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Glover L, Lilly AG, Justice AE, Howard AG, Staley BS, Wang Y, Kamens HM, Ferrier K, Bressler J, Loehr L, Raffield LM, Sims M, North KE, Fernández-Rhodes L. DNA methylation near MAD1L1, KDM2B, and SOCS3 mediates the effect of socioeconomic status on elevated body mass index in African American adults. Hum Mol Genet 2024; 33:1748-1757. [PMID: 39079086 PMCID: PMC11458006 DOI: 10.1093/hmg/ddae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/15/2024] [Indexed: 10/09/2024] Open
Abstract
Obesity and poverty disproportionally affect African American persons. Epigenetic mechanisms could partially explain the association between socioeconomic disadvantage and body mass index (BMI). We examined the extent to which epigenetic mechanisms mediate the effect of socioeconomic status (SES) on BMI. Using data from African American adults from the Atherosclerosis Risk in Communities (ARIC) Study (n = 2664, mean age = 57 years), education, income, and occupation were used to create a composite SES score at visit 1 (1987-1989). We conducted two methylation-wide association analyses to identify associations between SES (visit 1), BMI and cytosine-phosphate-guanine (CpG) sites measured at a subsequent visit (1990-1995). We then utilized structural equation modeling (SEM) to test whether identified sites mediated the association between earlier SES and BMI in sex-stratified models adjusted for demographic and risk factor covariates. Independent replication and meta-analyses were conducted using the Jackson Heart Study (JHS, n = 874, mean age 51 years, 2000-2004). Three CpG sites near MAD1L1, KDM2B, and SOCS3 (cg05095590, cg1370865, and cg18181703) were suggestively associated (P-value < 1.3×10-5) in ARIC and at array-wide significance (P-value < 1.3×10-7) in a combined meta-analysis of ARIC with JHS. SEM of these three sites revealed significant indirect effects in females (P-value < 5.8×10-3), each mediating 7%-20% of the total effect of SES on BMI. Nominally significant indirect effects were observed for two sites near MAD1L1 and KDM2B in males (P-value < 3.4×10-2), mediating -17 and -22% of the SES-BMI effect. These results provide further evidence that epigenetic modifications may be a potential pathway through which SES may "get under the skin" and contribute to downstream health disparities.
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Affiliation(s)
- LáShauntá Glover
- Department of Population Health Sciences, 215 Morris Street, Duke University School of Medicine, Durham, NC 27701, United States
| | - Adam G Lilly
- Department of Sociology, 102 Emerson Drive, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Carolina Population Center, 123 West Franklin Street, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, United States
| | - Anne E Justice
- Department of Population Health Sciences, 100 Academy Avenue, Geisinger Health, Danville, PA, United States
| | - Annie Green Howard
- Carolina Population Center, 123 West Franklin Street, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, United States
- Department of Biostatistics, 135 Dauer Drive, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Brooke S Staley
- Carolina Population Center, 123 West Franklin Street, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, United States
- Department of Epidemiology, 135 Dauer Drive, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Yujie Wang
- Department of Epidemiology, 135 Dauer Drive, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Helen M Kamens
- Department of Biobehavioral Health, 219 Biobehavioral Health Building, 296 Henderson Drive, College of Health and Human Development, Pennsylvania State University, University Park, PA 16802, United States
| | - Kendra Ferrier
- Department of Biomedical Informatics, 1890 North Revere Court, University of Colorado Anshutz Medical Campus, Aurora, CO, 80045, United States
| | - Jan Bressler
- Department of Epidemiology, Human Genetics & Environmental Sciences, 1200 Pressler Street, UTHealth Houston School of Public Health, Houston, TX 77030, United States
| | - Laura Loehr
- Department of Epidemiology, 135 Dauer Drive, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Laura M Raffield
- Department of Genetics, 120 Mason Farm Road, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Mario Sims
- Department of Social Medicine, Population, and Public Health, 900 University Avenue, University of California Riverside, Riverside, CA 92521, United States
| | - Kari E North
- Department of Epidemiology, 135 Dauer Drive, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Lindsay Fernández-Rhodes
- Department of Epidemiology, 135 Dauer Drive, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
- Department of Biobehavioral Health, 219 Biobehavioral Health Building, 296 Henderson Drive, College of Health and Human Development, Pennsylvania State University, University Park, PA 16802, United States
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Yusipov I, Kalyakulina A, Trukhanov A, Franceschi C, Ivanchenko M. Map of epigenetic age acceleration: A worldwide analysis. Ageing Res Rev 2024; 100:102418. [PMID: 39002646 DOI: 10.1016/j.arr.2024.102418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
We present a systematic analysis of epigenetic age acceleration based on by far the largest collection of publicly available DNA methylation data for healthy samples (93 datasets, 23 K samples), focusing on the geographic (25 countries) and ethnic (31 ethnicities) aspects around the world. We employed the most popular epigenetic tools for assessing age acceleration and examined their quality metrics and ability to extrapolate to epigenetic data from different tissue types and age ranges different from the training data of these models. In most cases, the models proved to be inconsistent with each other and showed different signs of age acceleration, with the PhenoAge model tending to systematically underestimate and different versions of the GrimAge model tending to systematically overestimate the age prediction of healthy subjects. Referring to data availability and consistency, most countries and populations are still not represented in GEO, moreover, different datasets use different criteria for determining healthy controls. Because of this, it is difficult to fully isolate the contribution of "geography/environment", "ethnicity" and "healthiness" to epigenetic age acceleration. Among the explored metrics, only the DunedinPACE, which measures aging rate, appears to adequately reflect the standard of living and socioeconomic indicators in countries, although it has a limited application to blood methylation data only. Invariably, by epigenetic age acceleration, males age faster than females in most of the studied countries and populations.
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Affiliation(s)
- Igor Yusipov
- Artificial Intelligence Research Center, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia; Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
| | - Alena Kalyakulina
- Artificial Intelligence Research Center, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia; Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
| | - Arseniy Trukhanov
- Mriya Life Institute, National Academy of Active Longevity, Moscow 124489, Russia.
| | - Claudio Franceschi
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
| | - Mikhail Ivanchenko
- Artificial Intelligence Research Center, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia; Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
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3
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Ki MR, Youn S, Kim DH, Pack SP. Natural Compounds for Preventing Age-Related Diseases and Cancers. Int J Mol Sci 2024; 25:7530. [PMID: 39062777 PMCID: PMC11276798 DOI: 10.3390/ijms25147530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 07/01/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Aging is a multifaceted process influenced by hereditary factors, lifestyle, and environmental elements. As time progresses, the human body experiences degenerative changes in major functions. The external and internal signs of aging manifest in various ways, including skin dryness, wrinkles, musculoskeletal disorders, cardiovascular diseases, diabetes, neurodegenerative disorders, and cancer. Additionally, cancer, like aging, is a complex disease that arises from the accumulation of various genetic and epigenetic alterations. Circadian clock dysregulation has recently been identified as an important risk factor for aging and cancer development. Natural compounds and herbal medicines have gained significant attention for their potential in preventing age-related diseases and inhibiting cancer progression. These compounds demonstrate antioxidant, anti-inflammatory, anti-proliferative, pro-apoptotic, anti-metastatic, and anti-angiogenic effects as well as circadian clock regulation. This review explores age-related diseases, cancers, and the potential of specific natural compounds in targeting the key features of these conditions.
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Affiliation(s)
- Mi-Ran Ki
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea; (M.-R.K.); (S.Y.); (D.H.K.)
- Institute of Industrial Technology, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea
| | - Sol Youn
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea; (M.-R.K.); (S.Y.); (D.H.K.)
| | - Dong Hyun Kim
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea; (M.-R.K.); (S.Y.); (D.H.K.)
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea; (M.-R.K.); (S.Y.); (D.H.K.)
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Hogan CM, Merrill SM, Hernandez Valencia E, McHayle AA, Sisitsky MD, McDermott JM, Parent J. The Impact of Early Life Adversity on Peripubertal Accelerated Epigenetic Aging and Psychopathology. J Am Acad Child Adolesc Psychiatry 2024:S0890-8567(24)00352-6. [PMID: 38969335 DOI: 10.1016/j.jaac.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 04/24/2024] [Accepted: 06/26/2024] [Indexed: 07/07/2024]
Abstract
OBJECTIVE To examine longitudinal associations between early life threat and deprivation on epigenetic age acceleration at ages 9 and 15 years, and to examine associations of age acceleration on later internalizing and externalizing symptoms. METHOD The study examines a large (n = 2,039) and racially diverse (Black/African American = 44%, Latino = 18%, White = 5%) sample from a national dataset. Epigenetic age acceleration was estimated using the pediatric buccal epigenetic clock. Early life threat and deprivation were measured using composites from the Parent-Child Conflict Tactics Scale and county-level violent and property crime rate data. Internalizing and externalizing symptoms came from parent-reported Child Behavior Checklist. Path analysis models examined associations of threat and deprivation at age 3 years on epigenetic age acceleration at ages 9 and 15. Experiences of threat were further broken down into threat experienced in the home and in the community. RESULTS Home threat experienced at age 3 years predicted age acceleration at 9 and 15, and community threat experienced at 3 predicted age acceleration at 15, but not at 9. Deprivation was not a significant predictor of accelerated aging. Age acceleration at age 9 predicted externalizing, but not internalizing, symptoms at age 15. Community threat had a direct effect on externalizing. No association emerged with internalizing. CONCLUSION Findings revealed that threat, not deprivation, was predictive of age acceleration, demonstrating support for this pattern longitudinally, using an epigenetic clock that is accurate in children. The findings provide critical nuance to the examination of threat, and highlight associated risks and possible intervention points for externalizing symptoms.
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Affiliation(s)
| | - Sarah M Merrill
- Warren Alpert Medical School at Brown University, Providence, Rhode Island
| | | | - Allison A McHayle
- Warren Alpert Medical School at Brown University, Providence, Rhode Island
| | | | | | - Justin Parent
- Warren Alpert Medical School at Brown University, Providence, Rhode Island; University of Rhode Island, Kingston, Rhode Island; Emma Pendleton Bradley Hospital, East Providence, Rhode Island
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5
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Villa C, Combi R. Epigenetics in Alzheimer's Disease: A Critical Overview. Int J Mol Sci 2024; 25:5970. [PMID: 38892155 PMCID: PMC11173284 DOI: 10.3390/ijms25115970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Epigenetic modifications have been implicated in a number of complex diseases as well as being a hallmark of organismal aging. Several reports have indicated an involvement of these changes in Alzheimer's disease (AD) risk and progression, most likely contributing to the dysregulation of AD-related gene expression measured by DNA methylation studies. Given that DNA methylation is tissue-specific and that AD is a brain disorder, the limitation of these studies is the ability to identify clinically useful biomarkers in a proxy tissue, reflective of the tissue of interest, that would be less invasive, more cost-effective, and easily obtainable. The age-related DNA methylation changes have also been used to develop different generations of epigenetic clocks devoted to measuring the aging in different tissues that sometimes suggests an age acceleration in AD patients. This review critically discusses epigenetic changes and aging measures as potential biomarkers for AD detection, prognosis, and progression. Given that epigenetic alterations are chemically reversible, treatments aiming at reversing these modifications will be also discussed as promising therapeutic strategies for AD.
