M, Chiriatti L, Novelli A, Micalizzi A, Matraxia M, Menale L, Faletra F, Prontera P, Pilotta A, Bedeschi MF, Capolino R, Baban A, Seri M, Mammì C, Zampino G, Digilio MC, Dallapiccola B, Priolo M, Tartaglia M. Genome-Wide DNA Methylation Profiling Solves Uncertainty in Classifying NSD1 Variants. Genes (Basel) 2022; 13:2163. [PMID: 36421837 PMCID: PMC9690023 DOI: 10.3390/genes13112163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND Inactivating NSD1 mutations causing Sotos syndrome have been previously associated with a specific genome-wide DNA methylation (DNAm) pattern. Sotos syndrome is characterized by phenotypic overlap with other overgrowth syndromes, and a definite diagnosis might not be easily reached due to the high prevalence of variants of unknown significance (VoUS) that are identified in patients with a suggestive phenotype. OBJECTIVE we performed microarray DNAm profiling in a set of 11 individuals with a clinical suspicion of Sotos syndrome and carrying an NSD1 VoUS or previously unreported variants to solve uncertainty in defining pathogenicity of the observed variants. The impact of the training cohort size on sensitivity and prediction confidence of the classifier was assessed. RESULTS The Sotos syndrome-specific DNAm signature was validated in six individuals with a clinical diagnosis of Sotos syndrome and carrying bona fide pathogenic NSD1 variants. Applying this approach to the remaining 11 individuals with NSD1 variants, we succeeded in confirming pathogenicity in eight subjects and excluding the diagnosis of Sotos syndrome in three. The sensitivity and prediction confidence of the classifier based on the different sizes of the training sets did not show substantial differences, though the overall performance was improved by using a data balancing strategy. CONCLUSIONS The present approach solved uncertainty in cases with NDS1 VoUS, further demonstrating the clinical utility of DNAm profiling.
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Affiliation(s)
- Marco Ferilli
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Andrea Ciolfi
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Lucia Pedace
- Department of Pediatric Onco-Haematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marcello Niceta
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | - Simone Pizzi
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Evelina Miele
- Department of Pediatric Onco-Haematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Camilla Cappelletti
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Cecilia Mancini
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Tiziana Galluccio
- Department of Pediatric Onco-Haematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marco Andreani
- Department of Pediatric Onco-Haematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Maria Iascone
- Medical Genetics Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Luigi Chiriatti
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Alessia Micalizzi
- Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marta Matraxia
- Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Lucia Menale
- Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Flavio Faletra
- Medical Genetics Unit, IRCCS Burlo Garofolo, 34137 Trieste, Italy
| | - Paolo Prontera
- Maternal-Infantile Department, University Hospital of Perugia, 06156 Perugia, Italy
| | - Alba Pilotta
- Auxo-Endocrinology, Diabetology and Medical Genetic Unit, Department of Paediatrics, ASST Spedali Civili, 25123 Brescia, Italy
| | - Maria Francesca Bedeschi
- Medical Genetic Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Clinica Mangiagalli, 20122 Milan, Italy
| | - Rossella Capolino
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Anwar Baban
- Medical and Surgical Department of Pediatric Cardiology, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marco Seri
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Corrado Mammì
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy
| | - Giuseppe Zampino
- Dipartimento Scienze della Vita, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Maria Cristina Digilio
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Bruno Dallapiccola
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Manuela Priolo
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy
| | - Marco Tartaglia
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
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Bedside tracking of functional autonomic age in preterm infants. Pediatr Res 2022:10.1038/s41390-022-02376-2. [PMID: 36376508 DOI: 10.1038/s41390-022-02376-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/27/2022] [Accepted: 10/23/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Preterm birth predisposes infants to adverse outcomes that, without early intervention, impacts their long-term health. To assist bedside monitoring, we developed a tool to track the autonomic maturation of the preterm by assessing heart rate variability (HRV) changes during intensive care. METHODS Electrocardiogram (ECG) recordings were longitudinally recorded in 67 infants (26-38 weeks postmenstrual age (PMA)). Supervised machine learning was used to generate a functional autonomic age (FAA), by combining 50 computed HRV features from successive 5-minute ECG epochs (median of 23 epochs per infant). Performance of the FAA was assessed by correlation to PMA, clinical outcomes and the infant's functional brain age (FBA), an index of maturation derived from the electroencephalogram. RESULTS The FAA was strongly correlated to PMA (r = 0.86, 95% CI: 0.83-0.93) with a mean absolute error (MAE) of 1.66 weeks and also accurately estimated FBA (MAE = 1.58 weeks, n = 54 infants). The relationship between PMA and FAA was not confounded by neurodevelopmental outcome (p = 0.18, n = 45), sex (p = 0.88, n = 56), patent ductus arteriosus (p = 0.08, n = 56), IVH (p = 0.63, n = 56) or body weight at birth (p = 0.95, n = 56). CONCLUSIONS The FAA, an index derived from the ubiquitous ECG signal, offers direct avenues towards estimating autonomic maturation at the bedside during intensive care monitoring. IMPACT The development of a tool to track functional autonomic age in preterm infants based on heart rate variability features in the electrocardiogram provides a rapid and specialized view of autonomic maturation at the bedside. Functional autonomic age is linked closely to postmenstrual age and central nervous system function response, as determined by its relationship to functional brain age from the electroencephalogram. Tracking functional autonomic age during neonatal intensive care unit monitoring offers a unique insight into cardiovascular health in infants born extremely preterm and their maturational trajectories to term age.
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Bolhuis E, Belsky J, Frankenhuis WE, Shalev I, Hastings WJ, Tollenaar MS, O’Donnell KJ, McGill MG, Pokhvisneva I, Lin DT, MacIsaac JL, Kobor MS, de Weerth C, Beijers R. Attachment insecurity and the biological embedding of reproductive strategies: Investigating the role of cellular aging. Biol Psychol 2022; 175:108446. [DOI: 10.1016/j.biopsycho.2022.108446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/15/2022] [Accepted: 10/16/2022] [Indexed: 11/02/2022]
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El-Ahwany E, Hassan M, Elzallat M, Abdelsalam L, El-Sawy MAH, Seyam M. Association of Sat-a and Alu methylation status with HCV-induced chronic liver disease and hepatocellular carcinoma. Virus Res 2022; 321:198928. [PMID: 36100006 DOI: 10.1016/j.virusres.2022.198928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 09/02/2022] [Accepted: 09/09/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The combination of epigenetic and genetic abnormalities contributes together to the development of liver cancer. The methylation status of the repetitive elements (REs) in DNA has been investigated in a variety of human illnesses. However, the methylation patterns of Sat-α and Alu REs in chronic liver disease (CLD) and hepatocellular carcinoma (HCC) caused by hepatitis C virus (HCV) have never been studied before. METHODOLOGY In this study, 3 groups of participants including 50 patients having HCV-induced CLD, 50 patients having HCV-induced HCC, and 46 healthy subjects were subjected to measurement of Sat-α and Alu methylation using the quantitative MethyLight assay. RESULTS Sat-α and Alu methylation percentages decreased significantly in both CLD and HCC, compared to control. Also, a significant Sat-α hypomethylation was detected in HCC, compared to CLD. In addition, Sat-α and Alu methylation showed a significant decline as lesion size grew. However, only Sat-α hypomethylation was significantly increased in association with portal vein thrombosis and the MELD score. Sat-α methylation percentage had the highest sensitivity and specificity for diagnosing HCC (100% and 84.4%) followed by α-fetoprotein (80% and 84.4%) and Alu methylation (66% and 61.5%). Furthermore, there was a strong positive correlation between Sat-α and Alu methylation. CONCLUSIONS Measuring Sat-α and Alu methylation provides us with a new tool for early detecting HCV-induced CLD and hepatocarcinogenesis. Sat-α has the potential to be utilized as an independent predictive parameter for HCC development and progression because of its ability to distinguish between CLD and HCC with their different MELD scores.
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Affiliation(s)
- Eman El-Ahwany
- Immunology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Marwa Hassan
- Immunology Department, Theodor Bilharz Research Institute, Giza, Egypt.
| | - Mohamed Elzallat
- Immunology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Lobna Abdelsalam
- Human Genetics Department, Faculty of Medicine, Cairo University, Cairo, Egypt; Human Genetics Department, Faculty of Medicine, University of North Carolina, USA
| | | | - Moataz Seyam
- Hepato-Gastroenterology Department, Theodor Bilharz Research Institute, Giza, Egypt
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119
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Epigenetic clock: A promising biomarker and practical tool in aging. Ageing Res Rev 2022; 81:101743. [PMID: 36206857 DOI: 10.1016/j.arr.2022.101743] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 09/13/2022] [Accepted: 09/30/2022] [Indexed: 01/31/2023]
Abstract
As a complicated process, aging is characterized by various changes at the cellular, subcellular and nuclear levels, one of which is epigenetic aging. With increasing awareness of the critical role that epigenetic alternations play in aging, DNA methylation patterns have been employed as a measure of biological age, currently referred to as the epigenetic clock. This review provides a comprehensive overview of the epigenetic clock as a biomarker of aging and a useful tool to manage healthy aging. In this burgeoning scientific field, various kinds of epigenetic clocks continue to emerge, including Horvath's clock, Hannum's clock, DNA PhenoAge, and DNA GrimAge. We hereby present the most classic epigenetic clocks, as well as their differences. Correlations of epigenetic age with morbidity, mortality and other factors suggest the potential of epigenetic clocks for risk prediction and identification in the context of aging. In particular, we summarize studies on promising age-reversing interventions, with epigenetic clocks employed as a practical tool in the efficacy evaluation. We also discuss how the lack of higher-quality information poses a major challenge, and offer some suggestions to address existing obstacles. Hopefully, our review will help provide an appropriate understanding of the epigenetic clocks, thereby enabling novel insights into the aging process and how it can be manipulated to promote healthy aging.
