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Porter HL, Brown CA, Roopnarinesingh X, Giles CB, Georgescu C, Freeman WM, Wren JD. Many chronological aging clocks can be found throughout the epigenome: Implications for quantifying biological aging. Aging Cell 2021; 20:e13492. [PMID: 34655509 PMCID: PMC8590098 DOI: 10.1111/acel.13492] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 08/19/2021] [Accepted: 09/09/2021] [Indexed: 01/01/2023] Open
Abstract
Epigenetic alterations are a hallmark of aging and age-related diseases. Computational models using DNA methylation data can create "epigenetic clocks" which are proposed to reflect "biological" aging. Thus, it is important to understand the relationship between predictive clock sites and aging biology. To do this, we examined over 450,000 methylation sites from 9,699 samples. We found ~20% of the measured genomic cytosines can be used to make many different epigenetic clocks whose age prediction performance surpasses that of telomere length. Of these predictive sites, the average methylation change over a lifetime was small (~1.5%) and these sites were under-represented in canonical regions of epigenetic regulation. There was only a weak association between "accelerated" epigenetic aging and disease. We also compare tissue-specific and pan-tissue clock performance. This is critical to applying clocks both to new sample sets in basic research, as well as understanding if clinically available tissues will be feasible samples to evaluate "epigenetic aging" in unavailable tissues (e.g., brain). Despite the reproducible and accurate age predictions from DNA methylation data, these findings suggest they may have limited utility as currently designed in understanding the molecular biology of aging and may not be suitable as surrogate endpoints in studies of anti-aging interventions. Purpose-built clocks for specific tissues age ranges or phenotypes may perform better for their specific purpose. However, if purpose-built clocks are necessary for meaningful predictions, then the utility of clocks and their application in the field needs to be considered in that context.
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Affiliation(s)
- Hunter L. Porter
- Oklahoma Medical Research FoundationOklahomaOKUSA
- University of Oklahoma Health Sciences CenterOklahomaOKUSA
- Oklahoma Center for Geroscience and Healthy Brain AgingOklahomaOKUSA
| | - Chase A. Brown
- Oklahoma Medical Research FoundationOklahomaOKUSA
- University of Oklahoma Health Sciences CenterOklahomaOKUSA
| | - Xiavan Roopnarinesingh
- Oklahoma Medical Research FoundationOklahomaOKUSA
- University of Oklahoma Health Sciences CenterOklahomaOKUSA
| | - Cory B. Giles
- Oklahoma Medical Research FoundationOklahomaOKUSA
- University of Oklahoma Health Sciences CenterOklahomaOKUSA
- Oklahoma Center for Geroscience and Healthy Brain AgingOklahomaOKUSA
| | | | - Willard M. Freeman
- Oklahoma Medical Research FoundationOklahomaOKUSA
- University of Oklahoma Health Sciences CenterOklahomaOKUSA
| | - Jonathan D. Wren
- Oklahoma Medical Research FoundationOklahomaOKUSA
- University of Oklahoma Health Sciences CenterOklahomaOKUSA
- Oklahoma Center for Geroscience and Healthy Brain AgingOklahomaOKUSA
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302
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Herrero-Roldán S, Rodrigo MJ, Hernández-Cabrera JA, Mitchell C, López M, Alcoba-Florez J, Fisher J, Espinosa F, León I. Reduction in Epigenetic Age Acceleration Is Related to Empathy in Mothers with Neglectful Caregiving. Brain Sci 2021; 11:brainsci11111376. [PMID: 34827375 PMCID: PMC8615407 DOI: 10.3390/brainsci11111376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/01/2021] [Accepted: 10/18/2021] [Indexed: 11/16/2022] Open
Abstract
DNA methylation clocks are used as molecular estimators of epigenetic age, but with little evidence in mothers and none in neglectful mothering. We investigated differences in epigenetic age acceleration (EAA) and the role of empathy using the PhenoAge clock. We collected saliva samples from mothers with extreme disregard for their child's needs (50 in the neglect group, NG) and mothers with non-neglectful caregiving (87 in the control group, CG). Mothers completed an empathy scale, along with questionnaires of their own childhood maltreatment, adverse life events and psychiatric disorders. Sociodemographic variables potentially affecting EAA were also measured. The ANCOVA solution showed a significant increase in EAA in the NG compared to the CG, after adjustment for maternal age, number of pregnancies, financial assistance, adverse events, childhood maltreatment and psychiatric disorder. The group interaction effects showed a reduction in EAA for greater empathic concern and for a higher education level both as positive factors, and an increment in EAA for mothers living in a two-parent family as a risk factor, all in the NG. Our findings open the search for protective factors of EAA associated with caregiver behavior to reduce health vulnerabilities and poor social functioning, especially for mothers at risk of maladaptive caregiving.
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Affiliation(s)
- Silvia Herrero-Roldán
- Instituto Universitario de Neurociencia, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain; (S.H.-R.); (M.J.R.); (J.A.H.-C.); (F.E.)
- Facultad de Psicología, Universidad de La Laguna, 38071 San Cristóbal de La Laguna, Spain
| | - María José Rodrigo
- Instituto Universitario de Neurociencia, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain; (S.H.-R.); (M.J.R.); (J.A.H.-C.); (F.E.)
- Facultad de Psicología, Universidad de La Laguna, 38071 San Cristóbal de La Laguna, Spain
| | - Juan A. Hernández-Cabrera
- Instituto Universitario de Neurociencia, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain; (S.H.-R.); (M.J.R.); (J.A.H.-C.); (F.E.)
- Facultad de Psicología, Universidad de La Laguna, 38071 San Cristóbal de La Laguna, Spain
| | - Colter Mitchell
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48109, USA; (C.M.); (J.F.)
- Population Studies Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maykel López
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland;
| | - Julia Alcoba-Florez
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, 38010 San Cristóbal de La Laguna, Spain;
| | - Jonah Fisher
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48109, USA; (C.M.); (J.F.)
| | - Fernanda Espinosa
- Instituto Universitario de Neurociencia, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain; (S.H.-R.); (M.J.R.); (J.A.H.-C.); (F.E.)
- Facultad de Psicología, Universidad de La Laguna, 38071 San Cristóbal de La Laguna, Spain
| | - Inmaculada León
- Instituto Universitario de Neurociencia, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain; (S.H.-R.); (M.J.R.); (J.A.H.-C.); (F.E.)
- Facultad de Psicología, Universidad de La Laguna, 38071 San Cristóbal de La Laguna, Spain
- Correspondence: ; Tel.: +34-9223-17506
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303
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Samoilova EM, Belopasov VV, Ekusheva EV, Zhang C, Troitskiy AV, Baklaushev VP. Epigenetic Clock and Circadian Rhythms in Stem Cell Aging and Rejuvenation. J Pers Med 2021; 11:1050. [PMID: 34834402 PMCID: PMC8620936 DOI: 10.3390/jpm11111050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/12/2022] Open
Abstract
This review summarizes the current understanding of the interaction between circadian rhythms of gene expression and epigenetic clocks characterized by the specific profile of DNA methylation in CpG-islands which mirror the senescence of all somatic cells and stem cells in particular. Basic mechanisms of regulation for circadian genes CLOCK-BMAL1 as well as downstream clock-controlled genes (ССG) are also discussed here. It has been shown that circadian rhythms operate by the finely tuned regulation of transcription and rely on various epigenetic mechanisms including the activation of enhancers/suppressors, acetylation/deacetylation of histones and other proteins as well as DNA methylation. Overall, up to 20% of all genes expressed by the cell are subject to expression oscillations associated with circadian rhythms. Additionally included in the review is a brief list of genes involved in the regulation of circadian rhythms, along with genes important for cell aging, and oncogenesis. Eliminating some of them (for example, Sirt1) accelerates the aging process, while the overexpression of Sirt1, on the contrary, protects against age-related changes. Circadian regulators control a number of genes that activate the cell cycle (Wee1, c-Myc, p20, p21, and Cyclin D1) and regulate histone modification and DNA methylation. Approaches for determining the epigenetic age from methylation profiles across CpG islands in individual cells are described. DNA methylation, which characterizes the function of the epigenetic clock, appears to link together such key biological processes as regeneration and functioning of stem cells, aging and malignant transformation. Finally, the main features of adult stem cell aging in stem cell niches and current possibilities for modulating the epigenetic clock and stem cells rejuvenation as part of antiaging therapy are discussed.
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Affiliation(s)
- Ekaterina M. Samoilova
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, 115682 Moscow, Russia; (A.V.T.); (V.P.B.)
| | | | - Evgenia V. Ekusheva
- Academy of Postgraduate Education of the Federal Scientific and Clinical Center for Specialized Types of Medical Care and Medical Technologies, FMBA of Russia, 125371 Moscow, Russia;
| | - Chao Zhang
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China;
| | - Alexander V. Troitskiy
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, 115682 Moscow, Russia; (A.V.T.); (V.P.B.)
| | - Vladimir P. Baklaushev
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, 115682 Moscow, Russia; (A.V.T.); (V.P.B.)
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304
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NEOage clocks - epigenetic clocks to estimate post-menstrual and postnatal age in preterm infants. Aging (Albany NY) 2021; 13:23527-23544. [PMID: 34655469 PMCID: PMC8580352 DOI: 10.18632/aging.203637] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/28/2021] [Indexed: 02/02/2023]
Abstract
Epigenetic clocks based on DNA methylation (DNAm) can accurately predict chronological age and are thought to capture biological aging. A variety of epigenetic clocks have been developed for different tissue types and age ranges, but none have focused on postnatal age prediction for preterm infants. Epigenetic estimators of biological age might be especially informative in epidemiologic studies of neonates since DNAm is highly dynamic during the neonatal period and this is a key developmental window. Additionally, markers of biological aging could be particularly important for those born preterm since they are at heightened risk of developmental impairments. We aimed to fill this gap by developing epigenetic clocks for neonatal aging in preterm infants. As part of the Neonatal Neurobehavior and Outcomes in Very Preterm Infants (NOVI) study, buccal cells were collected at NICU discharge to profile DNAm levels in 542 very preterm infants. We applied elastic net regression to identify four epigenetic clocks (NEOage Clocks) predictive of post-menstrual and postnatal age, compatible with the Illumina EPIC and 450K arrays. We observed high correlations between predicted and reported ages (0.93 - 0.94) with root mean squared errors (1.28 - 1.63 weeks). Epigenetic estimators of neonatal aging in preterm infants can be useful tools to evaluate biological maturity and associations with neonatal and long-term morbidities.
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305
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Secci R, Hartmann A, Walter M, Grabe HJ, Van der Auwera-Palitschka S, Kowald A, Palmer D, Rimbach G, Fuellen G, Barrantes I. Biomarkers of geroprotection and cardiovascular health: An overview of omics studies and established clinical biomarkers in the context of diet. Crit Rev Food Sci Nutr 2021; 63:2426-2446. [PMID: 34648415 DOI: 10.1080/10408398.2021.1975638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The slowdown, inhibition, or reversal of age-related decline (as a composite of disease, dysfunction, and, ultimately, death) by diet or natural compounds can be defined as dietary geroprotection. While there is no single reliable biomarker to judge the effects of dietary geroprotection, biomarker signatures based on omics (epigenetics, gene expression, microbiome composition) are promising candidates. Recently, omic biomarkers started to supplement established clinical ones such as lipid profiles and inflammatory cytokines. In this review, we focus on human data. We first summarize the current take on genetic biomarkers based on epidemiological studies. However, most of the remaining biomarkers that we describe, whether omics-based or clinical, are related to intervention studies. Then, because of their promising potential in the context of dietary geroprotection, we focus on the effects of berry-based interventions, which up to now have been mostly described employing clinical markers. We provide an aggregation and tabulation of all the recent systematic reviews and meta-analyses that we could find related to this topic. Finally, we present evidence for the importance of the "nutribiography," that is, the influence that an individual's history of diet and natural compound consumption can have on the effects of dietary geroprotection.