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Affiliation(s)
| | - Romina Combi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
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6
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Karetnikov DI, Romanov SE, Baklaushev VP, Laktionov PP. Age Prediction Using DNA Methylation Heterogeneity Metrics. Int J Mol Sci 2024; 25:4967. [PMID: 38732187 PMCID: PMC11084170 DOI: 10.3390/ijms25094967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
Dynamic changes in genomic DNA methylation patterns govern the epigenetic developmental programs and accompany the organism's aging. Epigenetic clock (eAge) algorithms utilize DNA methylation to estimate the age and risk factors for diseases as well as analyze the impact of various interventions. High-throughput bisulfite sequencing methods, such as reduced-representation bisulfite sequencing (RRBS) or whole genome bisulfite sequencing (WGBS), provide an opportunity to identify the genomic regions of disordered or heterogeneous DNA methylation, which might be associated with cell-type heterogeneity, DNA methylation erosion, and allele-specific methylation. We systematically evaluated the applicability of five scores assessing the variability of methylation patterns by evaluating within-sample heterogeneity (WSH) to construct human blood epigenetic clock models using RRBS data. The best performance was demonstrated by the model based on a metric designed to assess DNA methylation erosion with an MAE of 3.686 years. We also trained a prediction model that uses the average methylation level over genomic regions. Although this region-based model was relatively more efficient than the WSH-based model, the latter required the analysis of just a few short genomic regions and, therefore, could be a useful tool to design a reduced epigenetic clock that is analyzed by targeted next-generation sequencing.
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Affiliation(s)
- Dmitry I. Karetnikov
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Stanislav E. Romanov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Vladimir P. Baklaushev
- Federal Center for Brain and Neurotechnologies, Federal Medical and Biological Agency of Russia, 117513 Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Department of Medical Nanobiotechnology, Medical and Biological Faculty, Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, 117997 Moscow, Russia
| | - Petr P. Laktionov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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7
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Castagnola MJ, Medina-Paz F, Zapico SC. Uncovering Forensic Evidence: A Path to Age Estimation through DNA Methylation. Int J Mol Sci 2024; 25:4917. [PMID: 38732129 PMCID: PMC11084977 DOI: 10.3390/ijms25094917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Age estimation is a critical aspect of reconstructing a biological profile in forensic sciences. Diverse biochemical processes have been studied in their correlation with age, and the results have driven DNA methylation to the forefront as a promising biomarker. DNA methylation, an epigenetic modification, has been extensively studied in recent years for developing age estimation models in criminalistics and forensic anthropology. Epigenetic clocks, which analyze DNA sites undergoing hypermethylation or hypomethylation as individuals age, have paved the way for improved prediction models. A wide range of biomarkers and methods for DNA methylation analysis have been proposed, achieving different accuracies across samples and cell types. This review extensively explores literature from the past 5 years, showing scientific efforts toward the ultimate goal: applying age prediction models to assist in human identification.
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Affiliation(s)
- María Josefina Castagnola
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Francisco Medina-Paz
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Sara C. Zapico
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
- Department of Anthropology and Laboratories of Analytical Biology, National Museum of Natural History, MRC 112, Smithsonian Institution, Washington, DC 20560, USA
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8
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Lê BM, Hatch D, Yang Q, Shah N, Luyster FS, Garrett ME, Tanabe P, Ashley-Koch AE, Knisely MR. Characterizing epigenetic aging in an adult sickle cell disease cohort. Blood Adv 2024; 8:47-55. [PMID: 37967379 PMCID: PMC10784677 DOI: 10.1182/bloodadvances.2023011188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/20/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023] Open
Abstract
ABSTRACT Sickle cell disease (SCD) affects ∼100 000 predominantly African American individuals in the United States, causing significant cellular damage, increased disease complications, and premature death. However, the contribution of epigenetic factors to SCD pathophysiology remains relatively unexplored. DNA methylation (DNAm), a primary epigenetic mechanism for regulating gene expression in response to the environment, is an important driver of normal cellular aging. Several DNAm epigenetic clocks have been developed to serve as a proxy for cellular aging. We calculated the epigenetic ages of 89 adults with SCD (mean age, 30.64 years; 60.64% female) using 5 published epigenetic clocks: Horvath, Hannum, PhenoAge, GrimAge, and DunedinPACE. We hypothesized that in chronic disease, such as SCD, individuals would demonstrate epigenetic age acceleration, but the results differed depending on the clock used. Recently developed clocks more consistently demonstrated acceleration (GrimAge, DunedinPACE). Additional demographic and clinical phenotypes were analyzed to explore their association with epigenetic age estimates. Chronological age was significantly correlated with epigenetic age in all clocks (Horvath, r = 0.88; Hannum, r = 0.89; PhenoAge, r = 0.85; GrimAge, r = 0.88; DunedinPACE, r = 0.34). The SCD genotype was associated with 2 clocks (PhenoAge, P = .02; DunedinPACE, P < .001). Genetic ancestry, biological sex, β-globin haplotypes, BCL11A rs11886868, and SCD severity were not associated. These findings, among the first to interrogate epigenetic aging in adults with SCD, demonstrate epigenetic age acceleration with recently developed epigenetic clocks but not older-generation clocks. Further development of epigenetic clocks may improve their predictive ability and utility for chronic diseases such as SCD.
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Affiliation(s)
- Brandon M. Lê
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | | | - Qing Yang
- School of Nursing, Duke University, Durham, NC
| | - Nirmish Shah
- Department of Medicine, Division of Pediatric Hematology/Oncology, Duke University, Durham, NC
| | | | - Melanie E. Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | | | | | - Allison E. Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
- Department of Medicine, Duke University Medical Center, Durham, NC
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Kawamura T, Radak Z, Tabata H, Akiyama H, Nakamura N, Kawakami R, Ito T, Usui C, Jokai M, Torma F, Kim H, Miyachi M, Torii S, Suzuki K, Ishii K, Sakamoto S, Oka K, Higuchi M, Muraoka I, McGreevy KM, Horvath S, Tanisawa K. Associations between cardiorespiratory fitness and lifestyle-related factors with DNA methylation-based ageing clocks in older men: WASEDA'S Health Study. Aging Cell 2024; 23:e13960. [PMID: 37584423 PMCID: PMC10776125 DOI: 10.1111/acel.13960] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/17/2023] Open
Abstract
DNA methylation-based age estimators (DNAm ageing clocks) are currently one of the most promising biomarkers for predicting biological age. However, the relationships between cardiorespiratory fitness (CRF), measured directly by expiratory gas analysis, and DNAm ageing clocks are largely unknown. We investigated the relationships between CRF and the age-adjusted value from the residuals of the regression of DNAm ageing clock to chronological age (DNAmAgeAcceleration: DNAmAgeAccel) and attempted to determine the relative contribution of CRF to DNAmAgeAccel in the presence of other lifestyle factors. DNA samples from 144 Japanese men aged 65-72 years were used to appraise first- (i.e., DNAmHorvath and DNAmHannum) and second- (i.e., DNAmPhenoAge, DNAmGrimAge, and DNAmFitAge) generation DNAm ageing clocks. Various surveys and measurements were conducted, including physical fitness, body composition, blood biochemical parameters, nutrient intake, smoking, alcohol consumption, disease status, sleep status, and chronotype. Both oxygen uptake at ventilatory threshold (VO2 /kg at VT) and peak oxygen uptake (VO2 /kg at Peak) showed a significant negative correlation with GrimAgeAccel, even after adjustments for chronological age and smoking and drinking status. Notably, VO2 /kg at VT and VO2 /kg at Peak above the reference value were also associated with delayed GrimAgeAccel. Multiple regression analysis showed that calf circumference, serum triglyceride, carbohydrate intake, and smoking status, rather than CRF, contributed more to GrimAgeAccel and FitAgeAccel. In conclusion, although the contribution of CRF to GrimAgeAccel and FitAgeAccel is relatively low compared to lifestyle-related factors such as smoking, the results suggest that the maintenance of CRF is associated with delayed biological ageing in older men.
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Affiliation(s)
- Takuji Kawamura
- Waseda Institute for Sport Sciences, Waseda UniversitySaitamaJapan
- Research Centre for Molecular Exercise ScienceHungarian University of Sports ScienceBudapestHungary
| | - Zsolt Radak
- Research Centre for Molecular Exercise ScienceHungarian University of Sports ScienceBudapestHungary
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
| | - Hiroki Tabata
- Waseda Institute for Sport Sciences, Waseda UniversitySaitamaJapan
- Sportology CentreJuntendo University Graduate School of MedicineTokyoJapan
| | - Hiroshi Akiyama
- Graduate School of Sport SciencesWaseda UniversitySaitamaJapan
| | | | - Ryoko Kawakami
- Waseda Institute for Sport Sciences, Waseda UniversitySaitamaJapan
- Physical Fitness Research Institute, Meiji Yasuda Life Foundation of Health and WelfareTokyoJapan
| | - Tomoko Ito
- Waseda Institute for Sport Sciences, Waseda UniversitySaitamaJapan
- Department of Food and NutritionTokyo Kasei UniversityTokyoJapan
| | - Chiyoko Usui
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
| | - Matyas Jokai
- Research Centre for Molecular Exercise ScienceHungarian University of Sports ScienceBudapestHungary
| | - Ferenc Torma
- Faculty of Health and Sport SciencesUniversity of TsukubaIbarakiJapan
| | - Hyeon‐Ki Kim
- Research Centre for Molecular Exercise ScienceHungarian University of Sports ScienceBudapestHungary
| | | | - Suguru Torii
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
| | | | - Kaori Ishii
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
| | - Shizuo Sakamoto
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
- Faculty of Sport ScienceSurugadai UniversitySaitamaJapan
| | - Koichiro Oka
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
| | | | - Isao Muraoka
- Faculty of Sport SciencesWaseda UniversitySaitamaJapan
| | - Kristen M. McGreevy
- Department of Biostatistics, Fielding School of Public HealthUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public HealthUniversity of California Los AngelesLos AngelesCaliforniaUSA
- Department of Human Genetics, David Geffen School of MedicineUniversity of California Los AngelesLos AngelesCaliforniaUSA
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10
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Refn MR, Andersen MM, Kampmann ML, Tfelt-Hansen J, Sørensen E, Larsen MH, Morling N, Børsting C, Pereira V. Longitudinal changes and variation in human DNA methylation analysed with the Illumina MethylationEPIC BeadChip assay and their implications on forensic age prediction. Sci Rep 2023; 13:21658. [PMID: 38066081 PMCID: PMC10709620 DOI: 10.1038/s41598-023-49064-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
DNA methylation, a pivotal epigenetic modification, plays a crucial role in regulating gene expression and is known to undergo dynamic changes with age. The present study investigated epigenome-wide methylation profiles in 64 individuals over two time points, 15 years apart, using the Illumina EPIC850k arrays. A mixed-effects model identified 2821 age-associated differentially methylated CpG positions (aDMPs) with a median rate of change of 0.18% per year, consistent with a 10-15% change during a human lifespan. Significant variation in the baseline DNA methylation levels between individuals of similar ages as well as inconsistent direction of change with time across individuals were observed for all the aDMPs. Twenty-three of the 2821 aDMPs were previously incorporated into forensic age prediction models. These markers displayed larger changes in DNA methylation with age compared to all the aDMPs and less variation among individuals. Nevertheless, the forensic aDMPs also showed inter-individual variations in the direction of DNA methylation changes. Only cg16867657 in ELOVL2 exhibited a uniform direction of the age-related change among the investigated individuals, which supports the current knowledge that CpG sites in ELOVL2 are the best markers for age prediction.