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Higham J, Kerr L, Zhang Q, Walker RM, Harris SE, Howard DM, Hawkins EL, Sandu AL, Steele JD, Waiter GD, Murray AD, Evans KL, McIntosh AM, Visscher PM, Deary IJ, Cox SR, Sproul D. Local CpG density affects the trajectory and variance of age-associated DNA methylation changes. Genome Biol 2022; 23:216. [PMID: 36253871 PMCID: PMC9575273 DOI: 10.1186/s13059-022-02787-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is an epigenetic mark associated with the repression of gene promoters. Its pattern in the genome is disrupted with age and these changes can be used to statistically predict age with epigenetic clocks. Altered rates of aging inferred from these clocks are observed in human disease. However, the molecular mechanisms underpinning age-associated DNA methylation changes remain unknown. Local DNA sequence can program steady-state DNA methylation levels, but how it influences age-associated methylation changes is unknown. RESULTS We analyze longitudinal human DNA methylation trajectories at 345,895 CpGs from 600 individuals aged between 67 and 80 to understand the factors responsible for age-associated epigenetic changes at individual CpGs. We show that changes in methylation with age occur at 182,760 loci largely independently of variation in cell type proportions. These changes are especially apparent at 8322 low CpG density loci. Using SNP data from the same individuals, we demonstrate that methylation trajectories are affected by local sequence polymorphisms at 1487 low CpG density loci. More generally, we find that low CpG density regions are particularly prone to change and do so variably between individuals in people aged over 65. This differs from the behavior of these regions in younger individuals where they predominantly lose methylation. CONCLUSIONS Our results, which we reproduce in two independent groups of individuals, demonstrate that local DNA sequence influences age-associated DNA methylation changes in humans in vivo. We suggest that this occurs because interactions between CpGs reinforce maintenance of methylation patterns in CpG dense regions.
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Affiliation(s)
- Jonathan Higham
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Lyndsay Kerr
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Qian Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Present address: Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Present address: School of Psychology, University of Exeter, Edinburgh, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - David M Howard
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Emma L Hawkins
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Anca-Larisa Sandu
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - J Douglas Steele
- Division of Imaging Science and Technology, Medical School, University of Dundee, Dundee, UK
| | - Gordon D Waiter
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Alison D Murray
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Ian J Deary
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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Foolchand A, Mazaleni S, Ghazi T, Chuturgoon AA. A Review: Highlighting the Links between Epigenetics, COVID-19 Infection, and Vitamin D. Int J Mol Sci 2022; 23:12292. [PMID: 36293144 PMCID: PMC9603374 DOI: 10.3390/ijms232012292] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
The highly transmittable and infectious COVID-19 remains a major threat worldwide, with the elderly and comorbid individuals being the most vulnerable. While vaccines are currently available, therapeutic drugs will help ease the viral outbreak and prevent serious health outcomes. Epigenetic modifications regulate gene expression through changes in chromatin structure and have been linked to viral pathophysiology. Since epigenetic modifications contribute to the life cycle of the virus and host immune responses to infection, epigenetic drugs are promising treatment targets to ameliorate COVID-19. Deficiency of the multifunctional secosteroid hormone vitamin D is a global health threat. Vitamin D and its receptor function to regulate genes involved in immunity, apoptosis, proliferation, differentiation, and inflammation. Amassed evidence also indicates the biological relations of vitamin D with reduced disease risk, while its receptor can be modulated by epigenetic mechanisms. The immunomodulatory effects of vitamin D suggest a role for vitamin D as a COVID-19 therapeutic agent. Therefore, this review highlights the epigenetic effects on COVID-19 and vitamin D while also proposing a role for vitamin D in COVID-19 infections.
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Affiliation(s)
| | | | - Terisha Ghazi
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Howard College Campus, Durban 4041, South Africa
| | - Anil A. Chuturgoon
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Howard College Campus, Durban 4041, South Africa
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Bergstedt J, Azzou SAK, Tsuo K, Jaquaniello A, Urrutia A, Rotival M, Lin DTS, MacIsaac JL, Kobor MS, Albert ML, Duffy D, Patin E, Quintana-Murci L. The immune factors driving DNA methylation variation in human blood. Nat Commun 2022; 13:5895. [PMID: 36202838 PMCID: PMC9537159 DOI: 10.1038/s41467-022-33511-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/21/2022] [Indexed: 11/08/2022] Open
Abstract
Epigenetic changes are required for normal development, yet the nature and respective contribution of factors that drive epigenetic variation in humans remain to be fully characterized. Here, we assessed how the blood DNA methylome of 884 adults is affected by DNA sequence variation, age, sex and 139 factors relating to life habits and immunity. Furthermore, we investigated whether these effects are mediated or not by changes in cellular composition, measured by deep immunophenotyping. We show that DNA methylation differs substantially between naïve and memory T cells, supporting the need for adjustment on these cell-types. By doing so, we find that latent cytomegalovirus infection drives DNA methylation variation and provide further support that the increased dispersion of DNA methylation with aging is due to epigenetic drift. Finally, our results indicate that cellular composition and DNA sequence variation are the strongest predictors of DNA methylation, highlighting critical factors for medical epigenomics studies.
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Affiliation(s)
- Jacob Bergstedt
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France.
- Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - Sadoune Ait Kaci Azzou
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
| | - Kristin Tsuo
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
| | - Anthony Jaquaniello
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
| | | | - Maxime Rotival
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
| | - David T S Lin
- Edwin S.H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Julia L MacIsaac
- Edwin S.H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Michael S Kobor
- Edwin S.H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | | - Darragh Duffy
- Institut Pasteur, Université Paris Cité, Translational Immunology Unit, Institut Pasteur, Paris, France
| | - Etienne Patin
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France.
| | - Lluís Quintana-Murci
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France.
- Chair of Human Genomics and Evolution, Collège de France, Paris, France.
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Daunay A, Hardy LM, Bouyacoub Y, Sahbatou M, Touvier M, Blanché H, Deleuze JF, How-Kit A. Centenarians consistently present a younger epigenetic age than their chronological age with four epigenetic clocks based on a small number of CpG sites. Aging (Albany NY) 2022; 14:7718-7733. [PMID: 36202132 PMCID: PMC9596211 DOI: 10.18632/aging.204316] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
Abstract
Aging is a progressive time-dependent biological process affecting differentially individuals, who can sometimes present exceptional longevity. Epigenetic alterations are one of the hallmarks of aging, which comprise the epigenetic drift and clock at DNA methylation level. In the present study, we estimated the DNA methylation-based age (DNAmage) using four epigenetic clocks based on a small number of CpGs in French centenarians and semi-supercentenarians (CSSC, n=214) as well as nonagenarians' and centenarians' offspring (NCO, n=143) compared to individuals from the French general population (CG, n=149). DNA methylation analysis of the nine CpGs included in the epigenetic clocks showed high correlation with chronological age (-0.66>R>0.54) and also the presence of an epigenetic drift for four CpGs that was only visible in CSSC. DNAmage analysis showed that CSSC and to a lesser extend NCO present a younger DNAmage than their chronological age (15-28.5 years for CSSC, 4.4-11.5 years for NCO and 4.2-8.2 years for CG), which were strongly significant in CSSC compared to CG (p-values<2.2e-16). These differences suggest that epigenetic aging and potentially biological aging are slowed in exceptionally long-lived individuals and that epigenetic clocks based on a small number of CpGs are sufficient to reveal alterations of the global epigenetic clock.
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Affiliation(s)
- Antoine Daunay
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France
| | - Lise M Hardy
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France
| | - Yosra Bouyacoub
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France
| | - Mourad Sahbatou
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France
| | - Mathilde Touvier
- Sorbonne Paris Nord University, Nutritional Epidemiology Research Team (EREN), Epidemiology and Statistics Research Center Inserm U1153, Inrae U1125, Cnam, University of Paris (CRESS), Bobigny, France
| | - Hélène Blanché
- Laboratory of Excellence GenMed, Paris, France.,Centre de Ressources Biologiques, CEPH Biobank, Foundation Jean Dausset - CEPH, Paris, France
| | - Jean-François Deleuze
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France.,Laboratory of Excellence GenMed, Paris, France.,Centre de Ressources Biologiques, CEPH Biobank, Foundation Jean Dausset - CEPH, Paris, France.,Centre National de Recherche en Génomique Humaine, CEA, Institut François Jacob, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Foundation Jean Dausset - CEPH, Paris, France
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Zhou A, Wu Z, Zaw Phyo AZ, Torres D, Vishwanath S, Ryan J. Epigenetic aging as a biomarker of dementia and related outcomes: a systematic review. Epigenomics 2022; 14:1125-1138. [PMID: 36154448 DOI: 10.2217/epi-2022-0209] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background: Biological aging may be a robust biomarker of dementia or cognitive performance. This systematic review synthesized the evidence for an association between epigenetic aging and dementia, mild cognitive impairment and cognitive function. Methods: A systematic search was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Results: 30 eligible articles were included. There was no strong evidence that accelerated epigenetic aging was associated with dementia/mild cognitive impairment (n = 7). There was some evidence of an association with poorer cognition (n = 20), particularly with GrimAge acceleration, but this was inconsistent and varied across cognitive domains. A meta-analysis was not performed due to high study heterogeneity. Conclusion: There is insufficient evidence to indicate that current epigenetic aging clocks can be clinically useful biomarkers of dementia or cognitive aging.