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Affiliation(s)
- Riccardo Secci
- Junior Research Group Translational Bioinformatics, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Alexander Hartmann
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | - Michael Walter
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Rostock, University of Rostock, Rostock, Germany.,Institute of Laboratory Medicine, Clinical Chemistry, and Pathobiochemistry, Charite University Medical Center, Berlin, Germany
| | - Hans Jörgen Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany.,German Centre for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, Germany
| | - Sandra Van der Auwera-Palitschka
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany.,German Centre for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, Germany
| | - Axel Kowald
- Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock University Medical Center, Rostock, Germany
| | - Daniel Palmer
- Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock University Medical Center, Rostock, Germany
| | - Gerald Rimbach
- Institute of Human Nutrition and Food Science, University of Kiel, Kiel, Germany
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock University Medical Center, Rostock, Germany
| | - Israel Barrantes
- Junior Research Group Translational Bioinformatics, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
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306
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Kocabas Ş, Sanlier N. A comprehensive overview of the complex relationship between epigenetics, bioactive components, cancer, and aging. Crit Rev Food Sci Nutr 2021:1-13. [PMID: 34623201 DOI: 10.1080/10408398.2021.1986803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Among age-related diseases, the incidence of cancer increases significantly due to the overlap of some molecular pathways between cancer and aging. While the genetic influence on the human lifespan is estimated to be about 20-25%, epigenetic changes play an important role in modulating individual health status, aging. Aging and age-related conditions are processes that can be modified by both genetic, environmental factors, including dietary habits. Epigenetics is a new discipline has significant potential to be applied for the prevention, management of certain carcinomas and diseases. Epigenetic modifications may play an important role in disease occurrence and pathogenesis. Some nutritional components can be significantly effective in the prevention of breast, skin, esophagus, colorectal, prostate, pancreatic, lung cancers. It contains minerals, vitamins, and some bioactive components (curcumin, indole 3 carbinol, di-indolylmethane, sulforaphane, epigallocatechin-3-gallate, genistein, resveratrol, pterostilbene, apigenin, etc.) regulatory processes. However, compelling evidence suggests that dietary habits can manipulate the aging process and/or its consequences, have health benefits. Aging processes become complex when combined with the relational role of bioactive nutritional components on gene expression. In this review, the relationship between epigenetic processes caused by DNA methylylation, histone modification, non-coding m-RNA, and telomerase activity, the risk of aging and cancer is discussed.
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Affiliation(s)
- Şule Kocabas
- Department of Nutrition and Dietetics, School of Health Sciences, Ankara Medipol University, Altındağ, Ankara, Turkey
| | - Nevin Sanlier
- Department of Nutrition and Dietetics, School of Health Sciences, Ankara Medipol University, Altındağ, Ankara, Turkey
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307
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Lohman T, Bains G, Berk L, Lohman E. Predictors of Biological Age: The Implications for Wellness and Aging Research. Gerontol Geriatr Med 2021; 7:23337214211046419. [PMID: 34595331 PMCID: PMC8477681 DOI: 10.1177/23337214211046419] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/14/2021] [Accepted: 08/18/2021] [Indexed: 12/26/2022] Open
Abstract
As healthspan and lifespan research breakthroughs have become more commonplace, the need for valid, practical markers of biological age is becoming increasingly paramount. The accessibility and affordability of biological age predictors that can reveal information about mortality and morbidity risk, as well as remaining years of life, has profound clinical and research implications. In this review, we examine 5 groups of aging biomarkers capable of providing accurate biological age estimations. The unique capabilities of these biomarkers have far reaching implications for the testing of both pharmaceutical and non-pharmaceutical interventions designed to slow or reverse biological aging. Additionally, the enhanced validity and availability of these tools may have increasingly relevant clinical value. The authors of this review explore those implications, with an emphasis on lifestyle modification research, and provide an overview of the current evidence regarding 5 biological age predictor categories: Telomere length, composite biomarkers, DNA methylation “epigenetic clocks,” transcriptional predictors of biological age, and functional age predictors.
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Affiliation(s)
- Trevor Lohman
- School of Allied Health Professions, Loma Linda University, Loma Linda, CA, USA
| | - Gurinder Bains
- School of Allied Health Professions, Loma Linda University, Loma Linda, CA, USA
| | - Lee Berk
- School of Allied Health Professions, Loma Linda University, Loma Linda, CA, USA
| | - Everett Lohman
- School of Allied Health Professions, Loma Linda University, Loma Linda, CA, USA
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308
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Horvath S, Zoller JA, Haghani A, Jasinska AJ, Raj K, Breeze CE, Ernst J, Vaughan KL, Mattison JA. Epigenetic clock and methylation studies in the rhesus macaque. GeroScience 2021; 43:2441-2453. [PMID: 34487267 PMCID: PMC8599607 DOI: 10.1007/s11357-021-00429-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/01/2021] [Indexed: 11/28/2022] Open
Abstract
Methylation levels at specific CpG positions in the genome have been used to develop accurate estimators of chronological age in humans, mice, and other species. Although epigenetic clocks are generally species-specific, the principles underpinning them appear to be conserved at least across the mammalian class. This is exemplified by the successful development of epigenetic clocks for mice and several other mammalian species. Here, we describe epigenetic clocks for the rhesus macaque (Macaca mulatta), the most widely used nonhuman primate in biological research. Using a custom methylation array (HorvathMammalMethylChip40), we profiled n = 281 tissue samples (blood, skin, adipose, kidney, liver, lung, muscle, and cerebral cortex). From these data, we generated five epigenetic clocks for macaques. These clocks differ with regard to applicability to different tissue types (pan-tissue, blood, skin), species (macaque only or both humans and macaques), and measure of age (chronological age versus relative age). Additionally, the age-based human-macaque clock exhibits a high age correlation (R = 0.89) with the vervet monkey (Chlorocebus sabaeus), another Old World species. Four CpGs within the KLF14 promoter were consistently altered with age in four tissues (adipose, blood, cerebral cortex, skin). Future studies will be needed to evaluate whether these epigenetic clocks predict age-related conditions in the rhesus macaque.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Anna J. Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA Los Angeles, USA
| | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, , Didcot, UK
| | | | - Jason Ernst
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Kelli L. Vaughan
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, 16701 Elmer School Rd., MD 20842 Dickerson, USA
| | - Julie A. Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, 16701 Elmer School Rd., MD 20842 Dickerson, USA
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309
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Lin WY, Wang YC, Teng IH, Liu C, Lou XY. Associations of five obesity metrics with epigenetic age acceleration: Evidence from 2,474 Taiwan Biobank participants. Obesity (Silver Spring) 2021; 29:1731-1738. [PMID: 34472716 DOI: 10.1002/oby.23255] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVE Obesity is associated with epigenetic age acceleration (EAA), resulting in an increased risk of many age-related disorders. However, most studies have focused on the relationship of EAA with BMI. Whether any other obesity metric is more relevant to EAA remains unknown. METHODS Here, the methylation ages of 2,474 Taiwan Biobank (TWB) participants were calculated according to Levine's phenotypic age (PhenoAge) and Lu's GrimAge. Residuals from regressing methylation age on chronological age were used to quantify PhenoEAA and GrimEAA. Five obesity metrics were evaluated, namely BMI, body fat percentage, waist circumference, hip circumference, and waist-hip ratio. Sex-stratified EAA was regressed on each of the five obesity metrics. RESULTS For male individuals, an increase of one SD in waist-hip ratio (0.06) was associated with a 0.602-year PhenoEAA (p = 6.3E-6) and a 0.481-year GrimEAA (p = 1.2E-8). For female individuals, every SD increase in BMI (3.7 kg/m2 ) was associated with a 0.600-year PhenoEAA (p = 3.3E-5) and a 0.305-year GrimEAA (p = 3.1E-5). CONCLUSIONS "Abdominal obesity" and "general obesity" are significantly associated with male and female EAA, respectively. The prevention of abdominal obesity and general obesity is associated with a lower risk of EAA in men and women, respectively.
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Affiliation(s)
- Wan-Yu Lin
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Master of Public Health Degree Program, College of Public Health, National Taiwan University, Taipei, Taiwan
- Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Yu-Cyuan Wang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - I-Hsuan Teng
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chi Liu
- Master Program in Statistics, National Taiwan University, Taipei, Taiwan
| | - Xiang-Yang Lou
- Department of Biostatistics, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida, USA
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310
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Raj K, Szladovits B, Haghani A, Zoller JA, Li CZ, Black P, Maddox D, Robeck TR, Horvath S. Epigenetic clock and methylation studies in cats. GeroScience 2021; 43:2363-2378. [PMID: 34463900 PMCID: PMC8599556 DOI: 10.1007/s11357-021-00445-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/17/2021] [Indexed: 12/21/2022] Open
Abstract
Human DNA methylation profiles have been used successfully to develop highly accurate biomarkers of aging ("epigenetic clocks"). Although these human epigenetic clocks are not immediately applicable to all species of the animal kingdom, the principles underpinning them appear to be conserved even in animals that are evolutionarily far removed from humans. This is exemplified by recent development of epigenetic clocks for mice and other mammalian species. Here, we describe epigenetic clocks for the domestic cat (Felis catus), based on methylation profiles of CpGs with flanking DNA sequences that are highly conserved between multiple mammalian species. Methylation levels of these CpGs are measured using a custom-designed Infinium array (HorvathMammalMethylChip40). From these, we present 3 epigenetic clocks for cats; of which, one applies only to blood samples from cats, while the remaining two dual-species human-cat clocks apply both to cats and humans. We demonstrate that these domestic cat clocks also lead to high age correlations in cheetahs, tigers, and lions. It is expected that these epigenetic clocks for cats possess the potential to be further developed for monitoring feline health as well as being used for identifying and validating anti-aging interventions.
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Affiliation(s)
- Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, UK
| | - Balazs Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, 695 Charles E. Young Drive South, Los Angeles, CA 90095 USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Gonda Building, Los Angeles, CA 90095 USA
| | - Caesar Z. Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Gonda Building, Los Angeles, CA 90095 USA
| | | | | | - Todd R. Robeck
- Corporate Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, 695 Charles E. Young Drive South, Los Angeles, CA 90095 USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Gonda Building, Los Angeles, CA 90095 USA
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311
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Epigenetic clock and methylation studies in vervet monkeys. GeroScience 2021; 44:699-717. [PMID: 34591235 PMCID: PMC9135907 DOI: 10.1007/s11357-021-00466-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/20/2021] [Indexed: 11/26/2022] Open
Abstract
DNA methylation-based biomarkers of aging have been developed for many mammals but not yet for the vervet monkey (Chlorocebus sabaeus), which is a valuable non-human primate model for biomedical studies. We generated novel DNA methylation data from vervet cerebral cortex, blood, and liver using highly conserved mammalian CpGs represented on a custom array (HorvathMammalMethylChip40). We present six DNA methylation-based estimators of age: vervet multi-tissue epigenetic clock and tissue-specific clocks for brain cortex, blood, and liver. In addition, we developed two dual species clocks (human-vervet clocks) for measuring chronological age and relative age, respectively. Relative age was defined as ratio of chronological age to maximum lifespan to address the species differences in maximum lifespan. The high accuracy of the human-vervet clocks demonstrates that epigenetic aging processes are evolutionary conserved in primates. When applying these vervet clocks to tissue samples from another primate species, rhesus macaque, we observed high age correlations but strong offsets. We characterized CpGs that correlate significantly with age in the vervet. CpG probes that gain methylation with age across tissues were located near the targets of Polycomb proteins SUZ12 and EED and genes possessing the trimethylated H3K27 mark in their promoters. The epigenetic clocks are expected to be useful for anti-aging studies in vervets.