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Affiliation(s)
- Mie Rath Refn
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Mikkel Meyer Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- The Department of Mathematical Sciences, Aalborg University, 9220, Aalborg, Denmark
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- The Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Margit Hørup Larsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
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Zeidan RS, McElroy T, Rathor L, Martenson MS, Lin Y, Mankowski RT. Sex differences in frailty among older adults. Exp Gerontol 2023; 184:112333. [PMID: 37993077 DOI: 10.1016/j.exger.2023.112333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/24/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
By definition, aging is a natural, gradual and continuous process. On the other hand, frailty reflects the increase in vulnerability to stressors and shortens the time without disease (health span) while longevity refers to the length of life (lifespan). The average life expectancy has significantly increased during the last few decades. A longer lifespan has been accompanied by an increase in frailty and decreased independence in older adults, with major differences existing between men and women. For example, women tend to live longer than men but also experience higher rates of frailty and disability. Sex differences prevent optimization of lifestyle interventions and therapies to effectively prevent frailty. Sex differences in frailty and aging are rooted in a complex interplay between uncontrollable (genetic, epigenetic, physiological), and controllable factors (psychosocial and lifestyle factors). Thus, understanding the underlying causes of sex differences in frailty and aging is essential for developing personalized interventions to promote healthy aging and improve quality of life in older men and women. In this review, we have discussed the key contributors and knowledge gaps related to sex differences in aging and frailty.
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Affiliation(s)
- Rola S Zeidan
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America; Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Taylor McElroy
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America; Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Laxmi Rathor
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Matthew S Martenson
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Yi Lin
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America.
| | - Robert T Mankowski
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, FL, United States of America.
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12
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Iannuzzi V, Sarno S, Sazzini M, Abondio P, Sala C, Bacalini MG, Gentilini D, Calzari L, Masciotta F, Garagnani P, Castellani G, Moretti E, Dasso MC, Sevini F, Franceschi ZA, Franceschi C, Pettener D, Luiselli D, Giuliani C. Epigenetic aging differences between Wichí and Criollos from Argentina: Insights from genomic history and ecology. Evol Med Public Health 2023; 11:397-414. [PMID: 37954982 PMCID: PMC10632719 DOI: 10.1093/emph/eoad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/07/2023] [Indexed: 11/14/2023] Open
Abstract
Background and objectives Epigenetic estimators based on DNA methylation levels have emerged as promising biomarkers of human aging. These estimators exhibit natural variations across human groups, but data about indigenous populations remain underrepresented in research. This study aims to investigate differences in epigenetic estimators between two distinct human populations, both residing in the Gran Chaco region of Argentina, the Native-American Wichí, and admixed Criollos who are descendants of intermarriages between Native Americans and the first European colonizers, using a population genetic approach. Methodology We analyzed 24 Wichí (mean age: 39.2 ± 12.9 yo) and 24 Criollos (mean age: 41.1 ± 14.0 yo) for DNA methylation levels using the Infinium MethylationEPIC (Illumina) to calculate 16 epigenetic estimators. Additionally, we examined genome-wide genetic variation using the HumanOmniExpress BeadChip (Illumina) to gain insights into the genetic history of these populations. Results Our results indicate that Native-American Wichí are epigenetically older compared to Criollos according to five epigenetic estimators. Analyses within the Criollos population reveal that global ancestry does not influence the differences observed, while local (chromosomal) ancestry shows positive associations between specific SNPs located in genomic regions over-represented by Native-American ancestry and measures of epigenetic age acceleration (AgeAccelHannum). Furthermore, we demonstrate that differences in population ecologies also contribute to observed epigenetic differences. Conclusions and implications Overall, our study suggests that while the genomic history may partially account for the observed epigenetic differences, non-genetic factors, such as lifestyle and ecological factors, play a substantial role in the variability of epigenetic estimators, thereby contributing to variations in human epigenetic aging.
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Affiliation(s)
- Vincenzo Iannuzzi
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Marco Sazzini
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, Italy
- Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate), Interdepartmental Centre, University of Bologna, Bologna, Italy
| | - Paolo Abondio
- Department of Cultural Heritage (DBC), University of Bologna, Ravenna Campus, Ravenna, Italy
| | - Claudia Sala
- Department of Medical and Surgical Science (DIMEC), University of Bologna, Bologna, Italy
| | | | - Davide Gentilini
- Department of Brain and Behavioral Sciences, Università di Pavia, Pavia, Italy
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Luciano Calzari
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Federica Masciotta
- Department of Statistical Sciences ‘Paolo Fortunati’, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Medical and Surgical Science (DIMEC), University of Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Gastone Castellani
- Department of Medical and Surgical Science (DIMEC), University of Bologna, Bologna, Italy
| | - Edgardo Moretti
- Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Instituto de Biología y Medicina Experimental de Cuyo, CCT CONICET, Argentina
| | - Maria Cristina Dasso
- Centro de Investigaciones en Antropología Filosófica y Cultural (CIAFIC), Buenos Aires, Argentina
| | - Federica Sevini
- Department of Medical and Surgical Science (DIMEC), University of Bologna, Bologna, Italy
| | | | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Davide Pettener
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Department of Cultural Heritage (DBC), University of Bologna, Ravenna Campus, Ravenna, Italy
| | - Cristina Giuliani
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, Italy
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Housini M, Zhou Z, Gutierrez J, Rao S, Jomaa R, Subasinghe K, Reid DM, Silzer T, Phillips N, O'Bryant S, Barber RC. Top Alzheimer's disease risk allele frequencies differ in HABS-HD Mexican- versus Non-Hispanic White Americans. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2023; 15:e12518. [PMID: 38155914 PMCID: PMC10752755 DOI: 10.1002/dad2.12518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/13/2023] [Accepted: 11/25/2023] [Indexed: 12/30/2023]
Abstract
INTRODUCTION: Here we evaluate frequencies of the top 10 Alzheimer's disease (AD) risk alleles for late-onset AD in Mexican American (MA) and non-Hispanic White (NHW) American participants enrolled in the Health and Aging Brain Study-Health Disparities Study cohort. METHODS: Using DNA extracted from this community-based diverse population, we calculated the genotype frequencies in each population to determine whether a significant difference is detected between the different ethnicities. DNA genotyping was performed per manufacturers' protocols. RESULTS: Allele and genotype frequencies for 9 of the 11 single nucleotide polymorphisms (two apolipoprotein E variants, CR1, BIN1, DRB1, NYAP1, PTK2B, FERMT2, and ABCA7) differed significantly between MAs and NHWs. DISCUSSION: The significant differences in frequencies of top AD risk alleles observed here across MAs and NHWs suggest that ethnicity-specific genetic risks for AD exist. Given our results, we are advancing additional projects to further elucidate ethnicity-specific differences in AD.
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Affiliation(s)
- Mohammad Housini
- Department of Pharmacology and NeuroscienceSchool of Biomedical SciencesUniversity of North Texas Health Science CenterFort WorthTexasUSA
- Department of Family Medicine & Manipulative MedicineTexas College of Osteopathic MedicineUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Zhengyang Zhou
- Department of Biostatistics and EpidemiologySchool of Public HealthUniversity of North Texas Health Science CenterFort WorthTexasUSA
- Institute for Translational ResearchUNT Health Science CenterFort WorthTexasUSA
| | - John Gutierrez
- Department of Internal MedicineTexas Institute for Graduate Medical Education and ResearchSan AntonioTexasUSA
| | - Sumedha Rao
- Department of Family Medicine & Manipulative MedicineTexas College of Osteopathic MedicineUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Rodwan Jomaa
- Department of Family Medicine & Manipulative MedicineTexas College of Osteopathic MedicineUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Kumudu Subasinghe
- Department of MicrobiologyImmunology and GeneticsSchool of Biomedical SciencesUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Danielle Marie Reid
- Department of MicrobiologyImmunology and GeneticsSchool of Biomedical SciencesUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Talisa Silzer
- Department of MicrobiologyImmunology and GeneticsSchool of Biomedical SciencesUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Nicole Phillips
- Institute for Translational ResearchUNT Health Science CenterFort WorthTexasUSA
- Department of MicrobiologyImmunology and GeneticsSchool of Biomedical SciencesUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Sid O'Bryant
- Department of Family Medicine & Manipulative MedicineTexas College of Osteopathic MedicineUniversity of North Texas Health Science CenterFort WorthTexasUSA
- Institute for Translational ResearchUNT Health Science CenterFort WorthTexasUSA
| | - Robert Clinton Barber
- Department of Family Medicine & Manipulative MedicineTexas College of Osteopathic MedicineUniversity of North Texas Health Science CenterFort WorthTexasUSA
- Institute for Translational ResearchUNT Health Science CenterFort WorthTexasUSA
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Freilich CD. How does loneliness "get under the skin" to become biologically embedded? BIODEMOGRAPHY AND SOCIAL BIOLOGY 2023; 68:115-148. [PMID: 37800557 PMCID: PMC10843517 DOI: 10.1080/19485565.2023.2260742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Loneliness is linked to declining physical health across cardiovascular, inflammatory, metabolic, and cognitive domains. As a result, loneliness is increasingly being recognized as a public health threat, though the mechanisms that have been studied do not yet explain all loneliness-related health risk. Potential mechanisms include loneliness having 1.) direct, causal impacts on health, possibly maintained by epigenetic modification, 2.) indirect effects mediated through health-limiting behaviors, and 3.) artifactual associations perhaps related to genetic overlap and reverse causation. In this scoping review, we examine the evidence surrounding each of these pathways, with a particular emphasis on emerging research on epigenetic effects, in order to evaluate how loneliness becomes biologically embedded. We conclude that there are significant gaps in our knowledge of how psychosocial stress may lead to physiological changes, so more work is needed to understand if, how, and when loneliness has a direct influence on health. Hypothalamic-pituitary adrenocortical axis disruptions that lead to changes in gene expression through methylation and the activity of transcription factor proteins are one promising area of research but are confounded by a number of unmeasured factors. Therefore, wok is needed using causally informative designs, such as twin and family studies and intensively longitudinal diary studies.
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15
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Jones JD, Martinez S, Gonzalez I, Odom GJ, Comer SD. No evidence of accelerated epigenetic aging among black heroin users: A case vs control analysis. ADDICTION NEUROSCIENCE 2023; 7:100096. [PMID: 37388854 PMCID: PMC10305791 DOI: 10.1016/j.addicn.2023.100096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
This study sought to assess the association between illicit opioid use and accelerated epigenetic aging (A.K.A. DNAm Age) among people of African ancestry who use heroin. DNA was obtained from participants with opioid use disorder (OUD) who confirmed heroin as their primary drug of choice. Clinical inventories of drug use included: the Addiction Severity Index (ASI) Drug-Composite Score (range: 0-1), and Drug Abuse Screening Test (DAST-10; range: 0-10). A control group of participants of African ancestry who did not use heroin was recruited and matched to heroin users on sex, age, socioeconomic level, and smoking status. Methylation data were assessed in an epigenetic clock to determined and compare Epigenetic Age to Chronological Age (i.e., age acceleration or deceleration). Data were obtained from 32 controls [mean age 36.3 (±7.5) years] and 64 heroin users [mean age 48.1 (±6.6) years]. The experimental group used heroin for an average of 18.1 (±10.6) years, reported use of 6.4 (±6.1) bags of heroin/day, with a mean DAST-10 score of 7.0 (±2.6) and ASI Score of 0.33 (±0.19). Mean age acceleration for heroin users [+0.56 (± 9.5) years] was significantly (p< 0.05) lower than controls [+5.19 (± 9.1) years]. This study did not find evidence that heroin use causes epigenetic age acceleration.