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Affiliation(s)
- Aoshuang Zhou
- Division of Epidemiology, Jockey Club School of Public Health & Primary Care, Chinese University of Hong Kong, Hong Kong, China
| | - Zimu Wu
- Biological Neuropsychiatry & Dementia Unit, School of Public Health & Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia
| | - Aung Zaw Zaw Phyo
- Biological Neuropsychiatry & Dementia Unit, School of Public Health & Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia
| | - Daniel Torres
- Biological Neuropsychiatry & Dementia Unit, School of Public Health & Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia
| | - Swarna Vishwanath
- Biological Neuropsychiatry & Dementia Unit, School of Public Health & Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia
| | - Joanne Ryan
- Biological Neuropsychiatry & Dementia Unit, School of Public Health & Preventive Medicine, Monash University, Melbourne, Victoria, 3004, Australia
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Parkinson's disease-associated, sex-specific changes in DNA methylation at PARK7 (DJ-1), SLC17A6 (VGLUT2), PTPRN2 (IA-2β), and NR4A2 (NURR1) in cortical neurons. NPJ Parkinsons Dis 2022; 8:120. [PMID: 36151217 PMCID: PMC9508164 DOI: 10.1038/s41531-022-00355-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 06/24/2022] [Indexed: 12/04/2022] Open
Abstract
Evidence for epigenetic regulation playing a role in Parkinson's disease (PD) is growing, particularly for DNA methylation. Approximately 90% of PD cases are due to a complex interaction between age, genes, and environmental factors, and epigenetic marks are thought to mediate the relationship between aging, genetics, the environment, and disease risk. To date, there are a small number of published genome-wide studies of DNA methylation in PD, but none accounted for cell type or sex in their analyses. Given the heterogeneity of bulk brain tissue samples and known sex differences in PD risk, progression, and severity, these are critical variables to account for. In this genome-wide analysis of DNA methylation in an enriched neuronal population from PD postmortem parietal cortex, we report sex-specific PD-associated methylation changes in PARK7 (DJ-1), SLC17A6 (VGLUT2), PTPRN2 (IA-2β), NR4A2 (NURR1), and other genes involved in developmental pathways, neurotransmitter packaging and release, and axon and neuron projection guidance.
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126
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Carratto TMT, Moraes VMS, Recalde TSF, Oliveira MLGD, Teixeira Mendes-Junior C. Applications of massively parallel sequencing in forensic genetics. Genet Mol Biol 2022; 45:e20220077. [PMID: 36121926 PMCID: PMC9514793 DOI: 10.1590/1678-4685-gmb-2022-0077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022] Open
Abstract
Massively parallel sequencing, also referred to as next-generation sequencing, has positively changed DNA analysis, allowing further advances in genetics. Its capability of dealing with low quantity/damaged samples makes it an interesting instrument for forensics. The main advantage of MPS is the possibility of analyzing simultaneously thousands of genetic markers, generating high-resolution data. Its detailed sequence information allowed the discovery of variations in core forensic short tandem repeat loci, as well as the identification of previous unknown polymorphisms. Furthermore, different types of markers can be sequenced in a single run, enabling the emergence of DIP-STRs, SNP-STR haplotypes, and microhaplotypes, which can be very useful in mixture deconvolution cases. In addition, the multiplex analysis of different single nucleotide polymorphisms can provide valuable information about identity, biogeographic ancestry, paternity, or phenotype. DNA methylation patterns, mitochondrial DNA, mRNA, and microRNA profiling can also be analyzed for different purposes, such as age inference, maternal lineage analysis, body-fluid identification, and monozygotic twin discrimination. MPS technology also empowers the study of metagenomics, which analyzes genetic material from a microbial community to obtain information about individual identification, post-mortem interval estimation, geolocation inference, and substrate analysis. This review aims to discuss the main applications of MPS in forensic genetics.
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Affiliation(s)
- Thássia Mayra Telles Carratto
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | - Vitor Matheus Soares Moraes
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | | | | | - Celso Teixeira Mendes-Junior
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
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Ashapkin V, Suvorov A, Pilsner JR, Krawetz SA, Sergeyev O. Age-associated epigenetic changes in mammalian sperm: implications for offspring health and development. Hum Reprod Update 2022; 29:24-44. [PMID: 36066418 PMCID: PMC9825272 DOI: 10.1093/humupd/dmac033] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 08/05/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Modern reproductive behavior in most developed countries is characterized by delayed parenthood. Older gametes are generally less fertile, accumulating and compounding the effects of varied environmental exposures that are modified by lifestyle factors. Clinicians are primarily concerned with advanced maternal age, while the influence of paternal age on fertility, early development and offspring health remains underappreciated. There is a growing trend to use assisted reproductive technologies for couples of advanced reproductive age. Thus, the number of children born from older gametes is increasing. OBJECTIVE AND RATIONALE We review studies reporting age-associated epigenetic changes in mammals and humans in sperm, including DNA methylation, histone modifications and non-coding RNAs. The interplay between environment, fertility, ART and age-related epigenetic signatures is explored. We focus on the association of sperm epigenetics on epigenetic and phenotype events in embryos and offspring. SEARCH METHODS Peer-reviewed original and review articles over the last two decades were selected using PubMed and the Web of Science for this narrative review. Searches were performed by adopting the two groups of main terms. The first group included 'advanced paternal age', 'paternal age', 'postponed fatherhood', 'late fatherhood', 'old fatherhood' and the second group included 'sperm epigenetics', 'sperm', 'semen', 'epigenetic', 'inheritance', 'DNA methylation', 'chromatin', 'non-coding RNA', 'assisted reproduction', 'epigenetic clock'. OUTCOMES Age is a powerful factor in humans and rodent models associated with increased de novo mutations and a modified sperm epigenome. Age affects all known epigenetic mechanisms, including DNA methylation, histone modifications and profiles of small non-coding (snc)RNA. While DNA methylation is the most investigated, there is a controversy about the direction of age-dependent changes in differentially hypo- or hypermethylated regions with advanced age. Successful development of the human sperm epigenetic clock based on cross-sectional data and four different methods for DNA methylation analysis indicates that at least some CpG exhibit a linear relationship between methylation levels and age. Rodent studies show a significant overlap between genes regulated through age-dependent differentially methylated regions and genes targeted by age-dependent sncRNA. Both age-dependent epigenetic mechanisms target gene networks enriched for embryo developmental, neurodevelopmental, growth and metabolic pathways. Thus, age-dependent changes in the sperm epigenome cannot be described as a stochastic accumulation of random epimutations and may be linked with autism spectrum disorders. Chemical and lifestyle exposures and ART techniques may affect the epigenetic aging of sperm. Although most epigenetic modifications are erased in the early mammalian embryo, there is growing evidence that an altered offspring epigenome and phenotype is linked with advanced paternal age due to the father's sperm accumulating epigenetic changes with time. It has been hypothesized that age-induced changes in the sperm epigenome are profound, physiological and dynamic over years, yet stable over days and months, and likely irreversible. WIDER IMPLICATIONS This review raises a concern about delayed fatherhood and age-associated changes in the sperm epigenome that may compromise reproductive health of fathers and transfer altered epigenetic information to subsequent generations. Prospective studies using healthy males that consider confounders are recommended. We suggest a broader discussion focused on regulation of the father's age in natural and ART conceptions is needed. The professional community should be informed and should raise awareness in the population and when counseling older men.
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Affiliation(s)
| | | | - J Richard Pilsner
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Oleg Sergeyev
- Correspondence address. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory, House 1, Building 40, Room 322, Moscow 119992, Russia. E-mail: https://orcid.org/0000-0002-5745-3348
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Yu T, Slone J, Liu W, Barnes R, Opresko PL, Wark L, Mai S, Horvath S, Huang T. Premature aging is associated with higher levels of 8-oxoguanine and increased DNA damage in the Polg mutator mouse. Aging Cell 2022; 21:e13669. [PMID: 35993394 PMCID: PMC9470903 DOI: 10.1111/acel.13669] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/07/2022] [Accepted: 06/24/2022] [Indexed: 01/24/2023] Open
Abstract
Mitochondrial dysfunction plays an important role in the aging process. However, the mechanism by which this dysfunction causes aging is not fully understood. The accumulation of mutations in the mitochondrial genome (or "mtDNA") has been proposed as a contributor. One compelling piece of evidence in support of this hypothesis comes from the PolgD257A/D257A mutator mouse (Polgmut/mut ). These mice express an error-prone mitochondrial DNA polymerase that results in the accumulation of mtDNA mutations, accelerated aging, and premature death. In this paper, we have used the Polgmut/mut model to investigate whether the age-related biological effects observed in these mice are triggered by oxidative damage to the DNA that compromises the integrity of the genome. Our results show that mutator mouse has significantly higher levels of 8-oxoguanine (8-oxoGua) that are correlated with increased nuclear DNA (nDNA) strand breakage and oxidative nDNA damage, shorter average telomere length, and reduced mtDNA integrity. Based on these results, we propose a model whereby the increased level of reactive oxygen species (ROS) associated with the accumulation of mtDNA mutations in Polgmut/mut mice results in higher levels of 8-oxoGua, which in turn lead to compromised DNA integrity and accelerated aging via increased DNA fragmentation and telomere shortening. These results suggest that mitochondrial play a central role in aging and may guide future research to develop potential therapeutics for mitigating aging process.