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Richmond RC, Sillero-Rejon C, Khouja JN, Prince C, Board A, Sharp G, Suderman M, Relton CL, Munafò M, Gage SH. Investigating the DNA methylation profile of e-cigarette use. Clin Epigenetics 2021; 13:183. [PMID: 34583751 PMCID: PMC8479883 DOI: 10.1186/s13148-021-01174-7] [Citation(s) in RCA: 3] [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: 04/12/2021] [Accepted: 09/18/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Little evidence exists on the health effects of e-cigarette use. DNA methylation may serve as a biomarker for exposure and could be predictive of future health risk. We aimed to investigate the DNA methylation profile of e-cigarette use. RESULTS Among 117 smokers, 117 non-smokers and 116 non-smoking vapers, we evaluated associations between e-cigarette use and epigenome-wide methylation from saliva. DNA methylation at 7 cytosine-phosphate-guanine sites (CpGs) was associated with e-cigarette use at p < 1 × 10-5 and none at p < 5.91 × 10-8. 13 CpGs were associated with smoking at p < 1 × 10-5 and one at p < 5.91 × 10-8. CpGs associated with e-cigarette use were largely distinct from those associated with smoking. There was strong enrichment of known smoking-related CpGs in the smokers but not the vapers. We also tested associations between e-cigarette use and methylation scores known to predict smoking and biological ageing. Methylation scores for smoking and biological ageing were similar between vapers and non-smokers. Higher levels of all smoking scores and a biological ageing score (GrimAge) were observed in smokers. A methylation score for e-cigarette use showed poor prediction internally (AUC 0.55, 0.41-0.69) and externally (AUC 0.57, 0.36-0.74) compared with a smoking score (AUCs 0.80) and was less able to discriminate lung squamous cell carcinoma from adjacent normal tissue (AUC 0.64, 0.52-0.76 versus AUC 0.73, 0.61-0.85). CONCLUSIONS The DNA methylation profile for e-cigarette use is largely distinct from that of cigarette smoking, did not replicate in independent samples, and was unable to discriminate lung cancer from normal tissue. The extent to which methylation related to long-term e-cigarette use translates into chronic effects requires further investigation.
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Affiliation(s)
- Rebecca C Richmond
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
| | - Carlos Sillero-Rejon
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- National Institute for Health Research Applied Research Collaboration West (NIHR ARC West), University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Jasmine N Khouja
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- School of Psychological Science, University of Bristol, Bristol, UK
| | - Claire Prince
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Alexander Board
- Department of Experimental Psychology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Gemma Sharp
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Marcus Munafò
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- School of Psychological Science, University of Bristol, Bristol, UK
| | - Suzanne H Gage
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Department of Psychological Sciences, University of Liverpool, Liverpool, UK
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Palla G, Pollner P, Börcsök J, Major A, Molnár B, Csabai I. Hierarchy and control of ageing-related methylation networks. PLoS Comput Biol 2021; 17:e1009327. [PMID: 34534207 PMCID: PMC8480875 DOI: 10.1371/journal.pcbi.1009327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/29/2021] [Accepted: 08/05/2021] [Indexed: 11/28/2022] Open
Abstract
DNA methylation provides one of the most widely studied biomarkers of ageing. Since the methylation of CpG dinucleotides function as switches in cellular mechanisms, it is plausible to assume that by proper adjustment of these switches age may be tuned. Though, adjusting hundreds of CpG methylation levels coherently may never be feasible and changing just a few positions may lead to biologically unstable state. A prominent example of methylation-based age estimators is provided by Horvath’s clock, based on 353 CpG dinucleotides, showing a high correlation (not necessarily causation) with chronological age across multiple tissue types. On this small subset of CpG dinucleotides we demonstrate how the adjustment of one methylation level leads to a cascade of changes at other sites. Among the studied subset, we locate the most important CpGs (and related genes) that may have a large influence on the rest of the sub-system. According to our analysis, the structure of this network is way more hierarchical compared to what one would expect based on ensembles of uncorrelated connections. Therefore, only a handful of CpGs is enough to modify the system towards a desired state. When propagation of the change over the network is taken into account, the resulting modification in the predicted age can be significantly larger compared to the effect of isolated CpG perturbations. By adjusting the most influential single CpG site and following the propagation of methylation level changes we can reach up to 5.74 years in virtual age reduction, significantly larger than without taking into account of the network control. Extending our approach to the whole methylation network may identify key nodes that have controller role in the ageing process. Aging affects all living organisms. In humans, the chronological age correlates with the methylation level of some locations of the DNA. Here we extract an interaction network between these ageing related sites, which shows signs of hierarchical organisation. In addition, modifications in the methylation of single sites of the DNA can impose cascades of changes at other sites over this network. Based on “gedanken-experiments” in a small subset of CpG sites we show that by tuning appropriately selected methylation levels the estimated biological age can be changed. When modifying the most influential locations, the resulting cascades of changes can set back the estimated biological age by more than 5 years. Our study also shows that compared to single site methylation perturbations, the propagation of the change over the interaction network leads to methylation change profiles which are more aligned with the natural direction of ageing in a high dimensional representation of the methylation levels.
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Affiliation(s)
- Gergely Palla
- Health Services Management Training Centre, Semmelweis University, Budapest, Hungary
- MTA-ELTE Statistical and Biological Physics Research Group, Dept. of Biological Physics, Eötvös University, Budapest, Hungary
| | - Péter Pollner
- Health Services Management Training Centre, Semmelweis University, Budapest, Hungary
- MTA-ELTE Statistical and Biological Physics Research Group, Dept. of Biological Physics, Eötvös University, Budapest, Hungary
- * E-mail:
| | - Judit Börcsök
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - András Major
- Dept. of Physics of Complex Systems, ELTE Eötvös University, Budapest, Hungary
| | - Béla Molnár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - István Csabai
- Dept. of Physics of Complex Systems, ELTE Eötvös University, Budapest, Hungary
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314
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Morrow CS, Porter TJ, Moore DL. Fluorescent tagging of endogenous proteins with CRISPR/Cas9 in primary mouse neural stem cells. STAR Protoc 2021; 2:100744. [PMID: 34430917 PMCID: PMC8369070 DOI: 10.1016/j.xpro.2021.100744] [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] [Indexed: 11/16/2022] Open
Abstract
Although exogenous overexpression of a protein fused to a fluorescent tag can provide insight for the protein's function, it also can produce artifacts attributed to its upregulation and may not fully report the endogenous regulation of the protein of interest. To circumvent these issues, we adapted a protocol to label endogenous proteins with fluorescent tags in primary adult mouse neural stem cells in vitro. Here, we describe reagent construction, reagent delivery, and a screening strategy to isolate edited cells. For complete details on the use and execution of this protocol, please refer to Morrow et al. (2020).
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Affiliation(s)
| | - Tiaira J. Porter
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Darcie L. Moore
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
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315
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Abstract
ABSTRACT Recent research efforts have provided compelling evidence of genome-wide DNA methylation alterations in pediatrics. It is currently well established that epigenetic clocks, composed of DNA methylation sites, can estimate the gestational and chronological age of cells and tissues from different ages. Also, extensive research is aimed at their correlation with early life exposure and pediatric diseases. This review aimed to systematically summarize the epigenetic clocks in the pediatric population. Publications were collected from PubMed and Web of Science databases up to Apr 2021. Epigenetic clocks, DNA methylation clocks, epigenetic age acceleration or deceleration, pediatric and the pediatric population were used as search criteria. Here, we first review the currently applicative pediatric epigenetic clocks. We then highlight the interpretation for epigenetic age deviations in the pediatric population and their association with external factors, developmental trajectories, and pediatric diseases. Considering the remaining unknown of pediatric clocks, research strategies into them are also discussed. In all, pediatric epigenetic clocks may act as potent tools to understand development, growth and diseases in early life.
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316
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Johnson AA, Shokhirev MN. Pan-Tissue Aging Clock Genes That Have Intimate Connections with the Immune System and Age-Related Disease. Rejuvenation Res 2021; 24:377-389. [PMID: 34486398 DOI: 10.1089/rej.2021.0012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In our recent transcriptomic meta-analysis, we used random forest machine learning to accurately predict age in human blood, bone, brain, heart, and retina tissues given gene inputs. Although each tissue-specific model utilized a unique number of genes for age prediction, we found that the following six genes were prioritized in all five tissues: CHI3L2, CIDEC, FCGR3A, RPS4Y1, SLC11A1, and VTCN1. Since being selected for age prediction in multiple tissues is unique, we decided to explore these pan-tissue clock genes in greater detail. In the present study, we began by performing over-representation and network topology-based enrichment analyses in the Gene Ontology Biological Process database. These analyses revealed that the immunological terms "response to protozoan," "immune response," and "positive regulation of immune system process" were significantly enriched by these clock inputs. Expression analyses in mouse and human tissues identified that these inputs are frequently upregulated or downregulated with age. A detailed literature search showed that all six genes had noteworthy connections to age-related disease. For example, mice deficient in Cidec are protected against various metabolic defects, while suppressing VTCN1 inhibits age-related cancers in mouse models. Using a large multitissue transcriptomic dataset, we additionally generate a novel, minimalistic aging clock that can predict human age using just these six genes as inputs. Taken all together, these six genes are connected to diverse aspects of aging.
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Affiliation(s)
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, California, USA
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317
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318
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Hoang TT, Qi C, Paul KC, Lee M, White JD, Richards M, Auerbach SS, Long S, Shrestha S, Wang T, Beane Freeman LE, Hofmann JN, Parks C, Xu CJ, Ritz B, Koppelman GH, London SJ. Epigenome-Wide DNA Methylation and Pesticide Use in the Agricultural Lung Health Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:97008. [PMID: 34516295 PMCID: PMC8437246 DOI: 10.1289/ehp8928] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND Pesticide exposure is associated with many long-term health outcomes; the potential underlying mechanisms are not well established for most associations. Epigenetic modifications, such as DNA methylation, may contribute. Individual pesticides may be associated with specific DNA methylation patterns but no epigenome-wide association study (EWAS) has evaluated methylation in relation to individual pesticides. OBJECTIVES We conducted an EWAS of DNA methylation in relation to several pesticide active ingredients. METHODS The Agricultural Lung Health Study is a case-control study of asthma, nested within the Agricultural Health Study. We analyzed blood DNA methylation measured using Illumina's EPIC array in 1,170 male farmers of European ancestry. For pesticides still on the market at blood collection (2009-2013), we evaluated nine active ingredients for which at least 30 participants reported past and current (within the last 12 months) use, as well as seven banned organochlorines with at least 30 participants reporting past use. We used robust linear regression to compare methylation at individual C-phosphate-G sites (CpGs) among users of a specific pesticide to never users. RESULTS Using family-wise error rate (p<9×10-8) or false-discovery rate (FDR<0.05), we identified 162 differentially methylated CpGs across 8 of 9 currently marketed active ingredients (acetochlor, atrazine, dicamba, glyphosate, malathion, metolachlor, mesotrione, and picloram) and one banned organochlorine (heptachlor). Differentially methylated CpGs were unique to each active ingredient, and a dose-response relationship with lifetime days of use was observed for most. Significant CpGs were enriched for transcription motifs and 28% of CpGs were associated with whole blood cis-gene expression, supporting functional effects of findings. We corroborated a previously reported association between dichlorodiphenyltrichloroethane (banned in the United States in 1972) and epigenetic age acceleration. DISCUSSION We identified differential methylation for several active ingredients in male farmers of European ancestry. These may serve as biomarkers of chronic exposure and could inform mechanisms of long-term health outcomes from pesticide exposure. https://doi.org/10.1289/EHP8928.