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Affiliation(s)
- Jermaine D. Jones
- Department of Psychiatry, Division on Substance Use Disorders, New York State Psychiatric Institute, and Columbia University Irving Medical Center, 1051 Riverside Drive, New York, NY 10032, USA
| | - Suky Martinez
- Department of Psychiatry, Division on Substance Use Disorders, New York State Psychiatric Institute, and Columbia University Irving Medical Center, 1051 Riverside Drive, New York, NY 10032, USA
| | - Ingrid Gonzalez
- Department of Biostatistics, Robert Stempel College of Public Health, Florida International University, 1200 SW 8th St, Miami, FL 33174, USA
| | - Gabriel J. Odom
- Department of Biostatistics, Robert Stempel College of Public Health, Florida International University, 1200 SW 8th St, Miami, FL 33174, USA
| | - Sandra D. Comer
- Department of Psychiatry, Division on Substance Use Disorders, New York State Psychiatric Institute, and Columbia University Irving Medical Center, 1051 Riverside Drive, New York, NY 10032, USA
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16
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Venkataraghavan S, Pankow JS, Boerwinkle E, Fornage M, Selvin E, Ray D. Epigenome-wide association study of incident type 2 diabetes in Black and White participants from the Atherosclerosis Risk in Communities Study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.09.23293896. [PMID: 37609313 PMCID: PMC10441493 DOI: 10.1101/2023.08.09.23293896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
DNA methylation studies of incident type 2 diabetes in US populations are limited, and to our knowledge none included individuals of African descent living in the US. We performed an epigenome-wide association analysis of blood-based methylation levels at CpG sites with incident type 2 diabetes using Cox regression in 2,091 Black and 1,029 White individuals from the Atherosclerosis Risk in Communities study. At an epigenome-wide significance threshold of 10-7, we detected 7 novel diabetes-associated CpG sites in C1orf151 (cg05380846: HR= 0.89, p = 8.4 × 10-12), ZNF2 (cg01585592: HR= 0.88, p = 1.6 × 10-9), JPH3 (cg16696007: HR= 0.87, p = 7.8 × 10-9), GPX6 (cg02793507: HR= 0.85, p = 2.7 × 10-8 and cg00647063: HR= 1.20, p = 2.5 × 10-8), chr17q25 (cg16865890: HR= 0.8, p = 6.9 × 10-8), and chr11p15 (cg13738793: HR= 1.11, p = 7.7 × 10-8). The CpG sites at C1orf151, ZNF2, JPH3 and GPX6, were identified in Black adults, chr17q25 was identified in White adults, and chr11p15 was identified upon meta-analyzing the two groups. The CpG sites at JPH3 and GPX6 were likely associated with incident type 2 diabetes independent of BMI. All the CpG sites, except at JPH3, were likely consequences of elevated glucose at baseline. We additionally replicated known type 2 diabetes-associated CpG sites including cg19693031 at TXNIP, cg00574958 at CPT1A, cg16567056 at PLBC2, cg11024682 at SREBF1, cg08857797 at VPS25, and cg06500161 at ABCG1, 3 of which were replicated in Black adults at the epigenome-wide threshold. We observed modest increase in type 2 diabetes variance explained upon addition of the significantly associated CpG sites to a Cox model that included traditional type 2 diabetes risk factors and fasting glucose (increase from 26.2% to 30.5% in Black adults; increase from 36.9% to 39.4% in White adults). We examined if groups of proximal CpG sites were associated with incident type 2 diabetes using a gene-region specific and a gene-region agnostic differentially methylated region (DMR) analysis. Our DMR analyses revealed several clusters of significant CpG sites, including a DMR consisting of a previously discovered CpG site at ADCY7 and promoter regions of TP63 which were differentially methylated across all race groups. This study illustrates improved discovery of CpG sites/regions by leveraging both individual CpG site and DMR analyses in an unexplored population. Our findings include genes linked to diabetes in experimental studies (e.g., GPX6, JPH3, and TP63), and future gene-specific methylation studies could elucidate the link between genes, environment, and methylation in the pathogenesis of type 2 diabetes.
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Affiliation(s)
- Sowmya Venkataraghavan
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - James S. Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of American
| | - Eric Boerwinkle
- The UTHealth School of Public Health, Houston, Texas, United States of America
| | - Myriam Fornage
- Brown Foundation Institute for Molecular Medicine, The University of Texas Health Science Center, Houston, Texas, United States of America
| | - Elizabeth Selvin
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Welch Center for Prevention, Epidemiology, & Clinical Research, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Debashree Ray
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
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Watkins SH, Testa C, Chen JT, De Vivo I, Simpkin AJ, Tilling K, Diez Roux AV, Davey Smith G, Waterman PD, Suderman M, Relton C, Krieger N. Epigenetic clocks and research implications of the lack of data on whom they have been developed: a review of reported and missing sociodemographic characteristics. ENVIRONMENTAL EPIGENETICS 2023; 9:dvad005. [PMID: 37564905 PMCID: PMC10411856 DOI: 10.1093/eep/dvad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/17/2023] [Accepted: 07/13/2023] [Indexed: 08/12/2023]
Abstract
Epigenetic clocks are increasingly being used as a tool to assess the impact of a wide variety of phenotypes and exposures on healthy ageing, with a recent focus on social determinants of health. However, little attention has been paid to the sociodemographic characteristics of participants on whom these clocks have been based. Participant characteristics are important because sociodemographic and socioeconomic factors are known to be associated with both DNA methylation variation and healthy ageing. It is also well known that machine learning algorithms have the potential to exacerbate health inequities through the use of unrepresentative samples - prediction models may underperform in social groups that were poorly represented in the training data used to construct the model. To address this gap in the literature, we conducted a review of the sociodemographic characteristics of the participants whose data were used to construct 13 commonly used epigenetic clocks. We found that although some of the epigenetic clocks were created utilizing data provided by individuals from different ages, sexes/genders, and racialized groups, sociodemographic characteristics are generally poorly reported. Reported information is limited by inadequate conceptualization of the social dimensions and exposure implications of gender and racialized inequality, and socioeconomic data are infrequently reported. It is important for future work to ensure clear reporting of tangible data on the sociodemographic and socioeconomic characteristics of all the participants in the study to ensure that other researchers can make informed judgements about the appropriateness of the model for their study population.
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Affiliation(s)
- Sarah Holmes Watkins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Christian Testa
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Jarvis T Chen
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Immaculata De Vivo
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Andrew J Simpkin
- School of Medicine, National University of Ireland Galway, Galway H91 TK33, Ireland
| | - Kate Tilling
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Ana V Diez Roux
- Department of Epidemiology and Biostatistics and Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA 19104, USA
| | - George Davey Smith
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Pamela D Waterman
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Matthew Suderman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Caroline Relton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Nancy Krieger
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
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18
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Ray M, Wallace MK, Grayson SC, Cummings MH, Davis JA, Scott J, Belcher SM, Davis TS, Conley YP. Epigenomic Links Between Social Determinants of Health and Symptoms: A Scoping Review. Biol Res Nurs 2023; 25:404-416. [PMID: 36537264 PMCID: PMC10404910 DOI: 10.1177/10998004221147300] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Social determinants of health (SDoH) impact health and wellness. The link between SDoH and adverse health outcomes, including symptom occurrence and severity, may be explained by an individual's physiologic response to one or more SDoH. One potential mechanism underlying this physiologic response linking SDoH and symptoms is the dynamic epigenome. The purpose of this scoping review of the literature was to examine differential susceptibility for symptoms by identifying and summarizing research linking SDoH and symptoms through epigenomic mechanisms. PubMed was searched to identify empirical research where at least one SDoH was an independent or dependent variable, at least one symptom was investigated, and the investigation included an epigenomic measure. Of the 484 articles initially retrieved, after thorough vetting, 41 articles met eligibility. The most studied symptom was depressive symptoms followed by anxiety, cognitive function, sleep dysfunction, and pain. The most frequently studied SDoH were: 1) stress, particularly early life stress and acculturative stress; and 2) trauma, predominantly childhood trauma. DNA methylation and telomere length were the most studied epigenomic measures. Four genes (SLC6A4, BDNF, NR3C1, OXTR) had evidence from multiple studies and across methodological approaches linking SDoH to symptoms. This review supports the inclusion of epigenomic approaches to better understand the link between SDoH and symptoms and provides evidence that SDoH impact telomere length and the methylation of genes involved in neurotransmitter signaling, neuronal survival, behavior, inflammation and stress response.
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Affiliation(s)
- Mitali Ray
- Health Promotion and Development, University of Pittsburgh School of Nursing, Pittsburgh, PA, USA
| | | | - Susan C. Grayson
- Health Promotion and Development, University of Pittsburgh School of Nursing, Pittsburgh, PA, USA
| | - Meredith H. Cummings
- Health Promotion and Development, University of Pittsburgh School of Nursing, Pittsburgh, PA, USA
| | - Jessica A. Davis
- Health Promotion and Development, University of Pittsburgh School of Nursing, Pittsburgh, PA, USA
| | - Jewel Scott
- College of Nursing, University of South Carolina, Columbia, SC, USA
| | - Sarah M. Belcher
- Health and Community Systems, University of Pittsburgh School of Nursing, Pittsburgh, PA, USA
| | - Tara S. Davis
- Health Promotion and Development, University of Pittsburgh School of Nursing, Pittsburgh, PA, USA
| | - Yvette P. Conley
- School of Nursing, University of Pittsburgh, Pittsburgh, PA, USA
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Milicic L, Porter T, Vacher M, Laws SM. Utility of DNA Methylation as a Biomarker in Aging and Alzheimer's Disease. J Alzheimers Dis Rep 2023; 7:475-503. [PMID: 37313495 PMCID: PMC10259073 DOI: 10.3233/adr-220109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/23/2023] [Indexed: 06/15/2023] Open
Abstract
Epigenetic mechanisms such as DNA methylation have been implicated in a number of diseases including cancer, heart disease, autoimmune disorders, and neurodegenerative diseases. While it is recognized that DNA methylation is tissue-specific, a limitation for many studies is the ability to sample the tissue of interest, which is why there is a need for a proxy tissue such as blood, that is reflective of the methylation state of the target tissue. In the last decade, DNA methylation has been utilized in the design of epigenetic clocks, which aim to predict an individual's biological age based on an algorithmically defined set of CpGs. A number of studies have found associations between disease and/or disease risk with increased biological age, adding weight to the theory of increased biological age being linked with disease processes. Hence, this review takes a closer look at the utility of DNA methylation as a biomarker in aging and disease, with a particular focus on Alzheimer's disease.
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Affiliation(s)
- Lidija Milicic
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
| | - Michael Vacher
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- CSIRO Health and Biosecurity, Australian e-Health Research Centre, Floreat, Western Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
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20
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Chan MHM, Merrill SM, Konwar C, Kobor MS. An integrative framework and recommendations for the study of DNA methylation in the context of race and ethnicity. DISCOVER SOCIAL SCIENCE AND HEALTH 2023; 3:9. [PMID: 37122633 PMCID: PMC10118232 DOI: 10.1007/s44155-023-00039-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023]
Abstract
Human social epigenomics research is critical to elucidate the intersection of social and genetic influences underlying racial and ethnic differences in health and development. However, this field faces major challenges in both methodology and interpretation with regard to disentangling confounded social and biological aspects of race and ethnicity. To address these challenges, we discuss how these constructs have been approached in the past and how to move forward in studying DNA methylation (DNAm), one of the best-characterized epigenetic marks in humans, in a responsible and appropriately nuanced manner. We highlight self-reported racial and ethnic identity as the primary measure in this field, and discuss its implications in DNAm research. Racial and ethnic identity reflects the biological embedding of an individual's sociocultural experience and environmental exposures in combination with the underlying genetic architecture of the human population (i.e., genetic ancestry). Our integrative framework demonstrates how to examine DNAm in the context of race and ethnicity, while considering both intrinsic factors-including genetic ancestry-and extrinsic factors-including structural and sociocultural environment and developmental niches-when focusing on early-life experience. We reviewed DNAm research in relation to health disparities given its relevance to race and ethnicity as social constructs. Here, we provide recommendations for the study of DNAm addressing racial and ethnic differences, such as explicitly acknowledging the self-reported nature of racial and ethnic identity, empirically examining the effects of genetic variants and accounting for genetic ancestry, and investigating race-related and culturally regulated environmental exposures and experiences. Supplementary Information The online version contains supplementary material available at 10.1007/s44155-023-00039-z.