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Affiliation(s)
- Tenghui Yu
- Department of PediatricsUniversity at BuffaloBuffaloNew YorkUSA,Human Aging Research Institute, School of Life ScienceNanchang UniversityNanchangChina,Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Jesse Slone
- Department of PediatricsUniversity at BuffaloBuffaloNew YorkUSA,Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Wensheng Liu
- Department of PediatricsUniversity at BuffaloBuffaloNew YorkUSA
| | - Ryan Barnes
- Department of Environmental and Occupational HealthUniversity of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer CenterPittsburghPennsylvaniaUSA
| | - Patricia L. Opresko
- Department of Environmental and Occupational HealthUniversity of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer CenterPittsburghPennsylvaniaUSA
| | - Landon Wark
- CancerCare Manitoba Research Institute, The Genomic Center for Cancer Research & DiagnosisUniversity of ManitobaWinnipegManitobaCanada
| | - Sabine Mai
- CancerCare Manitoba Research Institute, The Genomic Center for Cancer Research & DiagnosisUniversity of ManitobaWinnipegManitobaCanada
| | - Steve Horvath
- Human Genetics, David Geffen School of MedicineUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Taosheng Huang
- Department of PediatricsUniversity at BuffaloBuffaloNew YorkUSA,Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
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129
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Schaffner SL, Kobor MS. DNA methylation as a mediator of genetic and environmental influences on Parkinson's disease susceptibility: Impacts of alpha-Synuclein, physical activity, and pesticide exposure on the epigenome. Front Genet 2022; 13:971298. [PMID: 36061205 PMCID: PMC9437223 DOI: 10.3389/fgene.2022.971298] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder with a complex etiology and increasing prevalence worldwide. As PD is influenced by a combination of genetic and environment/lifestyle factors in approximately 90% of cases, there is increasing interest in identification of the interindividual mechanisms underlying the development of PD as well as actionable lifestyle factors that can influence risk. This narrative review presents an outline of the genetic and environmental factors contributing to PD risk and explores the possible roles of cytosine methylation and hydroxymethylation in the etiology and/or as early-stage biomarkers of PD, with an emphasis on epigenome-wide association studies (EWAS) of PD conducted over the past decade. Specifically, we focused on variants in the SNCA gene, exposure to pesticides, and physical activity as key contributors to PD risk. Current research indicates that these factors individually impact the epigenome, particularly at the level of CpG methylation. There is also emerging evidence for interaction effects between genetic and environmental contributions to PD risk, possibly acting across multiple omics layers. We speculated that this may be one reason for the poor replicability of the results of EWAS for PD reported to date. Our goal is to provide direction for future epigenetics studies of PD to build upon existing foundations and leverage large datasets, new technologies, and relevant statistical approaches to further elucidate the etiology of this disease.
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Affiliation(s)
- Samantha L. Schaffner
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
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130
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C. Silva T, Young JI, Zhang L, Gomez L, Schmidt MA, Varma A, Chen XS, Martin ER, Wang L. Cross-tissue analysis of blood and brain epigenome-wide association studies in Alzheimer's disease. Nat Commun 2022; 13:4852. [PMID: 35982059 PMCID: PMC9388493 DOI: 10.1038/s41467-022-32475-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/01/2022] [Indexed: 01/17/2023] Open
Abstract
To better understand DNA methylation in Alzheimer's disease (AD) from both mechanistic and biomarker perspectives, we performed an epigenome-wide meta-analysis of blood DNA methylation in two large independent blood-based studies in AD, the ADNI and AIBL studies, and identified 5 CpGs, mapped to the SPIDR, CDH6 genes, and intergenic regions, that are significantly associated with AD diagnosis. A cross-tissue analysis that combined these blood DNA methylation datasets with four brain methylation datasets prioritized 97 CpGs and 10 genomic regions that are significantly associated with both AD neuropathology and AD diagnosis. An out-of-sample validation using the AddNeuroMed dataset showed the best performing logistic regression model includes age, sex, immune cell type proportions, and methylation risk score based on prioritized CpGs in cross-tissue analysis (AUC = 0.696, 95% CI: 0.616 - 0.770, P-value = 2.78 × 10-5). Our study offers new insights into epigenetics in AD and provides a valuable resource for future AD biomarker discovery.
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Affiliation(s)
- Tiago C. Silva
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Juan I. Young
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lanyu Zhang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Lissette Gomez
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Michael A. Schmidt
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Achintya Varma
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - X. Steven Chen
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Eden R. Martin
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lily Wang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
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131
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Bergquist SH, Wang D, Smith AK, Roberts DL, Moore MA. Hormetic association between perceived stress and human epigenetic aging based on resilience capacity. Biogerontology 2022; 23:615-627. [PMID: 35960459 DOI: 10.1007/s10522-022-09985-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/03/2022] [Indexed: 11/02/2022]
Abstract
Chronic stress is associated with deleterious health outcomes and mortality risk. A potential mechanism by which stress affects healthspan and lifespan is acceleration of cellular aging. Biologic age prediction models, termed epigenetic clocks, have been developed to estimate biologic age differences among people with the same chronologic age. This study evaluates the simultaneous impact of perceived chronic stress and resilience on Grim Age acceleration. The perceived stress score (PSS) and Connor-Davidson Resilience Scale (CD-RISC) were used to measure chronic stress and resilience, respectively. DNA was extracted from whole blood and analyzed using the MethylationEPIC BeadChip. GrimAge estimates were calculated using the methylation age calculator. Forty-seven business executives were categorized by levels of high or low stress and resilience scores. Compared to participants with low stress and high resilience, those with low stress and low resilience demonstrated the strongest association with Grim Age acceleration (p = 0.044), after controlling for age and estimated cellular proportions. Interestingly, among participants with low resilience, those with high perceived stress had a weaker association with Grim Age acceleration than participants with low perceived stress. However, among participants with high resilience, low perceived stress had a weaker association with Grim Age acceleration than high perceived stress. Our findings suggest that the impact of perceived stress on epigenetic age acceleration may differ based on resilience capacity, with a potential paradoxical beneficial effect among those with low resilience.
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Affiliation(s)
- Sharon H Bergquist
- Department of Medicine, School of Medicine, Emory University, 1365 Clifton Rd, Atlanta, GA, A140030322, USA.
| | - Danyang Wang
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - David L Roberts
- Department of Medicine, School of Medicine, Emory University, 1365 Clifton Rd, Atlanta, GA, A140030322, USA
| | - Miranda A Moore
- Department of Medicine, School of Medicine, Emory University, 1365 Clifton Rd, Atlanta, GA, A140030322, USA.,Department of Family and Preventive Medicine, School of Medicine, Emory University, Atlanta, GA, USA
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132
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Vatov E, Zentgraf U, Ludewig U. Moderate DNA methylation changes associated with nitrogen remobilization and leaf senescence in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4733-4752. [PMID: 35552412 PMCID: PMC9366325 DOI: 10.1093/jxb/erac167] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The lifespan of plants is restricted by environmental and genetic components. Following the transition to reproductive growth, leaf senescence ends cellular life in monocarpic plants to remobilize nutrients to storage organs. In Arabidopsis, we initially observed altered leaf to seed ratios, faster senescence progression, altered leaf nitrogen recovery after transient nitrogen removal, and ultimately enhanced nitrogen remobilization from the leaves in two methylation mutants (ros1 and the triple dmr1/2 cmt3 knockout). Analysis of the DNA methylome in wild type Col-0 leaves identified an initial moderate decline of cytosine methylation with progressing leaf senescence, predominantly in the CG context. Late senescence was associated with moderate de novo methylation of cytosines, primarily in the CHH context. Relatively few differentially methylated regions, including one in the ROS1 promoter linked to down-regulation of ROS1, were present, but these were unrelated to known senescence-associated genes. Differential methylation patterns were identified in transcription factor binding sites, such as the W-boxes that are targeted by WRKYs. Methylation in artificial binding sites impaired transcription factor binding in vitro. However, it remains unclear how moderate methylome changes during leaf senescence are linked with up-regulated genes during senescence.