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Affiliation(s)
- Thanh T. Hoang
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Cancan Qi
- Department of Pediatric Pulmonology and Pediatric Allergy, University Medical Center Groningen, Beatrix Children’s Hospital, University of Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and Chronic Obstructive Pulmonary Disease, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Kimberly C. Paul
- Department of Epidemiology, University of California, Los Angeles Fielding School of Public Health, Los Angeles, California, USA
| | - Mikyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Julie D. White
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | | | - Scott S. Auerbach
- Biomolecular Screening Branch, National Toxicology Program, NIEHS, NIH, DHHS, Morrisville, North Carolina, USA
| | | | - Srishti Shrestha
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Tianyuan Wang
- Integrative Bioinformatics Support Group, NIH, DHHS, Research Triangle Park, North Carolina, USA
| | - Laura E. Beane Freeman
- Occupational and Environmental Epidemiology Branch, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
| | - Jonathan N. Hofmann
- Occupational and Environmental Epidemiology Branch, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
| | - Christine Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | | | - Cheng-Jian Xu
- Research Group of Bioinformatics and Computational Genomics, CiiM, Centre for individualized infection medicine, a joint venture between Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Gastroenterology, Hepatology and Endocrinology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Beate Ritz
- Department of Epidemiology, University of California, Los Angeles Fielding School of Public Health, Los Angeles, California, USA
- Department of Neurology, David Geffen School of Medicine, Los Angeles, California, USA
| | - Gerard H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergy, University Medical Center Groningen, Beatrix Children’s Hospital, University of Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and Chronic Obstructive Pulmonary Disease, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
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Grodstein F, Lemos B, Yu L, Klein HU, Iatrou A, Buchman AS, Shireby GL, Mill J, Schneider JA, De Jager PL, Bennett DA. The association of epigenetic clocks in brain tissue with brain pathologies and common aging phenotypes. Neurobiol Dis 2021; 157:105428. [PMID: 34153464 PMCID: PMC8373772 DOI: 10.1016/j.nbd.2021.105428] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 10/21/2022] Open
Abstract
Epigenetic clocks are calculated by combining DNA methylation states across select CpG sites to estimate biologic age, and have been noted as the most successful markers of biologic aging to date. Yet, limited research has considered epigenetic clocks calculated in brain tissue. We used DNA methylation states in dorsolateral prefrontal cortex specimens from 721 older participants of the Religious Orders Study and Rush Memory and Aging Project, to calculate DNA methylation age using four established epigenetic clocks: Hannum, Horvath, PhenoAge, GrimAge, and a new Cortical clock. The four established clocks were trained in blood samples (Hannum, PhenoAge, GrimAge) or using 51 human tissue and cell types (Horvath); the recent Cortical clock is the first trained in postmortem cortical tissue. Participants were recruited beginning in 1994 (Religious Orders Study) and 1997 (Memory and Aging Project), and followed annually with questionnaires and clinical evaluations; brain specimens were obtained for 80-90% of participants. Mean age at death was 88.0 (SD 6.7) years. We used linear regression, logistic regression, and linear mixed models, to examine relations of epigenetic clock ages to neuropathologic and clinical aging phenotypes, controlling for chronologic age, sex, education, and depressive symptomatology. Hannum, Horvath, PhenoAge and Cortical clock ages were related to pathologic diagnosis of Alzheimer's disease (AD), as well as to Aβ load (a hallmark pathology of Alzheimer's disease). However, associations were substantially stronger for the Cortical than other clocks; for example, each standard deviation (SD) increase in Hannum, Horvath, and PhenoAge clock age was related to approximately 30% greater likelihood of pathologic AD (all p < 0.05), while each SD increase in Cortical age was related to 90% greater likelihood of pathologic AD (odds ratio = 1.91, 95% confidence interval 1.38, 2.62). Moreover, Cortical age was significantly related to other AD pathology (eg, mean tau tangle density, p = 0.003), and to odds of neocortical Lewy body pathology (for each SD increase in Cortical age, odds ratio = 2.00, 95% confidence 1.27, 3.17), although no clocks were related to cerebrovascular neuropathology. Cortical age was the only epigenetic clock significantly associated with the clinical phenotypes examined, from dementia to cognitive decline (5 specific cognitive systems, and a global cognitive measure averaging 17 tasks) to Parkinsonian signs. Overall, our findings provide evidence of the critical necessity for bespoke clocks of brain aging for advancing research to understand, and eventually prevent, neurodegenerative diseases of aging.
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Affiliation(s)
- Francine Grodstein
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States of America.
| | - Bernardo Lemos
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, United States of America
| | - Lei Yu
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America
| | - Hans-Ulrich Klein
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Artemis Iatrou
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America
| | - Aron S Buchman
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America
| | - Gemma L Shireby
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America; Department of Pathology, Rush University Medical Center, Chicago, IL, United States of America
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, United States of America
| | - David A Bennett
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America
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320
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Simpson DJ, Chandra T. Epigenetic age prediction. Aging Cell 2021; 20:e13452. [PMID: 34415665 PMCID: PMC8441394 DOI: 10.1111/acel.13452] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022] Open
Abstract
Advanced age is the main common risk factor for cancer, cardiovascular disease and neurodegeneration. Yet, more is known about the molecular basis of any of these groups of diseases than the changes that accompany ageing itself. Progress in molecular ageing research was slow because the tools predicting whether someone aged slowly or fast (biological age) were unreliable. To understand ageing as a risk factor for disease and to develop interventions, the molecular ageing field needed a quantitative measure; a clock for biological age. Over the past decade, a number of age predictors utilising DNA methylation have been developed, referred to as epigenetic clocks. While they appear to estimate biological age, it remains unclear whether the methylation changes used to train the clocks are a reflection of other underlying cellular or molecular processes, or whether methylation itself is involved in the ageing process. The precise aspects of ageing that the epigenetic clocks capture remain hidden and seem to vary between predictors. Nonetheless, the use of epigenetic clocks has opened the door towards studying biological ageing quantitatively, and new clocks and applications, such as forensics, appear frequently. In this review, we will discuss the range of epigenetic clocks available, their strengths and weaknesses, and their applicability to various scientific queries.
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Affiliation(s)
- Daniel J. Simpson
- MRC Human Genetics UnitMRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Tamir Chandra
- MRC Human Genetics UnitMRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
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321
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Simons RL, Lei MK, Klopach E, Berg M, Zhang Y, Beach SSR. Re(Setting) Epigenetic Clocks: An Important Avenue Whereby Social Conditions Become Biologically Embedded across the Life Course. JOURNAL OF HEALTH AND SOCIAL BEHAVIOR 2021; 62:436-453. [PMID: 34528488 DOI: 10.1177/00221465211009309] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Research on biological embedding of the social environment has been expedited by increased availability of biomarkers. Recently, this arsenal of measures has been expanded to include epigenetic clocks that indicate in years the extent to which an individual is older or younger than their chronological age. These measures of biological aging, especially GrimAge, are robust predictors of both illness and time to death. Importantly for sociologists, several studies have linked social conditions to these indices of aging. The present study extends this research using longitudinal data from a sample of 223 black women participating in the Family and Community Health Study. We find that changes in income and living arrangements over an 11-year period predict changes in speed of biological aging. These results provide further support for the idea that epigenetic aging is a mechanism whereby social conditions become biologically embedded. The utility of epigenetic clocks for sociological studies of health are discussed.
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Affiliation(s)
| | | | | | - Mark Berg
- University of Iowa, Iowa City, IA, USA
| | - Yue Zhang
- University of Georgia, Athens, GA, USA
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322
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Yoo H, Park K, Lee J, Lee S, Choi Y. An Optimized Method for the Construction of a DNA Methylome from Small Quantities of Tissue or Purified DNA from Arabidopsis Embryo. Mol Cells 2021; 44:602-612. [PMID: 34462399 PMCID: PMC8424141 DOI: 10.14348/molcells.2021.0084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/25/2021] [Accepted: 06/08/2021] [Indexed: 12/29/2022] Open
Abstract
DNA methylation is an important epigenetic mechanism affecting genome structure, gene regulation, and the silencing of transposable elements. Cell- and tissue-specific methylation patterns are critical for differentiation and development in eukaryotes. Dynamic spatiotemporal methylation data in these cells or tissues is, therefore, of great interest. However, the construction of bisulfite sequencing libraries can be challenging if the starting material is limited or the genome size is small, such as in Arabidopsis. Here, we describe detailed methods for the purification of Arabidopsis embryos at all stages, and the construction of comprehensive bisulfite libraries from small quantities of input. We constructed bisulfite libraries by releasing embryos from intact seeds, using a different approach for each developmental stage, and manually picking single-embryo with microcapillaries. From these libraries, reliable Arabidopsis methylome data were collected allowing, on average, 11-fold coverage of the genome using as few as five globular, heart, and torpedo embryos as raw input material without the need for DNA purification step. On the other hand, purified DNA from as few as eight bending torpedo embryos or a single mature embryo is sufficient for library construction when RNase A is treated before DNA extraction. This method can be broadly applied to cells from different tissues or cells from other model organisms. Methylome construction can be achieved using a minimal amount of input material using our method; thereby, it has the potential to increase our understanding of dynamic spatiotemporal methylation patterns in model organisms.
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Affiliation(s)
- Hyunjin Yoo
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Kyunghyuk Park
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jaehoon Lee
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Seunga Lee
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yeonhee Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
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Franzen J, Nüchtern S, Tharmapalan V, Vieri M, Nikolić M, Han Y, Balfanz P, Marx N, Dreher M, Brümmendorf TH, Dahl E, Beier F, Wagner W. Epigenetic Clocks Are Not Accelerated in COVID-19 Patients. Int J Mol Sci 2021; 22:ijms22179306. [PMID: 34502212 PMCID: PMC8431654 DOI: 10.3390/ijms22179306] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 02/06/2023] Open
Abstract
Age is a major risk factor for severe outcome of the 2019 coronavirus disease (COVID-19). In this study, we followed the hypothesis that particularly patients with accelerated epigenetic age are affected by severe outcomes of COVID-19. We investigated various DNA methylation datasets of blood samples with epigenetic aging signatures and performed targeted bisulfite amplicon sequencing. Overall, epigenetic clocks closely correlated with the chronological age of patients, either with or without acute respiratory distress syndrome. Furthermore, lymphocytes did not reveal significantly accelerated telomere attrition. Thus, these biomarkers cannot reliably predict higher risk for severe COVID-19 infection in elderly patients.
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Affiliation(s)
- Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; (J.F.); (S.N.); (V.T.); (M.N.); (Y.H.)
| | - Selina Nüchtern
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; (J.F.); (S.N.); (V.T.); (M.N.); (Y.H.)
| | - Vithurithra Tharmapalan
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; (J.F.); (S.N.); (V.T.); (M.N.); (Y.H.)
| | - Margherita Vieri
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany; (M.V.); (T.H.B.); (F.B.)
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Miloš Nikolić
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; (J.F.); (S.N.); (V.T.); (M.N.); (Y.H.)
| | - Yang Han
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; (J.F.); (S.N.); (V.T.); (M.N.); (Y.H.)
| | - Paul Balfanz
- Department of Cardiology, Angiology and Intensive Care Medicine (Department of Internal Medicine I), University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany; (P.B.); (N.M.)
| | - Nikolaus Marx
- Department of Cardiology, Angiology and Intensive Care Medicine (Department of Internal Medicine I), University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany; (P.B.); (N.M.)
| | - Michael Dreher
- Department of Pneumology and Intensive Care Medicine, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany;
| | - Tim H. Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany; (M.V.); (T.H.B.); (F.B.)
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Edgar Dahl
- Institute of Pathology, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany;
- RWTH Centralized Biomaterial Bank (RWTH cBMB), Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany; (M.V.); (T.H.B.); (F.B.)
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; (J.F.); (S.N.); (V.T.); (M.N.); (Y.H.)
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), 52074 Aachen, Germany
- Correspondence:
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324
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Fransquet PD, Lacaze P, Saffery R, Shah RC, Vryer R, Murray A, Woods RL, Ryan J. Accelerated Epigenetic Aging in Peripheral Blood does not Predict Dementia Risk. Curr Alzheimer Res 2021; 18:443-451. [PMID: 34429046 DOI: 10.2174/1567205018666210823100721] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 04/08/2021] [Accepted: 06/15/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND There is strong evidence that epigenetic age acceleration is associated with increased risk of later-life diseases and all-cause mortality. However, there is currently limited evidence that suggests accelerated epigenetic age is associated with dementia risk. OBJECTIVE This study aims to clarify whether epigenetic biomarkers of accelerated aging can predict dementia risk, which is an important consideration as aging is the greatest risk factor for the disease. METHODS DNA methylation was measured in peripheral blood samples provided by 160 participants from the ASPirin in Reducing Events in the Elderly study, including 73 pre-symptomatic dementia cases and 87 controls matched for age, sex, and smoking and education status. Epigenetic age was calculated using Horvath, Hannum, GrimAge and PhenoAge DNA methylation clocks, and age acceleration (the disparity between chronological age and epigenetic age) was determined. RESULTS There was no difference in age acceleration between dementia cases and controls. In males, only Hannum's intrinsic epigenetic age acceleration was increased in pre-symptomatic dementia cases compared to controls (Δ +1.8 years, p = 0.03). CONCLUSION These findings provide no strong evidence that accelerated epigenetic aging measured in peripheral blood can predict dementia risk.