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Affiliation(s)
- Meingold Hiu-ming Chan
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC Canada
| | - Sarah M. Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC Canada
| | - Chaini Konwar
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC Canada
| | - Michael S. Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC Canada
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
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21
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Guez-Barber D, Eisch AJ, Cristancho AG. Developmental Brain Injury and Social Determinants of Health: Opportunities to Combine Preclinical Models for Mechanistic Insights into Recovery. Dev Neurosci 2023; 45:255-267. [PMID: 37080174 PMCID: PMC10614252 DOI: 10.1159/000530745] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/14/2023] [Indexed: 04/22/2023] Open
Abstract
Epidemiological studies show that social determinants of health are among the strongest factors associated with developmental outcomes after prenatal and perinatal brain injuries, even when controlling for the severity of the initial injury. Elevated socioeconomic status and a higher level of parental education correlate with improved neurologic function after premature birth. Conversely, children experiencing early life adversity have worse outcomes after developmental brain injuries. Animal models have provided vital insight into mechanisms perturbed by developmental brain injuries, which have indicated directions for novel therapeutics or interventions. Animal models have also been used to learn how social environments affect brain maturation through enriched environments and early adverse conditions. We recognize animal models cannot fully recapitulate human social circumstances. However, we posit that mechanistic studies combining models of developmental brain injuries and early life social environments will provide insight into pathways important for recovery. Some studies combining enriched environments with neonatal hypoxic injury models have shown improvements in developmental outcomes, but further studies are needed to understand the mechanisms underlying these improvements. By contrast, there have been more limited studies of the effects of adverse conditions on developmental brain injury extent and recovery. Uncovering the biological underpinnings for early life social experiences has translational relevance, enabling the development of novel strategies to improve outcomes through lifelong treatment. With the emergence of new technologies to analyze subtle molecular and behavioral phenotypes, here we discuss the opportunities for combining animal models of developmental brain injury with social construct models to deconvolute the complex interactions between injury, recovery, and social inequity.
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Affiliation(s)
- Danielle Guez-Barber
- Division of Child Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amelia J. Eisch
- Department of Anesthesiology and Critical Care, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ana G. Cristancho
- Division of Child Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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22
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Devall MA, Sun X, Eaton S, Cooper GS, Willis JE, Weisenberger DJ, Casey G, Li L. A Race-Specific, DNA Methylation Analysis of Aging in Normal Rectum: Implications for the Biology of Aging and Its Relationship to Rectal Cancer. Cancers (Basel) 2022; 15:cancers15010045. [PMID: 36612042 PMCID: PMC9817986 DOI: 10.3390/cancers15010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/01/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Approximately 90% of colorectal cancer (CRC) develop over the age of 50, highlighting the important role of aging in CRC risk. African Americans (AAs) shoulder a greater CRC burden than European Americans (EA) and are more likely to develop CRC at a younger age. The effects of aging in AA and EA normal rectal tissue have yet to be defined. Here, we performed epigenome-wide DNA methylation analysis in the first, large-scale biracial cohort of normal rectum (n = 140 samples). We identified increased epigenetic age acceleration in EA than AA rectum (p = 3.91 × 10-4) using linear regression. We also identified differentially methylated regions (DMRs) associated with chronological aging in AA and EA, separately using DMRcate. Next, a consensus set of regions associated with cancer was identified through DMR analysis of two rectal cancer cohorts. The vast majority of AA DMRs were present in our analysis of aging in rectum of EA subjects, though rates of epigenetic drift were significantly greater in AA (p = 1.94 × 10-45). However, 3.66-fold more DMRs were associated with aging in rectum of EA subjects, many of which were also associated with rectal cancer. Our findings reveal a novel relationship between race, age, DNA methylation and rectal cancer risk that warrants further investigation.
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Affiliation(s)
- Matthew A. Devall
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Xiangqing Sun
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen Eaton
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Gregory S. Cooper
- Department of Medicine, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Joseph E. Willis
- Department of Pathology, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Daniel J. Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence: ; Tel.: +1-434-982-3975
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23
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Dolinko AV, Schultz BM, Ghosh J, Kalliora C, Mainigi M, Coutifaris C, Sapienza C, Senapati S. Disrupted methylation patterns at birth persist in early childhood: a prospective cohort analysis. Clin Epigenetics 2022; 14:129. [PMID: 36243864 PMCID: PMC9568969 DOI: 10.1186/s13148-022-01348-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alterations in the epigenome are a risk factor in multiple disease states. We have demonstrated in the past that disruption of the epigenome during early pregnancy or periconception, as demonstrated by altered methylation, may be associated with both assisted reproductive technology and undesirable clinical outcomes at birth, such as low birth weight. We have previously defined this altered methylation, calculated based on statistical upper and lower limits of outlier CpGs compared to the population, as an 'outlier methylation phenotype' (OMP). Our aim in this study was to determine whether children thus identified as possessing an OMP at birth by DNA methylation in cord blood persist as outliers in early childhood based on salivary DNA methylation. RESULTS A total of 31 children were included in the analysis. Among 24 children for whom both cord blood DNA and salivary DNA were available, DNA methylation patterns, analyzed using the Illumina Infinium MethylationEPIC BeadChip (850 K), between cord blood at birth and saliva in childhood at age 6-12 years remain stable (R2 range 0.89-0.97). At birth, three out of 28 children demonstrated an OMP in multiple cord blood datasets and hierarchical clustering. Overall DNA methylation among all three OMP children identified as outliers at birth was remarkably stable (individual R2 0.908, 0.92, 0.915), even when only outlier CpG sites were considered (R2 0.694, 0.738, 0.828). CONCLUSIONS DNA methylation signatures in cord blood remain stable over time as demonstrated by a strong correlation with epigenetic salivary signatures in childhood. Future work is planned to identify whether a clinical phenotype is associated with OMP and, if so, could undesirable clinical outcomes in childhood and adulthood be predicted at birth.
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Affiliation(s)
- Andrey V Dolinko
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Bryant M Schultz
- Fels Cancer Institute for Personalized Medicine, Temple University, Philadelphia, PA, USA
| | - Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Temple University, Philadelphia, PA, USA
| | - Charikleia Kalliora
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Monica Mainigi
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Christos Coutifaris
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Carmen Sapienza
- Fels Cancer Institute for Personalized Medicine, Temple University, Philadelphia, PA, USA
| | - Suneeta Senapati
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA.
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24
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Freni-Sterrantino A, Fiorito G, d’Errico A, Virtanen M, Ala-Mursula L, Järvelin MR, Vineis P, Robinson O. Association between work characteristics and epigenetic age acceleration: cross-sectional results from UK - Understanding Society study. Aging (Albany NY) 2022; 14:7752-7773. [PMID: 36202116 PMCID: PMC9596217 DOI: 10.18632/aging.204327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/17/2022] [Indexed: 11/25/2022]
Abstract
Occupation-related stress and work characteristics are possible determinants of social inequalities in epigenetic aging but have been little investigated. Here, we investigate the association of several work characteristics with epigenetic age acceleration (AA) biomarkers. The study population included employed and unemployed men and women (n = 631) from the UK Understanding Society study. We evaluated the association of employment and work characteristics related to job type, job stability; job schedule; autonomy and influence at work; occupational physical activity; and feelings regarding the job with four epigenetic age acceleration biomarkers (Hannum, Horvath, PhenoAge, GrimAge) and pace of aging (DunedinPoAm, DunedinPACE). We fitted linear regression models, unadjusted and adjusted for established risk factors, and found the following associations for unemployment (years of acceleration): HorvathAA (1.51, 95% CI 0.08, 2.95), GrimAgeAA (1.53, 95% CI 0.16, 2.90) and 3.21 years for PhenoAA (95% CI 0.89, 5.33). Job insecurity increased PhenoAA (1.83, 95% CI 0.003, 3.67), while working at night was associated with an increase of 2.12 years in GrimAgeAA (95% CI 0.69, 3.55). We found effects of unemployment to be stronger in men and effects of night shift work to be stronger in women. These results provide evidence of associations between unemployment with accelerated ageing and suggest that insecure employment and night work may also increase age acceleration. Our findings have implications for policies relating to current changes in working conditions and highlight the utility of biological age biomarkers in studies in younger populations without long-term health information.
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Affiliation(s)
- Anna Freni-Sterrantino
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, United Kingdom,The Alan Turing Institute, John Dodson House, London NW1 2DB, United Kingdom
| | - Giovanni Fiorito
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, United Kingdom,Laboratory of Biostatistics, Department of Biomedical Sciences, University of Sassari, Sassari 07100, Italy
| | - Angelo d’Errico
- Department of Epidemiology, Local Health Unit TO 3, Turin 10095, Italy
| | - Marianna Virtanen
- School of Educational Sciences and Psychology, University of Eastern Finland, Joensuu FI-80101, Finland,Division of Insurance Medicine, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm 17177, Sweden
| | - Leena Ala-Mursula
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu 90014, Finland
| | - Marjo-Riitta Järvelin
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, United Kingdom,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu 90014, Finland
| | - Paolo Vineis
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, United Kingdom
| | - Oliver Robinson
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, United Kingdom,Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College of London, London W2 1PG, United Kingdom
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25
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Pacheco NL, Noren Hooten N, Zhang Y, Prince CS, Mode NA, Ezike N, Becker KG, Zonderman AB, Evans MK. Sex-specific transcriptome differences in a middle-aged frailty cohort. BMC Geriatr 2022; 22:651. [PMID: 35945487 PMCID: PMC9361278 DOI: 10.1186/s12877-022-03326-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Frailty is a clinical syndrome described as reduced physiological reserve and increased vulnerability. Typically examined in older adults, recent work shows frailty occurs in middle-aged individuals and is associated with increased mortality. Previous investigation of global transcriptome changes in a middle-aged cohort from the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) study demonstrated inflammatory genes and pathways were significantly altered by frailty status and race. Transcriptome differences in frailty by sex remain unclear. We sought to discover novel genes and pathways associated with sex and frailty in a diverse middle-aged cohort using RNA-Sequencing. METHODS Differential gene expression and pathway analyses were performed in peripheral blood mononuclear cells for 1) frail females (FRAF, n = 4) vs non-frail females (NORF, n = 4), 2) frail males (FRAM, n = 4) vs non-frail males (NORM, n = 4), 3) FRAM vs FRAF, and 4) NORM vs NORF. We evaluated exclusive significant genes and pathways, as well as overlaps, between the comparison groups. RESULTS Over 80% of the significant genes exclusive to FRAF vs NORF, FRAM vs NORM, and FRAM vs FRAF, respectively, were novel and associated with various biological functions. Pathways exclusive to FRAF vs NORF were associated with reduced inflammation, while FRAM vs NORM exclusive pathways were related to aberrant musculoskeletal physiology. Pathways exclusive to FRAM vs FRAF were associated with reduced cell cycle regulation and activated catabolism and Coronavirus pathogenesis. CONCLUSIONS Our results indicate sex-specific transcriptional changes occur in middle-aged frailty, enhancing knowledge on frailty progression and potential therapeutic targets to prevent frailty.