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Affiliation(s)
- Emil Vatov
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, D-70593, Germany
- Center for Molecular Biology of Plants (ZMBP), University of Tübingen, Tübingen, D-72076, Germany
| | - Ulrike Zentgraf
- Center for Molecular Biology of Plants (ZMBP), University of Tübingen, Tübingen, D-72076, Germany
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Reimann B, Martens DS, Wang C, Ghantous A, Herceg Z, Plusquin M, Nawrot TS. Interrelationships and determinants of aging biomarkers in cord blood. J Transl Med 2022; 20:353. [PMID: 35945616 PMCID: PMC9361565 DOI: 10.1186/s12967-022-03541-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Increasing evidence supports the concept of prenatal programming as an early factor in the aging process. DNA methylation age (DNAm age), global genome-wide DNA methylation (global methylation), telomere length (TL), and mitochondrial DNA content (mtDNA content) have independently been shown to be markers of aging, but their interrelationship and determinants at birth remain uncertain. METHODS We assessed the inter-correlation between the aging biomarkers DNAm age, global methylation, TL and mtDNA content using Pearson's correlation in 190 cord blood samples of the ENVIRONAGE birth cohort. TL and mtDNA content was measured via qPCR, while the DNA methylome was determined using the human 450K methylation Illumina microarray. Subsequently, DNAm age was calculated according to Horvath's epigenetic clock, and mean global, promoter, gene-body, and intergenic DNA methylation were determined. Path analysis, a form of structural equation modeling, was performed to disentangle the complex causal relationships among the aging biomarkers and their potential determinants. RESULTS DNAm age was inversely correlated with global methylation (r = -0.64, p < 0.001) and mtDNA content (r = - 0.16, p = 0.027). Cord blood TL was correlated with mtDNA content (r = 0.26, p < 0.001) but not with global methylation or DNAm age. Path analysis showed the strongest effect for global methylation on DNAm age with a decrease of 0.64 standard deviations (SD) in DNAm age for each SD (0.01%) increase in global methylation (p < 0.001). Among the applied covariates, newborn sex and season of delivery were the strongest determinants of aging biomarkers. CONCLUSIONS We provide insight into molecular aging signatures at the start of life, including their interrelations and determinants, showing that cord blood DNAm age is inversely associated with global methylation and mtDNA content but not with newborn telomere length. Our findings demonstrate that cord blood TL and DNAm age relate to different pathways/mechanisms of biological aging and can be influenced by environmental factors already at the start of life. These findings are relevant for understanding fetal programming and for the early prevention of noncommunicable diseases.
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Affiliation(s)
- Brigitte Reimann
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Dries S Martens
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Congrong Wang
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), Lyon, France
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), Lyon, France
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium.
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
- School of Public Health, Occupational and Environmental Medicine, KU Leuven, Leuven, Belgium
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134
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Baker EC, Earnhardt AL, Cilkiz KZ, Collins HC, Littlejohn BP, Cardoso RC, Ghaffari N, Long CR, Riggs PK, Randel RD, Welsh TH, Riley DG. DNA methylation patterns and gene expression from amygdala tissue of mature Brahman cows exposed to prenatal stress. Front Genet 2022; 13:949309. [PMID: 35991551 PMCID: PMC9389044 DOI: 10.3389/fgene.2022.949309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/30/2022] [Indexed: 11/23/2022] Open
Abstract
Prenatal stress can alter postnatal performance and temperament of cattle. These phenotypic effects may result from changes in gene expression caused by stress-induced epigenetic alterations. Specifically, shifts in gene expression caused by DNA methylation within the brain’s amygdala can result in altered behavior because it regulates fear, stress response and aggression in mammals Thus, the objective of this experiment was to identify DNA methylation and gene expression differences in the amygdala tissue of 5-year-old prenatally stressed (PNS) Brahman cows compared to control cows. Pregnant Brahman cows (n = 48) were transported for 2-h periods at 60 ± 5, 80 ± 5, 100 ± 5, 120 ± 5, and 140 ± 5 days of gestation. A non-transported group (n = 48) were controls (Control). Amygdala tissue was harvested from 6 PNS and 8 Control cows at 5 years of age. Overall methylation of gene body regions, promoter regions, and cytosine-phosphate-guanine (CpG) islands were compared between the two groups. In total, 202 genes, 134 promoter regions, and 133 CpG islands exhibited differential methylation (FDR ≤ 0.15). Following comparison of gene expression in the amygdala between the PNS and Control cows, 2 differentially expressed genes were identified (FDR ≤ 0.15). The minimal differences observed could be the result of natural changes of DNA methylation and gene expression as an animal ages, or because this degree of transportation stress was not severe enough to cause lasting effects on the offspring. A younger age may be a more appropriate time to assess methylation and gene expression differences produced by prenatal stress.
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Affiliation(s)
- Emilie C. Baker
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Audrey L. Earnhardt
- Department of Animal Science, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research, College Station, TX, United States
- Texas A&M AgriLife Research, Overton, TX, United States
| | - Kubra Z. Cilkiz
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Haley C. Collins
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Brittni P. Littlejohn
- Department of Animal Science, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research, Overton, TX, United States
| | - Rodolfo C. Cardoso
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Noushin Ghaffari
- Department of Computer Science, Prairie View A&M University, Prairie View, TX, United States
| | - Charles R. Long
- Department of Animal Science, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research, Overton, TX, United States
| | - Penny K. Riggs
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Ronald D. Randel
- Department of Animal Science, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research, Overton, TX, United States
| | - Thomas H. Welsh
- Department of Animal Science, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research, College Station, TX, United States
| | - David G. Riley
- Department of Animal Science, Texas A&M University, College Station, TX, United States
- *Correspondence: David G. Riley,
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Islam M, Strawn M, Behura SK. Fetal origin of sex‐bias brain aging. FASEB J 2022; 36:e22463. [DOI: 10.1096/fj.202200255rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023]
Affiliation(s)
- Maliha Islam
- Division of Animal Sciences University of Missouri Columbia Missouri USA
| | - Monica Strawn
- Division of Animal Sciences University of Missouri Columbia Missouri USA
| | - Susanta K. Behura
- Division of Animal Sciences University of Missouri Columbia Missouri USA
- MU Institute for Data Science and Informatics University of Missouri Columbia Missouri USA
- Interdisciplinary Neuroscience Program University of Missouri Columbia Missouri USA
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136
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Characterization of methylation patterns associated with lifestyle factors and vitamin D supplementation in a healthy elderly cohort from Southwest Sweden. Sci Rep 2022; 12:12670. [PMID: 35879377 PMCID: PMC9310683 DOI: 10.1038/s41598-022-15924-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/01/2022] [Indexed: 11/08/2022] Open
Abstract
Numerous studies have shown that lifestyle factors, such as regular physical activity and vitamin D intake, may remarkably improve overall health and mental wellbeing. This is especially important in older adults whose vitamin D deficiency occurs with a high prevalence. This study aimed to examine the influence of lifestyle and vitamin D on global DNA methylation patterns in an elderly cohort in Southwest of Sweden. We also sought to examine the methylation levels of specific genes involved in vitamin D's molecular and metabolic activated pathways. We performed a genome wide methylation analysis, using Illumina Infinium DNA Methylation EPIC 850kBeadChip array, on 277 healthy individuals from Southwest Sweden at the age of 70–95. The study participants also answered queries on lifestyle, vitamin intake, heart medication, and estimated health. Vitamin D intake did not in general affect methylation patterns, which is in concert with other studies. However, when comparing the group of individuals taking vitamin supplements, including vitamin D, with those not taking supplements, a difference in methylation in the solute carrier family 25 (SCL25A24) gene was found. This confirms a previous finding, where changes in expression of SLC25A24 were associated with vitamin D treatment in human monocytes. The combination of vitamin D intake and high physical activity increased methylation of genes linked to regulation of vitamin D receptor pathway, the Wnt pathway and general cancer processes. To our knowledge, this is the first study detecting epigenetic markers associated with the combined effects of vitamin D supplementation and high physical activity. These results deserve to be further investigated in an extended, interventional study cohort, where also the levels of 25(OH)D3 can be monitored.
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137
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Cao Y, Tian W, Wu J, Song X, Cao L, Luan X. DNA hypermethylation of NOTCH2NLC in neuronal intranuclear inclusion disease: a case-control study. J Neurol 2022; 269:6049-6057. [PMID: 35857137 DOI: 10.1007/s00415-022-11272-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/27/2022] [Accepted: 07/04/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND GGC repeat expansions in NOTCH2NLC gene have been recently proposed to cause neuronal intranuclear inclusion disease (NIID) via prevailing gain-of-function mechanism (protein and RNA toxicity). Nevertheless, increasing evidences suggest that epigenetics can also play a role in the pathogenesis of repeat-mediated disorders. METHODS In this study, using MethylTarget sequencing, we performed a quantitative analysis of the methylation status of 68 CpG sites located around the NOTCH2NLC promoter in 25 NIID patients and 25 age- and gender-matched healthy controls. We further explored the correlation of DNA methylation (DNAm) status with disease features and performed receiver operating characteristic (ROC) analysis. RESULTS DNAm levels of GGC repeats and adjacent CpG islands were higher in the NIID patients than in controls, independent of gender and family history. DNAm levels at 4 CpG sites (CpG_207, CpG_421, GpG_473 and CpG_523) were negatively correlated with age at onset, and DNAm levels at 7 CpG sites (CpG_25, CpG_298, CpG_336, CpG_374, CpG_411, CpG_421 and CpG_473) were positively correlated with GGC repeats. NIID patients had concomitant system symptoms besides nervous system symptoms, and negative correlations between NOTCH2NLC DNAm levels and the number of multi-systemic involvement were observed in the study. The area under the ROC curve at NOTCH2NLC DNAm level reached to 0.733 for the best cutoff point of 0.012. CONCLUSIONS Our findings suggested the aberrant DNAm status of the NOTCH2NLC promoter in NIID, and we explored the link between DNAm levels and disease features quantitatively for the first time, which may help to further explore pathogenic mechanism.