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Affiliation(s)
- P D Fransquet
- School of Public Health and Preventive Medicine, Monash University, Melbourne, 3004, Victoria, Australia
| | - P Lacaze
- School of Public Health and Preventive Medicine, Monash University, Melbourne, 3004, Victoria, Australia
| | - R Saffery
- Murdoch Children's Research Institute, Department of Paediatrics, The University of Melbourne, Parkville, 3052 Victoria, Australia
| | - R C Shah
- Department of Family Medicine and Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, United States
| | - R Vryer
- Murdoch Children's Research Institute, Department of Paediatrics, The University of Melbourne, Parkville, 3052 Victoria, Australia
| | - A Murray
- Berman Center for Outcomes and Clinical Research, Hennepin Healthcare Research Institute, Hennepin Healthcare, Division of Geriatrics, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, United States
| | - R L Woods
- School of Public Health and Preventive Medicine, Monash University, Melbourne, 3004, Victoria, Australia
| | - J Ryan
- School of Public Health and Preventive Medicine, Monash University, Melbourne, 3004, Victoria, Australia
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325
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Levy JJ, Chen Y, Azizgolshani N, Petersen CL, Titus AJ, Moen EL, Vaickus LJ, Salas LA, Christensen BC. MethylSPWNet and MethylCapsNet: Biologically Motivated Organization of DNAm Neural Networks, Inspired by Capsule Networks. NPJ Syst Biol Appl 2021; 7:33. [PMID: 34417465 PMCID: PMC8379254 DOI: 10.1038/s41540-021-00193-7] [Citation(s) in RCA: 3] [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: 09/17/2020] [Accepted: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
DNA methylation (DNAm) alterations have been heavily implicated in carcinogenesis and the pathophysiology of diseases through upstream regulation of gene expression. DNAm deep-learning approaches are able to capture features associated with aging, cell type, and disease progression, but lack incorporation of prior biological knowledge. Here, we present modular, user-friendly deep-learning methodology and software, MethylCapsNet and MethylSPWNet, that group CpGs into biologically relevant capsules-such as gene promoter context, CpG island relationship, or user-defined groupings-and relate them to diagnostic and prognostic outcomes. We demonstrate these models' utility on 3,897 individuals in the classification of central nervous system (CNS) tumors. MethylCapsNet and MethylSPWNet provide an opportunity to increase DNAm deep-learning analyses' interpretability by enabling a flexible organization of DNAm data into biologically relevant capsules.
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Affiliation(s)
- Joshua J Levy
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Emerging Diagnostic and Investigative Technologies, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA.
| | - Youdinghuan Chen
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Curtis L Petersen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- The Dartmouth Institute for Health Policy and Clinical Practice, Lebanon, NH, USA
| | - Alexander J Titus
- Department of Life Sciences, University of New Hampshire, Manchester, NH, USA
| | - Erika L Moen
- The Dartmouth Institute for Health Policy and Clinical Practice, Lebanon, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Louis J Vaickus
- Emerging Diagnostic and Investigative Technologies, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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326
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Godley LA. Anticipation in hematopoietic malignancies: biology, bias, or both? Leuk Lymphoma 2021; 62:3070-3072. [PMID: 34405775 DOI: 10.1080/10428194.2021.1966789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lucy A Godley
- Departments of Medicine and Human Genetics, Section of Hematology/Oncology, The University of Chicago, Chicago, IL, USA
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327
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Stead ER, Bjedov I. Balancing DNA repair to prevent ageing and cancer. Exp Cell Res 2021; 405:112679. [PMID: 34102225 PMCID: PMC8361780 DOI: 10.1016/j.yexcr.2021.112679] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/25/2021] [Accepted: 04/29/2021] [Indexed: 02/06/2023]
Abstract
DNA damage is a constant stressor to the cell. Persistent damage to the DNA over time results in an increased risk of mutation and an accumulation of mutations with age. Loss of efficient DNA damage repair can lead to accelerated ageing phenotypes or an increased cancer risk, and the trade-off between cancer susceptibility and longevity is often driven by the cell's response to DNA damage. High levels of mutations in DNA repair mutants often leads to excessive cell death and stem cell exhaustion which may promote premature ageing. Stem cells themselves have distinct characteristics that enable them to retain low mutation rates. However, when mutations do arise, stem cell clonal expansion can also contribute to age-related tissue dysfunction as well as heightened cancer risk. In this review, we will highlight increasing DNA damage and mutation accumulation as hallmarks common to both ageing and cancer. We will propose that anti-ageing interventions might be cancer preventative and discuss the mechanisms through which they may act.
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Affiliation(s)
- Eleanor Rachel Stead
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street London, London WC1E 6DD, UK
| | - Ivana Bjedov
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street London, London WC1E 6DD, UK; University College London, Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, Gower Street, London WC1E 6BT, UK.
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328
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Mandelblatt JS, Ahles TA, Lippman ME, Isaacs C, Adams-Campbell L, Saykin AJ, Cohen HJ, Carroll J. Applying a Life Course Biological Age Framework to Improving the Care of Individuals With Adult Cancers: Review and Research Recommendations. JAMA Oncol 2021; 7:1692-1699. [PMID: 34351358 PMCID: PMC8602673 DOI: 10.1001/jamaoncol.2021.1160] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance The practice of oncology will increasingly involve the care of a growing population of individuals with midlife and late-life cancers. Managing cancer in these individuals is complex, based on differences in biological age at diagnosis. Biological age is a measure of accumulated life course damage to biological systems, loss of reserve, and vulnerability to functional deterioration and death. Biological age is important because it affects the ability to manage the rigors of cancer therapy, survivors' function, and cancer progression. However, biological age is not always clinically apparent. This review presents a conceptual framework of life course biological aging, summarizes candidate measures, and describes a research agenda to facilitate clinical translation to oncology practice. Observations Midlife and late-life cancers are chronic diseases that may arise from cumulative patterns of biological aging occurring over the life course. Before diagnosis, each new patient was on a distinct course of biological aging related to past exposures, life experiences, genetics, and noncancer chronic disease. Cancer and its treatments may also be associated with biological aging. Several measures of biological age, including p16INK4a, epigenetic age, telomere length, and inflammatory and body composition markers, have been used in oncology research. One or more of these measures may be useful in cancer care, either alone or in combination with clinical history and geriatric assessments. However, further research will be needed before biological age assessment can be recommended in routine practice, including determination of situations in which knowledge about biological age would change treatment, ascertaining whether treatment effects on biological aging are short-lived or persistent, and testing interventions to modify biological age, decrease treatment toxic effects, and maintain functional abilities. Conclusions and Relevance Understanding differences in biological aging could ultimately allow clinicians to better personalize treatment and supportive care, develop tailored survivorship care plans, and prescribe preventive or ameliorative therapies and behaviors informed by aging mechanisms.
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Affiliation(s)
- Jeanne S Mandelblatt
- Department of Oncology, Cancer Prevention and Control Program, Georgetown-Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC.,Department of Medicine, Georgetown University Medical Center, Washington, DC
| | - Tim A Ahles
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Marc E Lippman
- Department of Medicine, Georgetown University Medical Center, Washington, DC.,Department of Oncology, Breast Cancer Program, Georgetown-Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Claudine Isaacs
- Department of Medicine, Georgetown University Medical Center, Washington, DC.,Department of Oncology, Breast Cancer Program, Georgetown-Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Lucile Adams-Campbell
- Department of Oncology, Cancer Prevention and Control Program, Georgetown-Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Andrew J Saykin
- Radiology and Imaging Sciences, Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana Alzheimer's Disease Research Center and the Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis
| | - Harvey J Cohen
- Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, North Carolina
| | - Judith Carroll
- UCLA Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, Jane and Terry Semel Institute for Neuroscience and Human Behavior, Jonsson Comprehensive Cancer Center, and Cousins Center for Psychoneuroimmunology, Los Angeles, California
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329
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APOBECs orchestrate genomic and epigenomic editing across health and disease. Trends Genet 2021; 37:1028-1043. [PMID: 34353635 DOI: 10.1016/j.tig.2021.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/17/2022]
Abstract
APOBEC proteins can deaminate cytosine residues in DNA and RNA. This can lead to somatic mutations, DNA breaks, RNA modifications, or DNA demethylation in a selective manner. APOBECs function in various cellular compartments and recognize different nucleic acid motifs and structures. They orchestrate a wide array of genomic and epigenomic modifications, thereby affecting various cellular functions positively or negatively, including immune editing, viral and retroelement restriction, DNA damage responses, DNA demethylation, gene expression, and tissue homeostasis. Furthermore, the cumulative increase in genomic and epigenomic editing with aging could also, at least in part, be attributed to APOBEC function. We synthesize our cumulative understanding of APOBEC activity in a unifying overview and discuss their genomic and epigenomic impact in physiological, pathological, and technological contexts.
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330
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Oblak L, van der Zaag J, Higgins-Chen AT, Levine ME, Boks MP. A systematic review of biological, social and environmental factors associated with epigenetic clock acceleration. Ageing Res Rev 2021; 69:101348. [PMID: 33930583 DOI: 10.1016/j.arr.2021.101348] [Citation(s) in RCA: 191] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
Aging involves a diverse set of biological changes accumulating over time that leads to increased risk of morbidity and mortality. Epigenetic clocks are now widely used to quantify biological aging, in order to investigate determinants that modify the rate of aging and to predict age-related outcomes. Numerous biological, social and environmental factors have been investigated for their relationship to epigenetic clock acceleration and deceleration. The aim of this review was to synthesize general trends concerning the associations between human epigenetic clocks and these investigated factors. We conducted a systematic review of all available literature and included 156 publications across 4 resource databases. We compiled a list of all presently existing blood-based epigenetic clocks. Subsequently, we created an extensive dataset of over 1300 study findings in which epigenetic clocks were utilized in blood tissue of human subjects to assess the relationship between these clocks and numeral environmental exposures and human traits. Statistical analysis was possible on 57 such relationships, measured across 4 different epigenetic clocks (Hannum, Horvath, Levine and GrimAge). We found that the Horvath, Hannum, Levine and GrimAge epigenetic clocks tend to agree in direction of effects, but vary in size. Body mass index, HIV infection, and male sex were significantly associated with acceleration of one or more epigenetic clocks. Acceleration of epigenetic clocks was also significantly related to mortality, cardiovascular disease, cancer and diabetes. Our findings provide a graphical and numerical synopsis of the past decade of epigenetic age estimation research and indicate areas where further attention could be focused in the coming years.
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331
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Campisi M, Liviero F, Maestrelli P, Guarnieri G, Pavanello S. DNA Methylation-Based Age Prediction and Telomere Length Reveal an Accelerated Aging in Induced Sputum Cells Compared to Blood Leukocytes: A Pilot Study in COPD Patients. Front Med (Lausanne) 2021; 8:690312. [PMID: 34368190 PMCID: PMC8342924 DOI: 10.3389/fmed.2021.690312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Aging is the predominant risk factor for most degenerative diseases, including chronic obstructive pulmonary disease (COPD). This process is however very heterogeneous. Defining the biological aging of individual tissues may contribute to better assess this risky process. In this study, we examined the biological age of induced sputum (IS) cells, and peripheral blood leukocytes in the same subject, and compared these to assess whether biological aging of blood leukocytes mirrors that of IS cells. Biological aging was assessed in 18 COPD patients (72.4 ± 7.7 years; 50% males). We explored mitotic and non-mitotic aging pathways, using telomere length (TL) and DNA methylation-based age prediction (DNAmAge) and age acceleration (AgeAcc) (i.e., difference between DNAmAge and chronological age). Data on demographics, life style and occupational exposure, lung function, and clinical and blood parameters were collected. DNAmAge (67.4 ± 5.80 vs. 61.6 ± 5.40 years; p = 0.0003), AgeAcc (-4.5 ± 5.02 vs. -10.8 ± 3.50 years; p = 0.0003), and TL attrition (1.05 ± 0.35 vs. 1.48 ± 0.21 T/S; p = 0.0341) are higher in IS cells than in blood leukocytes in the same patients. Blood leukocytes DNAmAge (r = 0.927245; p = 0.0026) and AgeAcc (r = 0.916445; p = 0.0037), but not TL, highly correlate with that of IS cells. Multiple regression analysis shows that both blood leukocytes DNAmAge and AgeAcc decrease (i.e., younger) in patients with FEV1% enhancement (p = 0.0254 and p = 0.0296) and combined inhaled corticosteroid (ICS) therapy (p = 0.0494 and p = 0.0553). In conclusion, new findings from our work reveal a differential aging in the context of COPD, by a direct quantitative comparison of cell aging in the airway with that in the more accessible peripheral blood leukocytes, providing additional knowledge which could offer a potential translation into the disease management.