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Affiliation(s)
- Natasha L Pacheco
- Laboratory of Epidemiology and Population Sciences, National Institute On Aging, National Institutes of Health, Baltimore, MD, USA
| | - Nicole Noren Hooten
- Laboratory of Epidemiology and Population Sciences, National Institute On Aging, National Institutes of Health, Baltimore, MD, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute On Aging, National Institutes of Health, Baltimore, MD, USA
| | - Calais S Prince
- Laboratory of Epidemiology and Population Sciences, National Institute On Aging, National Institutes of Health, Baltimore, MD, USA
| | - Nicolle A Mode
- Laboratory of Epidemiology and Population Sciences, National Institute On Aging, National Institutes of Health, Baltimore, MD, USA
| | - Ngozi Ezike
- Laboratory of Epidemiology and Population Sciences, National Institute On Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kevin G Becker
- Laboratory of Genetics and Genomics, National Institute On Aging, National Institutes of Health, Baltimore, MD, USA
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute On Aging, National Institutes of Health, Baltimore, MD, USA
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute On Aging, National Institutes of Health, Baltimore, MD, USA.
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26
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Shen B, Hernandez DG, Chitrala KN, Fanelli-Kuczmarski MT, Noren Hooten N, Pacheco NL, Mode NA, Zonderman AB, Ezike N, Evans MK. APOE gene region methylation is associated with cognitive performance in middle-aged urban adults. Neurobiol Aging 2022; 116:41-48. [PMID: 35561457 PMCID: PMC10878469 DOI: 10.1016/j.neurobiolaging.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/17/2022]
Abstract
Apolipoprotein (APOE) ε4 allele is a strong risk factor for Alzheimer's disease (AD) and cognitive decline. Epigenetic modifications such as DNA methylation (DNAm) play a central role in cognition. This study sought to identify DNAm sites in the APOE genomic region associated with cognitive performance in a racially diverse middle-aged cohort (n = 411). Cognitive performance was measured by 11 standard neuropsychological tests. Two CpG sites were associated with the Card Rotation and Benton Visual Retention cognitive tests. The methylation level of the CpG site cg00397545 was associated with Card Rotation Test score (p = 0.000177) and a novel CpG site cg10178308 was associated with Benton Visual Retention Test score (p = 0.000084). Significant associations were observed among the dietary inflammatory index, which reflects the inflammatory potential of the diet, cognitive performance and the methylation level of several CpG sites. Our results indicate that DNAm in the APOE genomic area is correlated with cognitive performance and may presage cognitive decline.
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Affiliation(s)
- Botong Shen
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Kumaraswamy Naidu Chitrala
- Fels Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Marie T Fanelli-Kuczmarski
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Nicole Noren Hooten
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Natasha L Pacheco
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Nicolle A Mode
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Ngozi Ezike
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Michele K Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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27
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Gomez-Verjan JC, Esparza-Aguilar M, Martin-Martin V, Salazar-Perez C, Cadena-Trejo C, Gutierrez-Robledo LM, Arroyo P. DNA methylation profile of a rural cohort exposed to early-adversity and malnutrition: An exploratory analysis. Exp Gerontol 2022; 167:111899. [PMID: 35907475 DOI: 10.1016/j.exger.2022.111899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 02/08/2022] [Accepted: 07/13/2022] [Indexed: 11/04/2022]
Abstract
Barker's hypothesis affirms that undernourishment in early-life induces metabolic reprogramming that compromises organism functions later in life, leading to age-related diseases. We are exposed to environmental and social conditions that impact our life trajectories, leading to ageing phenotypes as we grow. Epigenetic mechanisms constitute the link between both external stimuli and genetic programming. Studies have focused on describing the effect of early adverse events such as trauma, famines, or childhood labor on epigenetic markers in adulthood and the elderly. However, we lack information on epigenetic programming in individuals born in rural communities from underdeveloped countries, exposed to negative influences during fetal and postnatal development, particularly chronic malnutrition. Hence, in this exploratory analysis, we characterize the epigenome of individuals and some parents from Tlaltizapan (a rural community in Mexico originally studied almost 50 years ago) and collect anthropometric data on growth and development, as well on the living conditions of the families. Our results help build a biological hypothesis indicating that most of the epigenetic age measures of the subjects are significantly different among them. Interestingly, the most affected methylated regions correspond to pathways involved in neuronal system development, reproductive behaviour, learning and memory regulation.
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Affiliation(s)
- J C Gomez-Verjan
- Direccion de Investigación, Instituto Nacional de Geriatría, INGER, Mexico City, Mexico.
| | | | | | | | - C Cadena-Trejo
- Direccion de Investigación, Instituto Nacional de Geriatría, INGER, Mexico City, Mexico
| | | | - P Arroyo
- Direccion de Investigación, Instituto Nacional de Geriatría, INGER, Mexico City, Mexico
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28
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Attia MH. A cautionary note on altered pace of aging in the COVID-19 era. Forensic Sci Int Genet 2022; 59:102724. [PMID: 35598567 PMCID: PMC9112667 DOI: 10.1016/j.fsigen.2022.102724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/02/2022] [Accepted: 05/12/2022] [Indexed: 11/18/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is highly age-dependent due to hi-jacking the molecular control of the immune cells by the severe acute respiratory syndrome-corona virus 2 (SARS-CoV-2) leading to aberrant DNA methylation (DNAm) pattern of blood in comparison to normal individuals. These epigenetic modifications have been linked to perturbations to the epigenetic clock, development of long COVID-19 syndrome, and all-cause mortality risk. I reviewed the effects of COVID-19 on different molecular age markers such as the DNAm, telomere length (TL), and signal joint T-cell receptor excision circle (sjTREC). Integrating the accumulated clinical research data, COVID-19 and novel medical management may alter the pace of aging in adult individuals (<60 years). As such, COVID-19 might be a confounder in epigenetic age estimation similar to life style diversities, pathogens and pathologies which may influence the interpretation of DNAm data. Similarly, the SARS-CoV-2 affects T-lymphocyte function with possible influence on sjTREC levels. In contrast, TL measurements performed years before the SARS-CoV-2 pandemic proved that short TL predisposes to severe COVID- 19 independently from chronological age. However, the persistence of COVID-19 epigenetic scars and the durability of the immune response after vaccination and their effect on the ongoing pace of aging are still unknown. In the light of these data, the heterogeneous nature of the samples in these studies mandates a systematic evaluation of the currrent methods. SARS-CoV-2 may modify the reliability of the age estimation models in real casework because blood is the most common biological sample encountered in forensic contexts.
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29
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Meloni M, Moll T, Issaka A, Kuzawa CW. A biosocial return to race? A cautionary view for the postgenomic era. Am J Hum Biol 2022; 34:e23742. [PMID: 35275433 PMCID: PMC9286859 DOI: 10.1002/ajhb.23742] [Citation(s) in RCA: 2] [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: 12/22/2021] [Revised: 02/01/2022] [Accepted: 02/20/2022] [Indexed: 12/21/2022] Open
Abstract
Recent studies demonstrating epigenetic and developmental sensitivity to early environments, as exemplified by fields like the Developmental Origins of Health and Disease (DOHaD) and environmental epigenetics, are bringing new data and models to bear on debates about race, genetics, and society. Here, we first survey the historical prominence of models of environmental determinism in early formulations of racial thinking to illustrate how notions of direct environmental effects on bodies have been used to naturalize racial hierarchy and inequalities in the past. Next, we conduct a scoping review of postgenomic work in environmental epigenetics and DOHaD that looks at the role of race/ethnicity in human health (2000-2021). Although there is substantial heterogeneity in how race is conceptualized and interpreted across studies, we observe practices that may unwittingly encourage typological thinking, including: using DNA methylation as a novel marker of racial classification; neglect of variation and reversibility within supposedly homogenous racial groups; and a tendency to label and reify whole groups as pathologized or impaired. Even in the very different politico-economic and epistemic context of contemporary postgenomic science, these trends echo deeply held beliefs in Western thinking which claimed that different environments shape different bodies and then used this logic to argue for essential differences between Europeans and non-Europeans. We conclude with a series of suggestions on interpreting and reporting findings in these fields that we feel will help researchers harness this work to benefit disadvantaged groups while avoiding the inadvertent dissemination of new and old forms of stigma or prejudice.
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Affiliation(s)
- Maurizio Meloni
- Alfred Deakin Institute for Citizenship and GlobalisationDeakin University, Geelong Waurn Ponds CampusWaurn PondsVictoriaAustralia
| | - Tessa Moll
- Alfred Deakin Institute for Citizenship and GlobalisationDeakin University, Geelong Waurn Ponds CampusWaurn PondsVictoriaAustralia
- School of Public Health, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Ayuba Issaka
- School of Health and Social Development, Faculty of HealthDeakin University, Geelong Waurn Ponds CampusWaurn PondsVictoriaAustralia
| | - Christopher W. Kuzawa
- Department of Anthropology and Institute for Policy ResearchNorthwestern UniversityEvanstonIllinoisUSA
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30
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Perez NB, Vorderstrasse AA, Yu G, Melkus GD, Wright F, Ginsberg SD, Crusto CA, Sun YV, Taylor JY. Associations Between DNA Methylation Age Acceleration, Depressive Symptoms, and Cardiometabolic Traits in African American Mothers From the InterGEN Study. Epigenet Insights 2022; 15:25168657221109781. [PMID: 35784386 PMCID: PMC9247996 DOI: 10.1177/25168657221109781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/06/2022] [Indexed: 11/20/2022] Open
Abstract
Background African American women (AAW) have a high risk of both cardiometabolic (CM) illness and depressive symptoms. Depressive symptoms co-occur in individuals with CM illness at higher rates than the general population, and accelerated aging may explain this. In this secondary analysis, we examined associations between age acceleration; depressive symptoms; and CM traits (hypertension, diabetes mellitus [DM], and obesity) in a cohort of AAW. Methods Genomic and clinical data from the InterGEN cohort (n = 227) were used. Age acceleration was based on the Horvath method of DNA methylation (DNAm) age estimation. Accordingly, DNAm age acceleration (DNAm AA) was defined as the residuals from a linear regression of DNAm age on chronological age. Spearman's correlations, linear and logistic regression examined associations between DNAm AA, depressive symptoms, and CM traits. Results DNAm AA did not associate with total depressive symptom scores. DNAm AA correlated with specific symptoms including self-disgust/self-hate (-0.13, 95% CI -0.26, -0.01); difficulty with making decisions (-0.15, 95% CI -0.28, -0.02); and worry over physical health (0.15, 95% CI 0.02, 0.28), but were not statistically significant after multiple comparison correction. DNAm AA associated with obesity (0.08, 95% CI 1.02, 1.16), hypertension (0.08, 95% CI 1.01, 1.17), and DM (0.20, 95% CI 1.09, 1.40), after adjustment for potential confounders. Conclusions Associations between age acceleration and depressive symptoms may be highly nuanced and dependent on study design contexts. Factors other than age acceleration may explain the connection between depressive symptoms and CM traits. AAW with CM traits may be at increased risk of accelerated aging.