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Affiliation(s)
- Yuwen Cao
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Wotu Tian
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jingying Wu
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xingwang Song
- Institute of Neuroscience and Department of Neurology, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Cao
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.
| | - Xinghua Luan
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.
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Xu Y, Zhong L, Wei H, Li Y, Xie J, Xie L, Chen X, Guo X, Yin P, Li S, Zeng J, Li XJ, Lin L. Brain Region- and Age-Dependent 5-Hydroxymethylcytosine Activity in the Non-Human Primate. Front Aging Neurosci 2022; 14:934224. [PMID: 35912074 PMCID: PMC9326314 DOI: 10.3389/fnagi.2022.934224] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/15/2022] [Indexed: 11/24/2022] Open
Abstract
Because of the difficulty in collecting fresh brains of humans at different ages, it remains unknown how epigenetic regulation occurs in the primate brains during aging. In the present study, we examined the genomic distribution of 5hmC, an indicator of DNA methylation, in the brain regions of non-human primates (rhesus monkey) at the ages of 2 (juvenile), 8 (young adult), and 17 (old) years. We found that genomic 5hmC distribution was accumulated in the monkey brain as age increased and displayed unique patterns in the cerebellum and striatum in an age-dependent manner. We also observed a correlation between differentially hydroxymethylated regions (DhMRs) and genes that contribute to brain region-related functions and diseases. Our studies revealed, for the first time, the brain-region and age-dependent 5hmC modifications in the non-human primate and the association of these 5hmC modifications with brain region-specific function and potentially aging-related brain diseases.
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Affiliation(s)
- Yanru Xu
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Liying Zhong
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Huixian Wei
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Yuwei Li
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Jiaxiang Xie
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Leijie Xie
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Xiusheng Chen
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Xiangyu Guo
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Peng Yin
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Shihua Li
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Junwei Zeng
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiao-Jiang Li
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Li Lin
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
- *Correspondence: Li Lin
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Di Lena P, Sala C, Nardini C. Evaluation of different computational methods for DNA methylation-based biological age. Brief Bioinform 2022; 23:6632619. [PMID: 35794713 DOI: 10.1093/bib/bbac274] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/27/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
In recent years there has been a widespread interest in researching biomarkers of aging that could predict physiological vulnerability better than chronological age. Aging, in fact, is one of the most relevant risk factors for a wide range of maladies, and molecular surrogates of this phenotype could enable better patients stratification. Among the most promising of such biomarkers is DNA methylation-based biological age. Given the potential and variety of computational implementations (epigenetic clocks), we here present a systematic review of such clocks. Furthermore, we provide a large-scale performance comparison across different tissues and diseases in terms of age prediction accuracy and age acceleration, a measure of deviance from physiology. Our analysis offers both a state-of-the-art overview of the computational techniques developed so far and a heterogeneous picture of performances, which can be helpful in orienting future research.
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Affiliation(s)
- Pietro Di Lena
- Department of Computer Science and Engineering, University of Bologna, Mura Anteo Zamboni 7, 40126 Bologna, Italy
| | - Claudia Sala
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
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IL-7 promoted the development of thymic DN3 cells in aged mice via DNA demethylation of Bcl2 and c-Myc genes. Mol Immunol 2022; 147:21-29. [DOI: 10.1016/j.molimm.2022.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/11/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022]
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Gallego-Fabrega C, Muiño E, Cullell N, Cárcel-Márquez J, Lazcano U, Soriano-Tárraga C, Lledós M, Llucià-Carol L, Aguilera-Simón A, Marín R, Prats-Sánchez L, Camps-Renom P, Delgado-Mederos R, Martín-Campos JM, Delgado P, Martí-Fàbregas J, Montaner J, Krupinski J, Jiménez-Conde J, Roquer J, Fernández-Cadenas I. Biological Age Acceleration Is Lower in Women With Ischemic Stroke Compared to Men. Stroke 2022; 53:2320-2330. [PMID: 35209739 DOI: 10.1161/strokeaha.121.037419] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Stroke onset in women occurs later in life compared with men. The underlying mechanisms of these differences have not been established. Epigenetic clocks, based on DNA methylation (DNAm) profiles, are the most accurate biological age estimate. Epigenetic age acceleration (EAA) measures indicate whether an individual is biologically younger or older than expected. Our aim was to analyze whether sexual dichotomy at age of stroke onset is conditioned by EAA. METHODS We used 2 DNAm datasets from whole blood samples of case-control genetic studies of ischemic stroke (IS), a discovery cohort of 374 IS patients (N women=163, N men=211), from GRECOS (Genotyping Recurrence Risk of Stroke) and SEDMAN (Dabigatran Study in the Early Phase of Stroke, New Neuroimaging Markers and Biomarkers) studies and a replication cohort of 981 IS patients (N women=411, N men=570) from BASICMAR register. We compared chronological age, 2 DNAm-based biomarkers of aging and intrinsic and extrinsic epigenetic age acceleration EAA (IEAA and extrinsic EAA, respectively), in IS as well as in individual IS etiologic subtypes. Horvath and Hannum epigenetic clocks were used to assess the aging rate. A proteomic study using the SOMAScan multiplex assay was performed on 26 samples analyzing 1305 proteins. RESULTS Women present lower Hannum-extrinsic EAA values, whereas men have higher Hannum-extrinsic EAA values (women=-0.64, men=1.24, P=1.34×10-2); the same tendency was observed in the second cohort (women=-0.57, men=0.79, P=0.02). These differences seemed to be specific to cardioembolic and undetermined stroke subtypes. Additionally, 42 blood protein levels were associated with Hannum-extrinsic EAA (P<0.05), belonging to the immune effector process (P=1.54×10-6) and platelet degranulation (P<8.74×10-6) pathways. CONCLUSIONS This study shows that sex-specific underlying biological mechanisms associated with stroke onset could be due to differences in biological age acceleration between men and women.
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Affiliation(s)
- Cristina Gallego-Fabrega
- Stroke Unit, Department of Neurology Santa Creu i Sant Pau, Barcelona, Spain (C.G.-F., A.A.-S., R.M., L.P.-S., P.C.-R., R.D.-M., J.M.-F.)
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain (C.G.-F., E.M., N.C., J.C.-M., M.L., L.L.-C., J.M.M.-C., I.F.-C.)
| | - Elena Muiño
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain (C.G.-F., E.M., N.C., J.C.-M., M.L., L.L.-C., J.M.M.-C., I.F.-C.)
| | - Natalia Cullell
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain (C.G.-F., E.M., N.C., J.C.-M., M.L., L.L.-C., J.M.M.-C., I.F.-C.)
- Department of Neurology, Hospital Universitari MútuaTerrassa/Fundació Docència i Recerca MútuaTerrassa, Spain (N.C., J.K.)
| | - Jara Cárcel-Márquez
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain (C.G.-F., E.M., N.C., J.C.-M., M.L., L.L.-C., J.M.M.-C., I.F.-C.)
| | - Uxue Lazcano
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain (C.G.-F., E.M., N.C., J.C.-M., M.L., L.L.-C., J.M.M.-C., I.F.-C.)
- Department of Neurology, Hospital del Mar; Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain (U.L., C.S.-T., J.J., J.R.)
| | - Carolina Soriano-Tárraga
- Department of Neurology, Hospital del Mar; Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain (U.L., C.S.-T., J.J., J.R.)
- Department of Psychiatry, Washington University School of Medicine, Saint-Louis, MO (C.S.-T.)
| | - Miquel Lledós
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain (C.G.-F., E.M., N.C., J.C.-M., M.L., L.L.-C., J.M.M.-C., I.F.-C.)
| | - Laia Llucià-Carol
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain (C.G.-F., E.M., N.C., J.C.-M., M.L., L.L.-C., J.M.M.-C., I.F.-C.)
- Institute for Biomedical Research of Barcelona (IIBB), National Spanish Research Council (CSIC) (L.L.-C.)
| | - Ana Aguilera-Simón
- Stroke Unit, Department of Neurology Santa Creu i Sant Pau, Barcelona, Spain (C.G.-F., A.A.-S., R.M., L.P.-S., P.C.-R., R.D.-M., J.M.-F.)
| | - Rebeca Marín
- Stroke Unit, Department of Neurology Santa Creu i Sant Pau, Barcelona, Spain (C.G.-F., A.A.-S., R.M., L.P.-S., P.C.-R., R.D.-M., J.M.-F.)
| | - Luis Prats-Sánchez
- Stroke Unit, Department of Neurology Santa Creu i Sant Pau, Barcelona, Spain (C.G.-F., A.A.-S., R.M., L.P.-S., P.C.-R., R.D.-M., J.M.-F.)
| | - Pol Camps-Renom
- Stroke Unit, Department of Neurology Santa Creu i Sant Pau, Barcelona, Spain (C.G.-F., A.A.-S., R.M., L.P.-S., P.C.-R., R.D.-M., J.M.-F.)
| | - Raquel Delgado-Mederos
- Stroke Unit, Department of Neurology Santa Creu i Sant Pau, Barcelona, Spain (C.G.-F., A.A.-S., R.M., L.P.-S., P.C.-R., R.D.-M., J.M.-F.)
| | - Jesús M Martín-Campos
- Stroke Unit, Department of Neurology Santa Creu i Sant Pau, Barcelona, Spain (C.G.-F., A.A.-S., R.M., L.P.-S., P.C.-R., R.D.-M., J.M.-F.)