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Affiliation(s)
- Manuela Campisi
- Occupational Medicine, Department of Cardiac, Thoracic, and Vascular Sciences and Public Health, University Hospital of Padua, Padua, Italy
| | - Filippo Liviero
- Occupational Medicine, Department of Cardiac, Thoracic, and Vascular Sciences and Public Health, University Hospital of Padua, Padua, Italy
| | - Piero Maestrelli
- Occupational Medicine, Department of Cardiac, Thoracic, and Vascular Sciences and Public Health, University Hospital of Padua, Padua, Italy
| | - Gabriella Guarnieri
- Respiratory Pathophysiology Unit, Department of Cardiac, Thoracic, and Vascular Sciences and Public Health, University Hospital of Padua, Padua, Italy
| | - Sofia Pavanello
- Occupational Medicine, Department of Cardiac, Thoracic, and Vascular Sciences and Public Health, University Hospital of Padua, Padua, Italy
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332
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Pietri P, Stefanadis C. Cardiovascular Aging and Longevity: JACC State-of-the-Art Review. J Am Coll Cardiol 2021; 77:189-204. [PMID: 33446313 DOI: 10.1016/j.jacc.2020.11.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/25/2022]
Abstract
Cardiovascular aging and longevity are interrelated through many pathophysiological mechanisms. Many factors that promote atherosclerotic cardiovascular disease are also implicated in the aging process and vice versa. Indeed, cardiometabolic disorders such as hyperglycemia, insulin resistance, dyslipidemia, and arterial hypertension share common pathophysiological mechanisms with aging and longevity. Moreover, genetic modulators of longevity have a significant impact on cardiovascular aging. The current knowledge of genetic, molecular, and biochemical pathways of aging may serve as a substrate to introduce interventions that might delay cardiovascular aging, thus approaching the goal of longevity. In the present review, the authors describe pathophysiological links between cardiovascular aging and longevity and translate these mechanisms into clinical data by reporting genetic, dietary, and environmental characteristics from long-living populations.
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Affiliation(s)
- Panagiota Pietri
- Athens Medical School, University of Athens, Athens, Greece; Research Institute for Longevity and Aging-related diseases, Athens, Greece
| | - Christodoulos Stefanadis
- Athens Medical School, University of Athens, Athens, Greece; Research Institute for Longevity and Aging-related diseases, Athens, Greece.
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333
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McErlean P, Bell CG, Hewitt RJ, Busharat Z, Ogger PP, Ghai P, Albers GJ, Calamita E, Kingston S, Molyneaux PL, Beck S, Lloyd CM, Maher TM, Byrne AJ. DNA Methylome Alterations are Associated with Airway Macrophage Differentiation and Phenotype During Lung Fibrosis. Am J Respir Crit Care Med 2021; 204:954-966. [PMID: 34280322 DOI: 10.1164/rccm.202101-0004oc] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Airway macrophages (AMs) are key regulators of the lung environment and are implicated in the pathogenesis of idiopathic pulmonary fibrosis (IPF), a fatal respiratory disease with no cure. However, knowledge of epigenetics of AMs in IPF are limited. METHODS We undertook DNA methylation profiling using Illumina EPIC (850k) arrays in sorted AMs from Healthy (n=14) and IPF (n=30) donors. Cell-type deconvolution was performed using reference myeloid-cell DNA methylomes. MEASUREMENTS AND MAIN RESULTS Our analysis revealed epigenetic heterogeneity was a key characteristic of IPF-AMs. DNAm 'clock' analysis indicated epigenetic alterations in IPF-AMs was not associated with accelerated ageing. In differential DNAm analysis, we identified numerous differentially methylated positions (DMPs, n=11) and regions (DMRs, n=49) between healthy and IPF AMs respectively. DMPs and DMRs encompassed genes involved in lipid (LPCAT1) and glucose (PFKFB3) metabolism and importantly, DNAm status was associated with disease severity in IPF. CONCLUSIONS Collectively, our data identify that changes in the epigenome are associated with development and function of AMs in the IPF lung.
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Affiliation(s)
- Peter McErlean
- Imperial College London, 4615, London, United Kingdom of Great Britain and Northern Ireland
| | - Christopher G Bell
- William Harvey Research Institute, 105713, London, United Kingdom of Great Britain and Northern Ireland
| | - Richard J Hewitt
- National Heart and Lung Institute, Inflammation, Repair & Development, London, United Kingdom of Great Britain and Northern Ireland
| | - Zabreen Busharat
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
| | - Patricia P Ogger
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
| | - Poonam Ghai
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
| | - Gesa J Albers
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
| | - Emily Calamita
- Imperial College London, 4615, London, United Kingdom of Great Britain and Northern Ireland
| | - Shaun Kingston
- Royal Brompton Hospital, 156726, Interstitial Lung Disease Unit, London, United Kingdom of Great Britain and Northern Ireland
| | - Philip L Molyneaux
- Imperial College London, National Heart and Lung Institute, London, United Kingdom of Great Britain and Northern Ireland
| | - Stephan Beck
- University College London, 4919, London, United Kingdom of Great Britain and Northern Ireland
| | - Clare M Lloyd
- Imperial College, Leukocyte Biology, London, United Kingdom of Great Britain and Northern Ireland
| | - Toby M Maher
- Royal Brompton Hospital, 156726, Interstitial Lung Disease Unit, London, United Kingdom of Great Britain and Northern Ireland;
| | - Adam J Byrne
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
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334
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DNA Methylation and Intra-Clonal Heterogeneity: The Chronic Myeloid Leukemia Model. Cancers (Basel) 2021; 13:cancers13143587. [PMID: 34298798 PMCID: PMC8307727 DOI: 10.3390/cancers13143587] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 01/24/2023] Open
Abstract
Chronic Myeloid Leukemia (CML) is a model to investigate the impact of tumor intra-clonal heterogeneity in personalized medicine. Indeed, tyrosine kinase inhibitors (TKIs) target the BCR-ABL fusion protein, which is considered the major CML driver. TKI use has highlighted the existence of intra-clonal heterogeneity, as indicated by the persistence of a minority subclone for several years despite the presence of the target fusion protein in all cells. Epigenetic modifications could partly explain this heterogeneity. This review summarizes the results of DNA methylation studies in CML. Next-generation sequencing technologies allowed for moving from single-gene to genome-wide analyses showing that methylation abnormalities are much more widespread in CML cells. These data showed that global hypomethylation is associated with hypermethylation of specific sites already at diagnosis in the early phase of CML. The BCR-ABL-independence of some methylation profile alterations and the recent demonstration of the initial intra-clonal DNA methylation heterogeneity suggests that some DNA methylation alterations may be biomarkers of TKI sensitivity/resistance and of disease progression risk. These results also open perspectives for understanding the epigenetic/genetic background of CML predisposition and for developing new therapeutic strategies.
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335
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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336
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Vasan L, Park E, David LA, Fleming T, Schuurmans C. Direct Neuronal Reprogramming: Bridging the Gap Between Basic Science and Clinical Application. Front Cell Dev Biol 2021; 9:681087. [PMID: 34291049 PMCID: PMC8287587 DOI: 10.3389/fcell.2021.681087] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022] Open
Abstract
Direct neuronal reprogramming is an innovative new technology that involves the conversion of somatic cells to induced neurons (iNs) without passing through a pluripotent state. The capacity to make new neurons in the brain, which previously was not achievable, has created great excitement in the field as it has opened the door for the potential treatment of incurable neurodegenerative diseases and brain injuries such as stroke. These neurological disorders are associated with frank neuronal loss, and as new neurons are not made in most of the adult brain, treatment options are limited. Developmental biologists have paved the way for the field of direct neuronal reprogramming by identifying both intrinsic cues, primarily transcription factors (TFs) and miRNAs, and extrinsic cues, including growth factors and other signaling molecules, that induce neurogenesis and specify neuronal subtype identities in the embryonic brain. The striking observation that postmitotic, terminally differentiated somatic cells can be converted to iNs by mis-expression of TFs or miRNAs involved in neural lineage development, and/or by exposure to growth factors or small molecule cocktails that recapitulate the signaling environment of the developing brain, has opened the door to the rapid expansion of new neuronal reprogramming methodologies. Furthermore, the more recent applications of neuronal lineage conversion strategies that target resident glial cells in situ has expanded the clinical potential of direct neuronal reprogramming techniques. Herein, we present an overview of the history, accomplishments, and therapeutic potential of direct neuronal reprogramming as revealed over the last two decades.
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Affiliation(s)
- Lakshmy Vasan
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Eunjee Park
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Luke Ajay David
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Taylor Fleming
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
| | - Carol Schuurmans
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
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337
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Davison GW, Irwin RE, Walsh CP. The metabolic-epigenetic nexus in type 2 diabetes mellitus. Free Radic Biol Med 2021; 170:194-206. [PMID: 33429021 DOI: 10.1016/j.freeradbiomed.2020.12.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
The prevalence of type 2 diabetes mellitus (T2DM) continues to rise globally. Yet the aetiology and pathophysiology of this noncommunicable, polygenic disease, is poorly understood. Lifestyle factors, such as poor dietary intake, lack of exercise, and abnormal glycaemia, are purported to play a role in disease onset and progression, and these environmental factors may disrupt specific epigenetic mechanisms, leading to a reprogramming of gene transcription. The hyperglycaemic cell per se, alters epigenetics through chemical modifications to DNA and histones via metabolic intermediates such as succinate, α-ketoglutarate and O-GlcNAc. To illustrate, α-ketoglutarate is considered a salient co-factor in the activation of the ten-eleven translocation (TET) dioxygenases, which drives DNA demethylation. On the contrary, succinate and other mitochondrial tricarboxylic acid cycle intermediates, inhibit TET activity predisposing to a state of hypermethylation. Hyperglycaemia depletes intracellular ascorbic acid, and damages DNA by enhancing the production of reactive oxygen species (ROS); this compromised cell milieu exacerbates the oxidation of 5-methylcytosine alongside a destabilisation of TET. These metabolic connections may regulate DNA methylation, affecting gene transcription and pancreatic islet β-cell function in T2DM. This complex interrelationship between metabolism and epigenetic alterations may provide a conceptual foundation for understanding how pathologic stimuli modify and control the intricacies of T2DM. As such, this narrative review will comprehensively evaluate and detail the interplay between metabolism and epigenetic modifications in T2DM.
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Affiliation(s)
- Gareth W Davison
- Ulster University, Sport and Exercise Sciences Research Institute, Newtownabbey, Northern Ireland, UK.
| | - Rachelle E Irwin
- Ulster University, Genomic Medicine Research Group, Biomedical Sciences Research Institute, Coleraine, Northern Ireland, UK
| | - Colum P Walsh
- Ulster University, Genomic Medicine Research Group, Biomedical Sciences Research Institute, Coleraine, Northern Ireland, UK
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338
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The role of epigenetics in psychological resilience. Lancet Psychiatry 2021; 8:620-629. [PMID: 33915083 PMCID: PMC9561637 DOI: 10.1016/s2215-0366(20)30515-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/20/2022]
Abstract
There is substantial variation in people's responses to adversity, with a considerable proportion of individuals displaying psychological resilience. Epigenetic mechanisms are hypothesised to be one molecular pathway of how adverse and traumatic events can become biologically embedded and contribute to individual differences in resilience. However, not much is known regarding the role of epigenetics in the development of psychological resilience. In this Review, we propose a new conceptual model for the different functions of epigenetic mechanisms in psychological resilience. The model considers the initial establishment of the epigenome, epigenetic modification due to adverse and protective environments, the role of protective factors in counteracting adverse influences, and genetic moderation of environmentally induced epigenetic modifications. After reviewing empirical evidence for the various components of the model, we identify research that should be prioritised and discuss practical implications of the proposed model for epigenetic research on resilience.