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Affiliation(s)
| | | | - Gary Yu
- Rory Meyers College of Nursing, New
York University, New York, NY, USA
| | | | - Fay Wright
- Rory Meyers College of Nursing, New
York University, New York, NY, USA
| | - Stephen D Ginsberg
- Center for Dementia Research, Nathan
Kline Institute, Orangeburg, NY, USA
- NYU Grossman School of Medicine, New
York, NY, USA
| | - Cindy A Crusto
- Yale School of Medicine, Orange, CT,
USA
- Department of Psychology, University of
Pretoria, Pretoria, South Africa
| | - Yan V Sun
- Emory University School of Public
Health, Atlanta, GA, USA
- Atlanta VA Health Care System, Decatur,
GA, USA
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Beydoun MA, Noren Hooten N, Weiss J, Beydoun HA, Hossain S, Evans MK, Zonderman AB. Plasma neurofilament light and its association with all-cause mortality risk among urban middle-aged men and women. BMC Med 2022; 20:218. [PMID: 35692046 PMCID: PMC9190073 DOI: 10.1186/s12916-022-02425-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/31/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Neurofilament light chain (NfL) is released into the blood during neuronal damage. NfL is linked to mortality in neurological disorders, remaining unexplored in population studies. We investigated whether initial (v1) and annualized change (δ) in plasma NfL can predict all-cause mortality in middle-aged dementia-free urban adults. METHODS Longitudinal data were from 694 participants in the Healthy Aging in Neighborhoods of Diversity Across the Life Span study (HANDLS, mean agev1: 47.8 years, 42% male, 55.8% African American). Plasma NfL was measured prospectively at three visits. Analyses included Cox proportional hazards models for all-cause mortality risk and 4-way decomposition testing for interaction and mediation. RESULTS Unlike men, women exhibited a direct association between δNfL (above vs. below median) and all-cause mortality risk in both the minimally (HR = 3.91, 95% CI 1.10-13.9, p = 0.036) and fully adjusted models (HR = 4.92, 95% CI 1.26-19.2, p = 0.022), and for δNfL (per unit increase) in the full model (HR = 1.65, 95% CI 1.04-2.61, p = 0.034). In both models, and among women, 1 standard deviation of NfLv1 was associated with an increased all-cause mortality risk (reduced model: HR = 2.01, 95% CI 1.24-3.25, p = 0.005; full model: HR = 1.75, 95% CI 1.02-2.98, p = 0.041). Only few interactions were detected for cardio-metabolic risk factors. Notably, NfLv1 was shown to be a better prognostic indicator at normal hsCRP values among women, while HbA1c and δNfL interacted synergistically to determine mortality risk, overall. CONCLUSIONS These findings indicate that plasma NfL levels at baseline and over time can predict all-cause mortality in women and interacts with hsCRP and HbA1c to predict that risk.
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Affiliation(s)
- May A Beydoun
- Laboratory of Epidemiology and Population Sciences, NIA/NIH/IRP, 251 Bayview Blvd., Suite 100, Room #: 04B118, Baltimore, MD, 21224, USA.
| | - Nicole Noren Hooten
- Laboratory of Epidemiology and Population Sciences, NIA/NIH/IRP, 251 Bayview Blvd., Suite 100, Room #: 04B118, Baltimore, MD, 21224, USA
| | - Jordan Weiss
- Department of Demography, University of California, Berkeley, Berkeley, CA, USA
| | - Hind A Beydoun
- Department of Research Programs, Fort Belvoir Community Hospital, Fort Belvoir, VA, USA
| | - Sharmin Hossain
- Laboratory of Epidemiology and Population Sciences, NIA/NIH/IRP, 251 Bayview Blvd., Suite 100, Room #: 04B118, Baltimore, MD, 21224, USA
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, NIA/NIH/IRP, 251 Bayview Blvd., Suite 100, Room #: 04B118, Baltimore, MD, 21224, USA
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, NIA/NIH/IRP, 251 Bayview Blvd., Suite 100, Room #: 04B118, Baltimore, MD, 21224, USA
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Schmitz LL, Zhao W, Ratliff SM, Goodwin J, Miao J, Lu Q, Guo X, Taylor KD, Ding J, Liu Y, Levine M, Smith JA. The Socioeconomic Gradient in Epigenetic Ageing Clocks: Evidence from the Multi-Ethnic Study of Atherosclerosis and the Health and Retirement Study. Epigenetics 2022; 17:589-611. [PMID: 34227900 PMCID: PMC9235889 DOI: 10.1080/15592294.2021.1939479] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/02/2021] [Indexed: 12/25/2022] Open
Abstract
Epigenetic clocks have been widely used to predict disease risk in multiple tissues or cells. Their success as a measure of biological ageing has prompted research on the connection between epigenetic pathways of ageing and the socioeconomic gradient in health and mortality. However, studies examining social correlates of epigenetic ageing have yielded inconsistent results. We conducted a comprehensive, comparative analysis of associations between various dimensions of socioeconomic status (SES) (education, income, wealth, occupation, neighbourhood environment, and childhood SES) and eight epigenetic clocks in two well-powered US ageing studies: The Multi-Ethnic Study of Atherosclerosis (MESA) (n = 1,211) and the Health and Retirement Study (HRS) (n = 4,018). In both studies, we found robust associations between SES measures in adulthood and the GrimAge and DunedinPoAm clocks (Bonferroni-corrected p-value < 0.01). In the HRS, significant associations with the Levine and Yang clocks were also evident. These associations were only partially mediated by smoking, alcohol consumption, and obesity, which suggests that differences in health behaviours alone cannot explain the SES gradient in epigenetic ageing in older adults. Further analyses revealed concurrent associations between polygenic risk for accelerated intrinsic epigenetic ageing, SES, and the Levine clock, indicating that genetic risk and social disadvantage may contribute additively to faster biological aging.
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Affiliation(s)
- Lauren L. Schmitz
- Robert M. La Follette School of Public Affairs, University of Wisconsin-Madison, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, USA
| | - Scott M. Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, USA
| | - Julia Goodwin
- Department of Sociology, University of Wisconsin-Madison, USA
| | - Jiacheng Miao
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, USA
| | - Qiongshi Lu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, USA
- Department of Statistics, University of Wisconsin-Madison, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, USA
| | - Jingzhong Ding
- Gerontology and Geriatric Medicine, School of Medicine, Wake Forest University, USA
| | - Yongmei Liu
- Department of Medicine, School of Medicine, Duke University, USA
| | - Morgan Levine
- Department of Pathology, School of Medicine, Yale University, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, USA
- Survey Research Center, Institute for Social Research, University of Michigan, USA
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Morales Berstein F, McCartney DL, Lu AT, Tsilidis KK, Bouras E, Haycock P, Burrows K, Phipps AI, Buchanan DD, Cheng I, Martin RM, Davey Smith G, Relton CL, Horvath S, Marioni RE, Richardson TG, Richmond RC. Assessing the causal role of epigenetic clocks in the development of multiple cancers: a Mendelian randomization study. eLife 2022; 11:e75374. [PMID: 35346416 PMCID: PMC9049976 DOI: 10.7554/elife.75374] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
Background Epigenetic clocks have been associated with cancer risk in several observational studies. Nevertheless, it is unclear whether they play a causal role in cancer risk or if they act as a non-causal biomarker. Methods We conducted a two-sample Mendelian randomization (MR) study to examine the genetically predicted effects of epigenetic age acceleration as measured by HannumAge (nine single-nucleotide polymorphisms (SNPs)), Horvath Intrinsic Age (24 SNPs), PhenoAge (11 SNPs), and GrimAge (4 SNPs) on multiple cancers (i.e. breast, prostate, colorectal, ovarian and lung cancer). We obtained genome-wide association data for biological ageing from a meta-analysis (N = 34,710), and for cancer from the UK Biobank (N cases = 2671-13,879; N controls = 173,493-372,016), FinnGen (N cases = 719-8401; N controls = 74,685-174,006) and several international cancer genetic consortia (N cases = 11,348-122,977; N controls = 15,861-105,974). Main analyses were performed using multiplicative random effects inverse variance weighted (IVW) MR. Individual study estimates were pooled using fixed effect meta-analysis. Sensitivity analyses included MR-Egger, weighted median, weighted mode and Causal Analysis using Summary Effect Estimates (CAUSE) methods, which are robust to some of the assumptions of the IVW approach. Results Meta-analysed IVW MR findings suggested that higher GrimAge acceleration increased the risk of colorectal cancer (OR = 1.12 per year increase in GrimAge acceleration, 95% CI 1.04-1.20, p = 0.002). The direction of the genetically predicted effects was consistent across main and sensitivity MR analyses. Among subtypes, the genetically predicted effect of GrimAge acceleration was greater for colon cancer (IVW OR = 1.15, 95% CI 1.09-1.21, p = 0.006), than rectal cancer (IVW OR = 1.05, 95% CI 0.97-1.13, p = 0.24). Results were less consistent for associations between other epigenetic clocks and cancers. Conclusions GrimAge acceleration may increase the risk of colorectal cancer. Findings for other clocks and cancers were inconsistent. Further work is required to investigate the potential mechanisms underlying the results. Funding FMB was supported by a Wellcome Trust PhD studentship in Molecular, Genetic and Lifecourse Epidemiology (224982/Z/22/Z which is part of grant 218495/Z/19/Z). KKT was supported by a Cancer Research UK (C18281/A29019) programme grant (the Integrative Cancer Epidemiology Programme) and by the Hellenic Republic's Operational Programme 'Competitiveness, Entrepreneurship & Innovation' (OΠΣ 5047228). PH was supported by Cancer Research UK (C18281/A29019). RMM was supported by the NIHR Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol and by a Cancer Research UK (C18281/A29019) programme grant (the Integrative Cancer Epidemiology Programme). RMM is a National Institute for Health Research Senior Investigator (NIHR202411). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care. GDS and CLR were supported by the Medical Research Council (MC_UU_00011/1 and MC_UU_00011/5, respectively) and by a Cancer Research UK (C18281/A29019) programme grant (the Integrative Cancer Epidemiology Programme). REM was supported by an Alzheimer's Society project grant (AS-PG-19b-010) and NIH grant (U01 AG-18-018, PI: Steve Horvath). RCR is a de Pass Vice Chancellor's Research Fellow at the University of Bristol.
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Affiliation(s)
- Fernanda Morales Berstein
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Konstantinos K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College LondonLondonUnited Kingdom
- Department of Hygiene and Epidemiology, School of Medicine, University of IoanninaIoanninaGreece
| | - Emmanouil Bouras
- Department of Hygiene and Epidemiology, School of Medicine, University of IoanninaIoanninaGreece
| | - Philip Haycock
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Department of Epidemiology, School of Public Health, University of WashingtonSeattleUnited States
| | - Daniel D Buchanan
- Department of Clinical Pathology, Melbourne Medical School, University of MelbourneParkvilleAustralia
| | - Iona Cheng
- Cancer Prevention Institute of CaliforniaFremontUnited States
| | - Richard M Martin
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of BristolBristolUnited Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
- Department of Biostatistics, Fielding School of Public Health, University of California, Los AngelesLos AngelesUnited States
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
- Novo Nordisk Research CentreOxfordUnited Kingdom
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
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Akhabir L, Stringer R, Desai D, Mandhane PJ, Azad MB, Moraes TJ, Subbarao P, Turvey SE, Paré G, Anand SS, Anand SS, Atkinson SA, Azad MB, Becker AB, Brook J, Denburg JA, Desai D, de Souza RJ, Gupta M, Kobor M, Lefebvre DL, Lou W, Mandhane PJ, McDonald S, Mente A, Meyre D, Moraes TJ, Morrison K, Paré G, Sears MR, Subbarao P, Teo KK, Turvey SE, Wilson J, Yusuf S, Atkinson S, Wahi G, Zulyniak MA. DNA methylation changes in cord blood and the developmental origins of health and disease – a systematic review and replication study. BMC Genomics 2022; 23:221. [PMID: 35305575 PMCID: PMC8933946 DOI: 10.1186/s12864-022-08451-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 03/07/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Environmental exposures in utero which modify DNA methylation may have a long-lasting impact on health and disease in offspring. We aimed to identify and replicate previously published genomic loci where DNA methylation changes are attributable to in utero exposures in the NutriGen birth cohort studies Alliance.
Methods
We reviewed the literature to identify differentially methylated sites of newborn DNA which are associated with the following five traits of interest maternal diabetes, pre-pregnancy body mass index (BMI), diet during pregnancy, smoking, and gestational age. We then attempted to replicate these published associations in the Canadian Healthy Infant Longitudinal Development (CHILD) and the South Asian birth cohort (START) cord blood epigenome-wide data.