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain (C.G.-F., E.M., N.C., J.C.-M., M.L., L.L.-C., J.M.M.-C., I.F.-C.)
| | - Pilar Delgado
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research, Universitat Autònoma de Barcelona, Spain (P.D.)
| | | | - Joan Montaner
- Department of Neurology, Virgen del Rocío and Macarena Hospitals, Institute of Biomedicine of Seville (IBiS), Seville, Spain (J.M.)
| | - Jerzy Krupinski
- Department of Neurology, Hospital Universitari MútuaTerrassa/Fundació Docència i Recerca MútuaTerrassa, Spain (N.C., J.K.)
- Centre for Biomedicine, Manchester Metropolitan University, United Kingdom (J.K.)
| | - J Jiménez-Conde
- Department of Neurology, Hospital del Mar; Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain (U.L., C.S.-T., J.J., J.R.)
| | - Jaume Roquer
- Department of Neurology, Hospital del Mar; Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain (U.L., C.S.-T., J.J., J.R.)
| | - Israel Fernández-Cadenas
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain (C.G.-F., E.M., N.C., J.C.-M., M.L., L.L.-C., J.M.M.-C., I.F.-C.)
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Davis DL, Metzger DB, Vann PH, Wong JM, Subasinghe KH, Garlotte IK, Phillips NR, Shetty RA, Forster MJ, Sumien N. Sex differences in neurobehavioral consequences of methamphetamine exposure in adult mice. Psychopharmacology (Berl) 2022; 239:2331-2349. [PMID: 35347365 PMCID: PMC9232998 DOI: 10.1007/s00213-022-06122-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/16/2022] [Indexed: 11/24/2022]
Abstract
RATIONALE Recreational and medical use of stimulants is increasing, and their use may increase susceptibility to aging and promote neurobehavioral impairments. The long-term consequences of these psychostimulants and how they interact with age have not been fully studied. OBJECTIVES Our study investigated whether chronic exposure to the prototypical psychostimulant, methamphetamine (METH), at doses designed to emulate human therapeutic dosing, would confer a pro-oxidizing redox shift promoting long-lasting neurobehavioral impairments. METHODS Groups of 4-month-old male and female C57BL/6 J mice were administered non-contingent intraperitoneal injections of either saline or METH (1.4 mg/kg) twice a day for 4 weeks. Mice were randomly assigned to one experimental group: (i) short-term cognitive assessments (at 5 months), (ii) long-term cognitive assessments (at 9.5 months), and (ii) longitudinal motor assessments (at 5, 7, and 9 months). Brain regions were assessed for oxidative stress and markers of neurotoxicity after behavior testing. RESULTS Chronic METH exposure induced short-term effects on associative memory, gait speed, dopamine (DA) signaling, astrogliosis in females, and spatial learning and memory, balance, DA signaling, and excitotoxicity in males. There were no long-term effects of chronic METH on cognition; however, it decreased markers of excitotoxicity in the striatum and exacerbated age-associated motor impairments in males. CONCLUSION In conclusion, cognitive and motor functions were differentially and sex-dependently affected by METH exposure, and oxidative stress did not seem to play a role in the observed behavioral outcomes. Future studies are necessary to continue exploring the long-term neurobehavioral consequences of drug use in both sexes and the relationship between aging and drugs.
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Affiliation(s)
- Delaney L Davis
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, TX, USA
| | - Daniel B Metzger
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, TX, USA
| | - Philip H Vann
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, TX, USA
| | - Jessica M Wong
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, TX, USA
| | - Kumudu H Subasinghe
- Department of Microbiology, Immunology & Genetics, UNT HSC, Fort Worth, TX, USA
| | - Isabelle K Garlotte
- Department of Microbiology, Immunology & Genetics, UNT HSC, Fort Worth, TX, USA
| | - Nicole R Phillips
- Department of Microbiology, Immunology & Genetics, UNT HSC, Fort Worth, TX, USA
| | - Ritu A Shetty
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, TX, USA
| | - Michael J Forster
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, TX, USA
| | - Nathalie Sumien
- Department of Pharmacology & Neuroscience, UNT HSC, Fort Worth, TX, USA.
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Reale A, Tagliatesta S, Zardo G, Zampieri M. Counteracting aged DNA methylation states to combat ageing and age-related diseases. Mech Ageing Dev 2022; 206:111695. [PMID: 35760211 DOI: 10.1016/j.mad.2022.111695] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/09/2022] [Accepted: 06/22/2022] [Indexed: 12/18/2022]
Abstract
DNA methylation (DNAm) overwrites information about multiple extrinsic factors on the genome. Age is one of these factors. Age causes characteristic DNAm changes that are thought to be not only major drivers of normal ageing but also precursors to diseases, cancer being one of these. Although there is still much to learn about the relationship between ageing, age-related diseases and DNAm, we now know how to interpret some of the effects caused by age in the form of changes in methylation marks at specific loci. In fact, these changes form the basis of the so called "epigenetic clocks", which translate the genomic methylation profile into an "epigenetic age". Epigenetic age does not only estimate chronological age but can also predict the risk of chronic diseases and mortality. Epigenetic age is believed to be one of the most accurate metrics of biological age. Initial evidence has recently been gathered pointing to the possibility that the rate of epigenetic ageing can be slowed down or even reversed. In this review, we discuss some of the most relevant advances in this field. Expected outcome is that this approach can provide insights into how to preserve health and reduce the impact of ageing diseases in humans.
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Affiliation(s)
- Anna Reale
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
| | - Stefano Tagliatesta
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00161 Rome, Italy.
| | - Giuseppe Zardo
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
| | - Michele Zampieri
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
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Hao X, Zhang J, Chen G, Cao W, Chen H, Chen S. Aberrant expression of GSTM5 in lung adenocarcinoma is associated with DNA hypermethylation and poor prognosis. BMC Cancer 2022; 22:685. [PMID: 35729618 PMCID: PMC9214983 DOI: 10.1186/s12885-022-09711-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/27/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glutathione-S transferases (GSTs) comprise a series of critical enzymes involved in detoxification of endogenous or xenobiotic compounds. Among several GSTs, Glutathione S-transferases mu (GSTM) has been implicated in a number of cancer types. However, the prognostic value and potential functions of the GSTM family genes have not been investigated in lung adenocarcinoma (LUAD). METHODS We examined the expression of GSTM5 in LUAD and identified associations among GSTM5 expression, clinicopathological features, survival data from the Cancer Genome Atlas (TCGA). The correlation between GSTM5 DNA methylation and its expression was analyzed using the MEXPRESS tool and UCSC Xena browser. The methylation status of GSTM5 in the promoter region in lung cancer cells was measured by methylation-specific PCR (MSP). After 5-aza-2'-deoxycytidine treatment of lung cancer cells, expression of GSTM5, cell proliferation and migration were assessed by RT-PCR, CCK-8 and transwell assays, respectively. RESULTS The results showed that GSTM5 was abnormally down-regulated in LUAD patients' tissues, and patients with low GSTM5 expression level had significantly shorter OS. Cox regression analyses revealed that GSTM5 was associated with overall survival (OS) of LUAD patients, which expression was an independent prognostic indicator in terms of OS (hazard ratio: 0.848; 95% CI: 0.762-0.945; P = 0.003). In addition, we found the promoter region of GSTM5 was hypermethylated in the tumor tissue compared with adjacent normal tissues, and the average methylation level of GSTM5 were moderately correlated with its expression. Moreover, methylation-specific PCR also showed that the GSTM5 gene promoter was hypermethylated in lung cancer cells, and treatment with 5-Aza-CdR can restore the gene expression and inhibit cell proliferation and migration. Finally, Gene Set Enrichment Analysis (GSEA) revealed that low GSTM5 expression was significantly related to DNA repair pathways. CONCLUSION Our data demonstrate that low GSTM5 expression and its high DNA methylation status may act as a novel putative molecular target gene for LUAD.
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Affiliation(s)
- Xuewei Hao
- Department of Biochemistry, Inspection Institute, Harbin Medical University-Daqing, Daqing, China
| | - Jun Zhang
- School of Biomedical Sciences and Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Guoyou Chen
- Department of Biopharmaceutical Sciences, College of Pharmacy, Harbin Medical University-Daqing, No. 39 Xinyang Street, High-tech Zone, Daqing, 163319, Heilongjiang Province, China
| | - Weiwei Cao
- Department of Biopharmaceutical Sciences, College of Pharmacy, Harbin Medical University-Daqing, No. 39 Xinyang Street, High-tech Zone, Daqing, 163319, Heilongjiang Province, China
| | - Hongyang Chen
- Department of Biopharmaceutical Sciences, College of Pharmacy, Harbin Medical University-Daqing, No. 39 Xinyang Street, High-tech Zone, Daqing, 163319, Heilongjiang Province, China
| | - Shuo Chen
- Department of Biopharmaceutical Sciences, College of Pharmacy, Harbin Medical University-Daqing, No. 39 Xinyang Street, High-tech Zone, Daqing, 163319, Heilongjiang Province, China.