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339
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Prado NA, Brown JL, Zoller JA, Haghani A, Yao M, Bagryanova LR, Campana MG, E. Maldonado J, Raj K, Schmitt D, Robeck TR, Horvath S. Epigenetic clock and methylation studies in elephants. Aging Cell 2021; 20:e13414. [PMID: 34118182 PMCID: PMC8282242 DOI: 10.1111/acel.13414] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/15/2021] [Accepted: 05/08/2021] [Indexed: 11/30/2022] Open
Abstract
Age-associated DNA-methylation profiles have been used successfully to develop highly accurate biomarkers of age ("epigenetic clocks") in humans, mice, dogs, and other species. Here we present epigenetic clocks for African and Asian elephants. These clocks were developed using novel DNA methylation profiles of 140 elephant blood samples of known age, at loci that are highly conserved between mammalian species, using a custom Infinium array (HorvathMammalMethylChip40). We present epigenetic clocks for Asian elephants (Elephas maximus), African elephants (Loxodonta africana), and both elephant species combined. Two additional human-elephant clocks were constructed by combining human and elephant samples. Epigenome-wide association studies identified elephant age-related CpGs and their proximal genes. The products of these genes play important roles in cellular differentiation, organismal development, metabolism, and circadian rhythms. Intracellular events observed to change with age included the methylation of bivalent chromatin domains, and targets of polycomb repressive complexes. These readily available epigenetic clocks can be used for elephant conservation efforts where accurate estimates of age are needed to predict demographic trends.
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Affiliation(s)
- Natalia A. Prado
- Center for Species SurvivalSmithsonian Conservation Biology InstituteFront RoyalVAUSA
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDCUSA
| | - Janine L. Brown
- Center for Species SurvivalSmithsonian Conservation Biology InstituteFront RoyalVAUSA
| | - Joseph A. Zoller
- Department of BiostatisticsFielding School of Public HealthUniversity of CaliforniaLos AngelesCAUSA
| | - Amin Haghani
- Department of Human GeneticsDavid Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Mingjia Yao
- Department of BiostatisticsFielding School of Public HealthUniversity of CaliforniaLos AngelesCAUSA
| | - Lora R. Bagryanova
- Department of EpidemiologyFielding School of Public HealthUniversity of CaliforniaLos Angeles, Los AngelesCAUSA
| | - Michael G. Campana
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDCUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDCUSA
| | - Ken Raj
- Radiation Effects DepartmentCentre for Radiation, Chemical and Environmental HazardsPublic Health EnglandDidcotUK
| | - Dennis Schmitt
- College of AgricultureMissouri State UniversitySpringfieldMOUSA
| | | | - Steve Horvath
- Department of BiostatisticsFielding School of Public HealthUniversity of CaliforniaLos AngelesCAUSA
- Department of Human GeneticsDavid Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
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340
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Sedrak MS, Gilmore NJ, Carroll JE, Muss HB, Cohen HJ, Dale W. Measuring Biologic Resilience in Older Cancer Survivors. J Clin Oncol 2021; 39:2079-2089. [PMID: 34043454 PMCID: PMC8260901 DOI: 10.1200/jco.21.00245] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/24/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Affiliation(s)
| | | | - Judith E. Carroll
- University of California, Los Angeles, David Geffen School of Medicine, Jonsson Comprehensive Cancer Center, Jane & Terry Semel Institute for Neuroscience & Human Behavior, Department of Psychiatry & Biobehavioral Sciences, Cousins Center for Psychoneuroimmunology, Los Angeles, CA
| | - Hyman B. Muss
- Department of Medicine and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | | | - William Dale
- City of Hope National Medical Center, Duarte, CA
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341
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McCartney DL, Min JL, Richmond RC, Lu AT, Sobczyk MK, Davies G, Broer L, Guo X, Jeong A, Jung J, Kasela S, Katrinli S, Kuo PL, Matias-Garcia PR, Mishra PP, Nygaard M, Palviainen T, Patki A, Raffield LM, Ratliff SM, Richardson TG, Robinson O, Soerensen M, Sun D, Tsai PC, van der Zee MD, Walker RM, Wang X, Wang Y, Xia R, Xu Z, Yao J, Zhao W, Correa A, Boerwinkle E, Dugué PA, Durda P, Elliott HR, Gieger C, de Geus EJC, Harris SE, Hemani G, Imboden M, Kähönen M, Kardia SLR, Kresovich JK, Li S, Lunetta KL, Mangino M, Mason D, McIntosh AM, Mengel-From J, Moore AZ, Murabito JM, Ollikainen M, Pankow JS, Pedersen NL, Peters A, Polidoro S, Porteous DJ, Raitakari O, Rich SS, Sandler DP, Sillanpää E, Smith AK, Southey MC, Strauch K, Tiwari H, Tanaka T, Tillin T, Uitterlinden AG, Van Den Berg DJ, van Dongen J, Wilson JG, Wright J, Yet I, Arnett D, Bandinelli S, Bell JT, Binder AM, Boomsma DI, Chen W, Christensen K, Conneely KN, Elliott P, Ferrucci L, Fornage M, Hägg S, Hayward C, Irvin M, Kaprio J, Lawlor DA, Lehtimäki T, Lohoff FW, Milani L, Milne RL, Probst-Hensch N, Reiner AP, Ritz B, Rotter JI, Smith JA, Taylor JA, van Meurs JBJ, Vineis P, Waldenberger M, Deary IJ, Relton CL, Horvath S, Marioni RE. Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging. Genome Biol 2021; 22:194. [PMID: 34187551 PMCID: PMC8243879 DOI: 10.1186/s13059-021-02398-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/03/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Biological aging estimators derived from DNA methylation data are heritable and correlate with morbidity and mortality. Consequently, identification of genetic and environmental contributors to the variation in these measures in populations has become a major goal in the field. RESULTS Leveraging DNA methylation and SNP data from more than 40,000 individuals, we identify 137 genome-wide significant loci, of which 113 are novel, from genome-wide association study (GWAS) meta-analyses of four epigenetic clocks and epigenetic surrogate markers for granulocyte proportions and plasminogen activator inhibitor 1 levels, respectively. We find evidence for shared genetic loci associated with the Horvath clock and expression of transcripts encoding genes linked to lipid metabolism and immune function. Notably, these loci are independent of those reported to regulate DNA methylation levels at constituent clock CpGs. A polygenic score for GrimAge acceleration showed strong associations with adiposity-related traits, educational attainment, parental longevity, and C-reactive protein levels. CONCLUSION This study illuminates the genetic architecture underlying epigenetic aging and its shared genetic contributions with lifestyle factors and longevity.
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Affiliation(s)
- Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Josine L Min
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Maria K Sobczyk
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gail Davies
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Linda Broer
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ayoung Jeong
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jeesun Jung
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, USA
| | - Silva Kasela
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Seyma Katrinli
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Pei-Lun Kuo
- Longitudinal Study Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Pamela R Matias-Garcia
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland
| | - Marianne Nygaard
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Amit Patki
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott M Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Oliver Robinson
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Mette Soerensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Dianjianyi Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Matthijs D van der Zee
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Xiaochuan Wang
- Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, Victoria, 3004, Australia
| | - Yunzhang Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | - Rui Xia
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zongli Xu
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Eric Boerwinkle
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Pierre-Antoine Dugué
- Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, Victoria, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, 3168, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Melbourne, Victoria, 3010, Australia
| | - Peter Durda
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05446, USA
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
| | - Eco J C de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33521, Tampere, Finland
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Jacob K Kresovich
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Shengxu Li
- Children's Minnesota Research Institute, Children's Minnesota, Minneapolis, MN, 55404, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, USA
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, SE1 9RT, UK
| | - Dan Mason
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | | | - Jonas Mengel-From
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Ann Zenobia Moore
- Longitudinal Study Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Joanne M Murabito
- Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - James S Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Silvia Polidoro
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Dale P Sandler
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Elina Sillanpää
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Gerontology Research Center, Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, Victoria, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, 3168, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Melbourne, Victoria, 3010, Australia
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, 55101, Mainz, Germany
- Chair of Genetic Epidemiology, Institute for Medical Information Processing, Biometry, and Epidemiology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hemant Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, USA
| | - Toshiko Tanaka
- Longitudinal Study Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Therese Tillin
- MRC Unit for Lifelong Health and Ageing at UCL, London, UK
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - David J Van Den Berg
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - James G Wilson
- Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Idil Yet
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, 06100, Ankara, Turkey
| | - Donna Arnett
- Deans Office, College of Public Health, University of Kentucky, Lexington, UK
| | | | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Alexandra M Binder
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawai'i Cancer Center, University of Hawai'i, Honolulu, HI, USA
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Wei Chen
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Paul Elliott
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Luigi Ferrucci
- Longitudinal Study Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Rd. South, Edinburgh, EH4 2XU, UK
| | - Marguerite Irvin
- Dept of Epidemiology, University of Alabama at Birmingham, Birmingham, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland
| | - Falk W Lohoff
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, USA
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, Victoria, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, 3168, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Melbourne, Victoria, 3010, Australia
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Beate Ritz
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Jack A Taylor
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Paolo Vineis
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK.
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342
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Inflammation, epigenetics, and metabolism converge to cell senescence and ageing: the regulation and intervention. Signal Transduct Target Ther 2021; 6:245. [PMID: 34176928 PMCID: PMC8236488 DOI: 10.1038/s41392-021-00646-9] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/09/2021] [Accepted: 05/13/2021] [Indexed: 02/05/2023] Open
Abstract
Remarkable progress in ageing research has been achieved over the past decades. General perceptions and experimental evidence pinpoint that the decline of physical function often initiates by cell senescence and organ ageing. Epigenetic dynamics and immunometabolic reprogramming link to the alterations of cellular response to intrinsic and extrinsic stimuli, representing current hotspots as they not only (re-)shape the individual cell identity, but also involve in cell fate decision. This review focuses on the present findings and emerging concepts in epigenetic, inflammatory, and metabolic regulations and the consequences of the ageing process. Potential therapeutic interventions targeting cell senescence and regulatory mechanisms, using state-of-the-art techniques are also discussed.
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343
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Mayne B, Espinoza T, Roberts D, Butler GL, Brooks S, Korbie D, Jarman S. Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod. Mol Ecol Resour 2021; 21:2324-2332. [PMID: 34161658 PMCID: PMC8518777 DOI: 10.1111/1755-0998.13440] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/16/2021] [Accepted: 06/01/2021] [Indexed: 11/29/2022]
Abstract
Age‐based demography is fundamental to management of wild fish populations. Age estimates for individuals can determine rates of change in key life‐history parameters such as length, maturity, mortality and fecundity. These age‐based characteristics are critical for population viability analysis in endangered species and for developing sustainable harvest strategies. For teleost fish, age has traditionally been determined by counting increments formed in calcified structures such as otoliths. However, the collection of otoliths is lethal and therefore undesirable for threatened species. At a molecular level, age can be predicted by measuring DNA methylation. Here, we use previously identified age‐associated sites of DNA methylation in zebrafish (Danio rerio) to develop two epigenetic clocks for three threatened freshwater fish species. One epigenetic clock was developed for the Australian lungfish (Neoceratodus forsteri) and the second for the Murray cod (Maccullochellapeelii) and Mary River cod (Maccullochellamariensis). Age estimation models were calibrated using either known‐age individuals, ages derived from otoliths or bomb radiocarbon dating of scales. We demonstrate a high Pearson's correlation between the chronological and predicted age in both the Lungfish clock (cor = .98) and Maccullochella clock (cor = .92). The median absolute error rate for both epigenetic clocks was also low (Lungfish = 0.86 years; Maccullochella = 0.34 years). This study demonstrates the transferability of DNA methylation sites for age prediction between highly phylogenetically divergent fish species. Given the method is nonlethal and suited to automation, age prediction by DNA methylation has the potential to improve fisheries and other wildlife management settings.
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Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research Centre, Crawley, WA, Australia
| | - Thomas Espinoza
- Department of Natural Resources, Mines and Energy, Bundaberg, Qld, Australia
| | | | - Gavin L Butler
- Department of Primary Industries, Grafton Fisheries Centre, Grafton, NSW, Australia
| | - Steven Brooks
- Department of Agriculture, Fisheries and Forestry, Brisbane, Qld, Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld, Australia
| | - Simon Jarman
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
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344
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Campello L, Singh N, Advani J, Mondal AK, Corso-Diaz X, Swaroop A. Aging of the Retina: Molecular and Metabolic Turbulences and Potential Interventions. Annu Rev Vis Sci 2021; 7:633-664. [PMID: 34061570 DOI: 10.1146/annurev-vision-100419-114940] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Multifaceted and divergent manifestations across tissues and cell types have curtailed advances in deciphering the cellular events that accompany advanced age and contribute to morbidities and mortalities. Increase in human lifespan during the past century has heightened awareness of the need to prevent age-associated frailty of neuronal and sensory systems to allow a healthy and productive life. In this review, we discuss molecular and physiological attributes of aging of the retina, with a goal of understanding age-related impairment of visual function. We highlight the epigenome-metabolism nexus and proteostasis as key contributors to retinal aging and discuss lifestyle changes as potential modulators of retinal function. Finally, we deliberate promising intervention strategies for promoting healthy aging of the retina for improved vision. Expected final online publication date for the Annual Review of Vision Science, Volume 7 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Laura Campello
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Nivedita Singh
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Anupam K Mondal
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Ximena Corso-Diaz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
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345
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Kerepesi C, Zhang B, Lee SG, Trapp A, Gladyshev VN. Epigenetic clocks reveal a rejuvenation event during embryogenesis followed by aging. SCIENCE ADVANCES 2021; 7:eabg6082. [PMID: 34172448 PMCID: PMC8232908 DOI: 10.1126/sciadv.abg6082] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/12/2021] [Indexed: 05/05/2023]
Abstract
The notion that the germ line does not age goes back to the 19th-century ideas of August Weismann. However, being metabolically active, the germ line accumulates damage and other changes over time, i.e., it ages. For new life to begin in the same young state, the germ line must be rejuvenated in the offspring. Here, we developed a multi-tissue epigenetic clock and applied it, together with other aging clocks, to track changes in biological age during mouse and human prenatal development. This analysis revealed a significant decrease in biological age, i.e., rejuvenation, during early stages of embryogenesis, followed by an increase in later stages. We further found that pluripotent stem cells do not age even after extensive passaging and that the examined epigenetic age dynamics is conserved across species. Overall, this study uncovers a natural rejuvenation event during embryogenesis and suggests that the minimal biological age (ground zero) marks the beginning of organismal aging.
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Affiliation(s)
- Csaba Kerepesi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alexandre Trapp
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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346
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Robeck TR, Fei Z, Lu AT, Haghani A, Jourdain E, Zoller JA, Li CZ, Steinman KJ, DiRocco S, Schmitt T, Osborn S, Van Bonn B, Katsumata E, Mergl J, Almunia J, Rodriguez M, Haulena M, Dold C, Horvath S. Multi-species and multi-tissue methylation clocks for age estimation in toothed whales and dolphins. Commun Biol 2021; 4:642. [PMID: 34059764 PMCID: PMC8167141 DOI: 10.1038/s42003-021-02179-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/04/2021] [Indexed: 02/05/2023] Open
Abstract
The development of a precise blood or skin tissue DNA Epigenetic Aging Clock for Odontocete (OEAC) would solve current age estimation inaccuracies for wild odontocetes. Therefore, we determined genome-wide DNA methylation profiles using a custom array (HorvathMammalMethyl40) across skin and blood samples (n = 446) from known age animals representing nine odontocete species within 4 phylogenetic families to identify age associated CG dinucleotides (CpGs). The top CpGs were used to create a cross-validated OEAC clock which was highly correlated for individuals (r = 0.94) and for unique species (median r = 0.93). Finally, we applied the OEAC for estimating the age and sex of 22 wild Norwegian killer whales. DNA methylation patterns of age associated CpGs are highly conserved across odontocetes. These similarities allowed us to develop an odontocete epigenetic aging clock (OEAC) which can be used for species conservation efforts by provide a mechanism for estimating the age of free ranging odontocetes from either blood or skin samples.
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Affiliation(s)
- Todd R Robeck
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA.
| | - Zhe Fei
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Caesar Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Karen J Steinman
- Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA
| | | | | | | | | | | | - June Mergl
- Marineland of Canada, Niagara Falls, ON, Canada
| | - Javier Almunia
- Loro Parque Fundación, SA, Avenida Loro Parque, Puerto de la Cruz, Santa Cruz de Tenerife, Spain
| | | | | | - Christopher Dold
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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347
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Mayne B, Berry O, Jarman S. Optimal sample size for calibrating DNA methylation age estimators. Mol Ecol Resour 2021; 21:2316-2323. [PMID: 34053192 PMCID: PMC8518423 DOI: 10.1111/1755-0998.13437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022]
Abstract
Age is a fundamental parameter in wildlife management as it is used to determine the risk of extinction, manage invasive species, and regulate sustainable harvest. In a broad variety of vertebrates species, age can be determined by measuring DNA methylation. Animals with known ages are initially required during development, calibration, and validation of these epigenetic clocks. However, wild animals with known ages are frequently difficult to obtain. Here, we perform Monte‐Carlo simulations to determine the optimal sample size required to create an accurate calibration model for age estimation by elastic net regression modelling of cytosine‐phosphate‐guanine methylation data. Our results suggest a minimum calibration population size of 70, but ideally 134 individuals or more for accurate and precise models. We also provide estimates to the extent a model can be extrapolated beyond a distribution of ages that was used during calibration. The findings can assist researchers to better design age estimation models and decide if their model is adequate for determining key population attributes.
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Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Simon Jarman
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
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348
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ERCC5 quantification for age estimation of peripheral blood in a Chinese Han population. Leg Med (Tokyo) 2021; 52:101912. [PMID: 34090258 DOI: 10.1016/j.legalmed.2021.101912] [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: 01/29/2021] [Revised: 05/04/2021] [Accepted: 05/22/2021] [Indexed: 11/23/2022]
Abstract
Age estimation is an important topic of human identification in forensic practice, especially coming to biological samples in crime scene, such as blood, saliva, semen. As rate-limiting enzyme in Nucleotide excision repair (NER) that was associated with aging, Excision repair cross-complementation group 5 (ERCC5) was considered to be a candidate biomarker for individual age estimation. The ERCC5 mRNA and protein expression levels association with age have been demonstrated in our previous study. However, very little is known about relationship DNA-based quantification of ERCC5 with age. In this study, we detected ERCC5 level in peripheral blood from a Chinese Han population by SYBR qPCR assay to gain better insight into the quantitative relationship with age. The results showed ERCC5 level declined with individual age with a negative correlation(r = -0.8, R2 = 0.63, P < 0.001). The data model for age estimation based on ERCC5 level was Y = -31.352X + 14.436 ± 10.28 (Y: age, year; X: CqTBP-CqERCC5; standard error: year). The accuracy about the data model for age estimation was about 73.33%. The mean absolute difference (MAD) values were 8.22, 8.09 and 8.38 in total, male and female, respectively. Furthermore, ERCC5 quantification for age estimation was also applicable for stored blood samples under low temperature up to 6 months. It was suggested that the ERCC5 quantification was expected to be a valuable additional method for individual age estimation, especially in cases where traditional morphologic method is absent or inefficient in forensic practice.
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349
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Balnis J, Madrid A, Hogan KJ, Drake LA, Chieng HC, Tiwari A, Vincent CE, Chopra A, Vincent PA, Robek MD, Singer HA, Alisch RS, Jaitovich A. Blood DNA methylation and COVID-19 outcomes. Clin Epigenetics 2021; 13:118. [PMID: 34034806 PMCID: PMC8148415 DOI: 10.1186/s13148-021-01102-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/11/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND There are no prior reports that compare differentially methylated regions of DNA in blood samples from COVID-19 patients to samples collected before the SARS-CoV-2 pandemic using a shared epigenotyping platform. We performed a genome-wide analysis of circulating blood DNA CpG methylation using the Infinium Human MethylationEPIC BeadChip on 124 blood samples from hospitalized COVID-19-positive and COVID-19-negative patients and compared these data with previously reported data from 39 healthy individuals collected before the pandemic. Prospective outcome measures such as COVID-19-GRAM risk-score and mortality were combined with methylation data. RESULTS Global mean methylation levels did not differ between COVID-19 patients and healthy pre-pandemic controls. About 75% of acute illness-associated differentially methylated regions were located near gene promoter regions and were hypo-methylated in comparison with healthy pre-pandemic controls. Gene ontology analyses revealed terms associated with the immune response to viral infections and leukocyte activation; and disease ontology analyses revealed a predominance of autoimmune disorders. Among COVID-19-positive patients, worse outcomes were associated with a prevailing hyper-methylated status. Recursive feature elimination identified 77 differentially methylated positions predictive of COVID-19 severity measured by the GRAM-risk score. CONCLUSION Our data contribute to the awareness that DNA methylation may influence the expression of genes that regulate COVID-19 progression and represent a targetable process in that setting.
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Affiliation(s)
- Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin, Madison, WI, USA
| | - Lisa A Drake
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Hau C Chieng
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Anupama Tiwari
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Catherine E Vincent
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Amit Chopra
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Peter A Vincent
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Michael D Robek
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, USA
| | - Harold A Singer
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA.
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA.
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA.
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350
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Hartmann A, Hartmann C, Secci R, Hermann A, Fuellen G, Walter M. Ranking Biomarkers of Aging by Citation Profiling and Effort Scoring. Front Genet 2021; 12:686320. [PMID: 34093670 PMCID: PMC8176216 DOI: 10.3389/fgene.2021.686320] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/23/2021] [Indexed: 01/10/2023] Open
Abstract
Aging affects most living organisms and includes the processes that reduce health and survival. The chronological and the biological age of individuals can differ remarkably, and there is a lack of reliable biomarkers to monitor the consequences of aging. In this review we give an overview of commonly mentioned and frequently used potential aging-related biomarkers. We were interested in biomarkers of aging in general and in biomarkers related to cellular senescence in particular. To answer the question whether a biological feature is relevant as a potential biomarker of aging or senescence in the scientific community we used the PICO strategy known from evidence-based medicine. We introduced two scoring systems, aimed at reflecting biomarker relevance and measurement effort, which can be used to support study designs in both clinical and research settings.
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Affiliation(s)
- Alexander Hartmann
- Institute of Clinical Chemistry and Laboratory Medicine, Rostock University Medical Center, Rostock, Germany
| | - Christiane Hartmann
- Translational Neurodegeneration Section “Albrecht-Kossel”, Department of Neurology, Rostock University Medical Center, Rostock, Germany
- German Center for Neurodegenerative Diseases (DZNE) Rostock/Greifswald, Rostock, Germany
| | - Riccardo Secci
- Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock University Medical Center, Rostock, Germany
| | - Andreas Hermann
- Translational Neurodegeneration Section “Albrecht-Kossel”, Department of Neurology, Rostock University Medical Center, Rostock, Germany
- German Center for Neurodegenerative Diseases (DZNE) Rostock/Greifswald, Rostock, Germany
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock University Medical Center, Rostock, Germany
| | - Michael Walter
- Institute of Clinical Chemistry and Laboratory Medicine, Rostock University Medical Center, Rostock, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité –Berlin Institute of Health, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
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