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Epigenetic Variations in Chromatin Caused by the Combination of Bioregulators with Heavy Metals During Aging. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10427-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Gallego-Fabrega C, Muiño E, Cárcel-Márquez J, Llucià-Carol L, Lledós M, Martín-Campos JM, Cullell N, Fernández-Cadenas I. Genome-Wide Studies in Ischaemic Stroke: Are Genetics Only Useful for Finding Genes? Int J Mol Sci 2022; 23:6840. [PMID: 35743317 PMCID: PMC9224543 DOI: 10.3390/ijms23126840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 02/07/2023] Open
Abstract
Ischaemic stroke is a complex disease with some degree of heritability. This means that heritability factors, such as genetics, could be risk factors for ischaemic stroke. The era of genome-wide studies has revealed some of these heritable risk factors, although the data generated by these studies may also be useful in other disciplines. Analysis of these data can be used to understand the biological mechanisms associated with stroke risk and stroke outcome, to determine the causality between stroke and other diseases without the need for expensive clinical trials, or to find potential drug targets with higher success rates than other strategies. In this review we will discuss several of the most relevant studies regarding the genetics of ischaemic stroke and the potential use of the data generated.
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Affiliation(s)
- Cristina Gallego-Fabrega
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
| | - Elena Muiño
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
| | - Jara Cárcel-Márquez
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
| | - Laia Llucià-Carol
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
- Institute for Biomedical Research of Barcelona (IIBB), National Spanish Research Council (CSIC), 08036 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Miquel Lledós
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
| | - Jesús M. Martín-Campos
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
| | - Natalia Cullell
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
| | - Israel Fernández-Cadenas
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
- Stroke Pharmacogenomics and Genetics Group, Fundació MútuaTerrassa per la Docència i la Recerca, 08221 Terrassa, Spain
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O’Shea DM, Maynard T, Tremont G. DNA Methylation "GrimAge" Acceleration Mediates Sex/Gender Differences in Verbal Memory and Processing Speed: Findings From the Health and Retirement Study. J Gerontol A Biol Sci Med Sci 2022; 77:2402-2412. [PMID: 35715888 PMCID: PMC9799212 DOI: 10.1093/gerona/glac133] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Indexed: 01/20/2023] Open
Abstract
Whether sex/gender differences in rates of biological aging mediate sex/gender differences in cognition in older adults has not been fully examined. The aim of the current study was to investigate this association. Data from up to 1 928 participants (mean age = 75, standard deviation = 7.04, female = 57%) who took part in the 2016 Harmonized Cognitive Assessment Protocol and Venous Blood Study; substudies of the Health and Retirement Study were included in the current study. The residuals from 4 age-adjusted epigenetic clocks (Horvath, Hannum, PhenoAge, and GrimAge) were used to measure biological age acceleration. Sex/gender differences in cognition were tested using a series of analyses of covariance. Mediation analyses tested whether the measures of age acceleration accounted for these sex/gender differences, controlling for age, education, smoking status, and white blood cell count. Women outperformed men on measures of verbal learning, verbal memory, visual scanning, and processing speed. No other significant sex/gender differences were identified. Results from mediation analyses revealed that women's slower rates of GrimAge fully accounted for their faster processing speeds and partially accounted for their better performances on verbal learning, verbal memory, and visual scanning measures. None of the other measures of age acceleration were significant mediators. Accounting for sex/gender differences in biological aging may differentiate between cognitive sex/gender differences that are driven by universal (ie, age-related) versus sex-specific mechanisms. More broadly, these findings support the growing evidence that the GrimAge clock outperforms other clocks in predicting cognitive outcomes.
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Affiliation(s)
- Deirdre M O’Shea
- Address correspondence to: Deirdre M. O’Shea, PhD, Department of Psychiatry & Human Behavior, Warren Alpert Medical School, Brown University, 593 Eddy Street Building, 7th Floor, Providence, RI 02903, USA. E-mail:
| | | | - Geoffrey Tremont
- Department of Psychiatry & Human Behavior, Warren Alpert Medical School, Brown University, Providence, Rhode Island,USA,Rhode Island Hospital, Providence, Rhode Island, USA
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148
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Abstract
BACKGROUND Cardiovascular health (CVH) was defined by the American Heart Association as an integrative idealness of seven clinical or lifestyle factors. Based on populations of European ancestry, recent studies have shown that ideal CVH is associated with a slower aging rate. The aging rate is measured by levels of epigenetic age acceleration (EAA), usually obtained from the residuals of regressing DNA methylation (DNAm) age on chronological age. However, little has been known about the association of CVH with biological aging in Asian populations. METHODS AND RESULTS We here analyzed blood DNAm data and clinical/lifestyle factors of 2474 Taiwan Biobank (TWB) participants, to investigate the association of CVH with EAA. CVH was assessed by seven components: smoking status, physical activity, dietary habits, body mass index, total cholesterol, fasting glucose, and blood pressure levels. Four measures of EAA were applied, among which two were based on the first-generation DNAm clocks (HannumEAA and IEAA) and two were based on the second-generation clocks (PhenoEAA and GrimEAA). After excluding 276 individuals with cardiovascular diseases, we regressed EAA on the CVH score (ranging from 0 to 7, integrating the abovementioned seven components) while adjusting for sex, drinking status, and educational attainment. Our results showed that a decrease in one point in the CVH score was associated with a 0.350-year PhenoEAA (p = 4.5E-4) and a 0.499-year GrimEAA (p = 4.2E-15). By contrast, HannumEAA and IEAA were not significantly associated with the CVH score. We have obtained consistent results within each generation of epigenetic clocks. CONCLUSIONS This is one of the first studies to comprehensively investigate the associations of CVH with four epigenetic clocks. Our TWB data showed that ideal CVH is associated with lower levels of EAA calculated according to the second-generation epigenetic clocks (PhenoEAA and GrimEAA). Having an ideal CVH status can lower EAA and reduce the risk of aging-related disorders.
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149
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Shao X, Le Stunff C, Cheung W, Kwan T, Lathrop M, Pastinen T, Bougnères P. Differentially methylated CpGs in response to growth hormone administration in children with idiopathic short stature. Clin Epigenetics 2022; 14:65. [PMID: 35585611 PMCID: PMC9118695 DOI: 10.1186/s13148-022-01281-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/17/2022] [Indexed: 11/17/2022] Open
Abstract
Background Recombinant human growth hormone (rhGH) has shown a great growth-promoting potential in children with idiopathic short stature (ISS). However, the response to rhGH differs across individuals, largely due to genetic and epigenetic heterogeneity. Since epigenetic marks on the methylome can be dynamically influenced by GH, we performed a comprehensive pharmacoepigenomics analysis of DNA methylation changes associated with long-term rhGH administration in children with ISS.
Results We measured DNA methylation profiles before and after GH treatment (with a duration of ~ 18 months in average) on 47 healthy children using customized methylC-seq capture sequencing. Their changes were compared and associated with changes in plasma IGF1 by adjusting sex, age, treatment duration and estimated blood proportions. We observed a considerable inter-individual heterogeneity of DNA methylation changes responding to GH treatment. We identified 267 response-associated differentially methylated cytosines (DMCs) that were enriched in promoter regions, CpG islands and blood cell-type-specific regulatory elements. Furthermore, the genes associated with these DMCs were enriched in the biology process of “cell development,” “neuron differentiation” and “developmental growth,” and in the TGF-beta signaling pathway, PPAR Alpha pathway, endoderm differentiation pathway, adipocytokine signaling pathway as well as PI3K-Akt signaling pathway, and cAMP signaling pathway. Conclusion Our study provides a first insight in DNA methylation changes associated with rhGH administration, which may help understand mechanisms of epigenetic regulation on GH-responsive genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01281-z.
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Affiliation(s)
- Xiaojian Shao
- Digital Technologies Research Center, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada.
| | - Catherine Le Stunff
- UMR INSERM 1195 and Université Paris Saclay, Endocrinologie Pédiatrique, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Warren Cheung
- Genomic Medicine Center, Children's Mercy - Kansas City and Children's Mercy Research Institute, Kansas City, MO, 64108, USA
| | - Tony Kwan
- Department of Human Genetics, McGill University and McGill Genome Center, Montreal, QC, H3A 0G1, Canada
| | - Mark Lathrop
- Department of Human Genetics, McGill University and McGill Genome Center, Montreal, QC, H3A 0G1, Canada
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy - Kansas City and Children's Mercy Research Institute, Kansas City, MO, 64108, USA.
| | - Pierre Bougnères
- UMR INSERM 1195 and Université Paris Saclay, Endocrinologie Pédiatrique, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France.
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150
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Seale K, Horvath S, Teschendorff A, Eynon N, Voisin S. Making sense of the ageing methylome. Nat Rev Genet 2022; 23:585-605. [PMID: 35501397 DOI: 10.1038/s41576-022-00477-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2022] [Indexed: 12/22/2022]
Abstract
Over time, the human DNA methylation landscape accrues substantial damage, which has been associated with a broad range of age-related diseases, including cardiovascular disease and cancer. Various age-related DNA methylation changes have been described, including at the level of individual CpGs, such as differential and variable methylation, and at the level of the whole methylome, including entropy and correlation networks. Here, we review these changes in the ageing methylome as well as the statistical tools that can be used to quantify them. We detail the evidence linking DNA methylation to ageing phenotypes and the longevity strategies aimed at altering both DNA methylation patterns and machinery to extend healthspan and lifespan. Lastly, we discuss theories on the mechanistic causes of epigenetic ageing.
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Affiliation(s)
- Kirsten Seale
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Altos Labs, San Diego, CA, USA
| | - Andrew Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.,UCL Cancer Institute, University College London, London, UK
| | - Nir Eynon
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia.
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia.
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