Results
We screened 68 full-text articles and identified a total of 17 cord blood epigenome-wide association studies (EWAS) of the traits of interest. Out of the 290 CpG sites reported, 19 were identified in more than one study; all of them associated with maternal smoking. In CHILD and START EWAS, thousands of sites associated with gestational age were identified and maintained significance after correction for multiple testing. In CHILD, there was differential methylation observed for 8 of the published maternal smoking sites. No other traits tested (i.e., folate levels, gestational diabetes, birthweight) replicated in the CHILD or START cohorts.
Conclusions
Maternal smoking during pregnancy and gestational age are strongly associated with differential methylation in offspring cord blood, as assessed in the EWAS literature and our birth cohorts. There are a limited number of reported methylation sites associated in more than two independent studies related to pregnancy. Additional large studies of diverse populations with fine phenotyping are needed to produce robust epigenome-wide data in order to further elucidate the effect of intrauterine exposures on the infants’ methylome.
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35
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Becker J, Böhme P, Reckert A, Eickhoff SB, Koop BE, Blum J, Gündüz T, Takayama M, Wagner W, Ritz-Timme S. Evidence for differences in DNA methylation between Germans and Japanese. Int J Legal Med 2022; 136:405-413. [PMID: 34739581 PMCID: PMC8847189 DOI: 10.1007/s00414-021-02736-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/22/2021] [Indexed: 12/16/2022]
Abstract
As a contribution to the discussion about the possible effects of ethnicity/ancestry on age estimation based on DNA methylation (DNAm) patterns, we directly compared age-associated DNAm in German and Japanese donors in one laboratory under identical conditions. DNAm was analyzed by pyrosequencing for 22 CpG sites (CpGs) in the genes PDE4C, RPA2, ELOVL2, DDO, and EDARADD in buccal mucosa samples from German and Japanese donors (N = 368 and N = 89, respectively).Twenty of these CpGs revealed a very high correlation with age and were subsequently tested for differences between German and Japanese donors aged between 10 and 65 years (N = 287 and N = 83, respectively). ANCOVA was performed by testing the Japanese samples against age- and sex-matched German subsamples (N = 83 each; extracted 500 times from the German total sample). The median p values suggest a strong evidence for significant differences (p < 0.05) at least for two CpGs (EDARADD, CpG 2, and PDE4C, CpG 2) and no differences for 11 CpGs (p > 0.3).Age prediction models based on DNAm data from all 20 CpGs from German training data did not reveal relevant differences between the Japanese test samples and German subsamples. Obviously, the high number of included "robust CpGs" prevented relevant effects of differences in DNAm at two CpGs.Nevertheless, the presented data demonstrates the need for further research regarding the impact of confounding factors on DNAm in the context of ethnicity/ancestry to ensure a high quality of age estimation. One approach may be the search for "robust" CpG markers-which requires the targeted investigation of different populations, at best by collaborative research with coordinated research strategies.
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Affiliation(s)
- J Becker
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany.
| | - P Böhme
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - A Reckert
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - S B Eickhoff
- Institute for Systems Neuroscience, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
- Institute of Neuroscience and Medicine, Brain and Behaviour, (INM-7), Research Centre Jülich, 52428, Jülich, Germany
| | - B E Koop
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - J Blum
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - T Gündüz
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - M Takayama
- Department of Forensic Medicine, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
- Tokyo Medical Examiner's Office, Tokyo, Japan
| | - W Wagner
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, 52074, Aachen, Germany
| | - S Ritz-Timme
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
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Noren Hooten N, Pacheco NL, Smith JT, Evans MK. The accelerated aging phenotype: The role of race and social determinants of health on aging. Ageing Res Rev 2022; 73:101536. [PMID: 34883202 PMCID: PMC10862389 DOI: 10.1016/j.arr.2021.101536] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/12/2021] [Accepted: 12/03/2021] [Indexed: 02/06/2023]
Abstract
The pursuit to discover the fundamental biology and mechanisms of aging within the context of the physical and social environment is critical to designing interventions to prevent and treat its complex phenotypes. Aging research is critically linked to understanding health disparities because these inequities shape minority aging, which may proceed on a different trajectory than the overall population. Health disparities are characteristically seen in commonly occurring age-associated diseases such as cardiovascular and cerebrovascular disease as well as diabetes mellitus and cancer. The early appearance and increased severity of age-associated disease among African American and low socioeconomic status (SES) individuals suggests that the factors contributing to the emergence of health disparities may also induce a phenotype of 'premature aging' or 'accelerated aging' or 'weathering'. In marginalized and low SES populations with high rates of early onset age-associated disease the interaction of biologic, psychosocial, socioeconomic and environmental factors may result in a phenotype of accelerated aging biologically similar to premature aging syndromes with increased susceptibility to oxidative stress, premature accumulation of oxidative DNA damage, defects in DNA repair and higher levels of biomarkers of oxidative stress and inflammation. Health disparities, therefore, may be the end product of this complex interaction in populations at high risk. This review will examine the factors that drive both health disparities and the accelerated aging phenotype that ultimately contributes to premature mortality.
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Affiliation(s)
- Nicole Noren Hooten
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Natasha L Pacheco
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Jessica T Smith
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Michele K Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA.
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37
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Sleep Health among Racial/Ethnic groups and Strategies to achieve Sleep Health Equity. Respir Med 2022. [DOI: 10.1007/978-3-030-93739-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Shiau S, Arpadi SM, Shen Y, Cantos A, Ramon CV, Shah J, Jang G, Manly JJ, Brickman AM, Baccarelli AA, Yin MT. Epigenetic Aging Biomarkers Associated With Cognitive Impairment in Older African American Adults With Human Immunodeficiency Virus (HIV). Clin Infect Dis 2021; 73:1982-1991. [PMID: 34143869 PMCID: PMC8664485 DOI: 10.1093/cid/ciab563] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Accelerated epigenetic aging using DNA methylation (DNAm)-based biomarkers has been reported in people with human immunodeficiency virus (HIV, PWH), but limited data are available among African Americans (AA), women, and older PWH. METHODS DNAm was measured using Illumina EPIC Arrays for 107 (69 PWH and 38 HIV-seronegative controls) AA adults ≥60 years in New York City. Six DNAm-based biomarkers of aging were estimated: (1) epigenetic age acceleration (EAA), (2) extrinsic epigenetic age acceleration (EEAA), (3) intrinsic epigenetic age acceleration (IEAA), (4) GrimAge, (5) PhenoAge, and (6) DNAm-estimated telomere length (DNAm-TL). The National Institutes of Health (NIH) Toolbox Cognition Battery (domains: executive function, attention, working memory, processing speed, and language) and Montreal Cognitive Assessment (MoCA) were administered. Participants were assessed for frailty by the Fried criteria. RESULTS The PWH and control groups did not differ by sex, chronological age, or ethnicity. In total, 83% of PWH had a viral load <50 copies/mL, and 94% had a recent CD4 ≥200 cells/µL. The PWH group had a higher EAA, EEAA, GrimAge, and PhenoAge, and a lower DNAm-TL compared to the controls. IEAA was not different between groups. For PWH, there were significant negative correlations between IEAA and executive function, attention, and working memory and PhenoAge and attention. No associations between biomarkers and frailty were detected. CONCLUSIONS Evidence of epigenetic age acceleration was observed in AA older PWH using DNAm-based biomarkers of aging. There was no evidence of age acceleration independent of cell type National Institutes of Health composition (IEAA) associated with HIV, but this measure was associated with decreased cognitive function among PWH.
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Affiliation(s)
- Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA
| | - Stephen M Arpadi
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
- ICAP at Columbia, Mailman School of Public Health, Columbia University Irving Medical Center, New York, New York, USA
| | - Yanhan Shen
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Anyelina Cantos
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Christian Vivar Ramon
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Jayesh Shah
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Grace Jang
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Jennifer J Manly
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
- Taub Institute for Research in Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Adam M Brickman
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
- Taub Institute for Research in Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Irving Medical Center, New York, New York, USA
| | - Michael T Yin
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
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Heidegger A, Pisarek A, de la Puente M, Niederstätter H, Pośpiech E, Woźniak A, Schury N, Unterländer M, Sidstedt M, Junker K, Ventayol Garcia M, Laurent FX, Ulus A, Vannier J, Bastisch I, Hedman J, Sijen T, Branicki W, Xavier C, Parson W. Development and inter-laboratory validation of the VISAGE enhanced tool for age estimation from semen using quantitative DNA methylation analysis. Forensic Sci Int Genet 2021; 56:102596. [PMID: 34763164 DOI: 10.1016/j.fsigen.2021.102596] [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] [Received: 07/08/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/27/2022]
Abstract
The analysis of DNA methylation has become an established method for chronological age estimation. This has triggered interest in the forensic community to develop new methods for age estimation from biological crime scene material. Various assays are available for age estimation from somatic tissues, the majority from blood. Age prediction from semen requires different DNA methylation markers and the only assays currently developed for forensic analysis are based on SNaPshot or pyrosequencing. Here, we describe a new assay using massively parallel sequencing to analyse 13 candidate CpG sites targeted in two multiplex PCRs. The assay has been validated by five consortium laboratories of the VISible Attributes through GEnomics (VISAGE) project within a collaborative exercise and was tested for reproducible quantification of DNA methylation levels and sensitivity with DNA methylation controls. Furthermore, DNA extracts and stains on Whatman FTA cards from two semen samples were used to evaluate concordance and mimic casework samples. Overall, the assay yielded high read depths (> 1000 reads) at all 13 marker positions. The methylation values obtained indicated robust quantification with an average standard deviation of 2.8% at the expected methylation level of 50% across the 13 markers and a good performance with 50 ng DNA input into bisulfite conversion. The absolute difference of quantifications from one participating laboratory to the mean quantifications of concordance and semen stains of remaining laboratories was approximately 1%. These results demonstrated the assay to be robust and suitable for age estimation from semen in forensic investigations. In addition to the 13-marker assay, a more streamlined protocol combining only five age markers in one multiplex PCR was developed. Preliminary results showed no substantial differences in DNA methylation quantification between the two assays, indicating its applicability with the VISAGE age model for semen developed with data from the complete 13-marker tool.
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Affiliation(s)
- A Heidegger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - A Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - M de la Puente
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - H Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - E Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - A Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - N Schury
- Federal Criminal Police Office, Wiesbaden, Germany
| | | | - M Sidstedt
- National Forensic Centre (NFC), Swedish Police Authority, Linköping, Sweden
| | - K Junker
- National Forensic Centre (NFC), Swedish Police Authority, Linköping, Sweden
| | - M Ventayol Garcia
- Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
| | - F X Laurent
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, Ecully Cedex, France
| | - A Ulus
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, Ecully Cedex, France
| | - J Vannier
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, Ecully Cedex, France
| | - I Bastisch
- Federal Criminal Police Office, Wiesbaden, Germany
| | - J Hedman
- National Forensic Centre (NFC), Swedish Police Authority, Linköping, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - T Sijen
- Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands; University of Amsterdam, Swammerdam Institute of Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - W Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Central Forensic Laboratory of the Police, Warsaw, Poland
| | - C Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, State College, PA, USA.
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40
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Martínez-Magaña JJ, Genis-Mendoza AD, Santana D, Tóvilla-Zárate CA, Lanzagorta N, Nicolini H. [The presence of a psychiatric diagnosis could alter the epigenetic clock in monozygotic twins]. Rev Esp Geriatr Gerontol 2021; 56:361-363. [PMID: 34583863 DOI: 10.1016/j.regg.2021.07.001] [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: 02/06/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND The acceleration of the epigenetic clock has been associated with a reduction in life expectancy. Individuals diagnosed with a psychiatric disorder have a reduction in life expectancy, and some studies have correlated it with accelerated aging. OBJECTIVE The present study aims to explore whether the presence of any psychiatric disorder could accelerate the epigenetic clock in monozygotic twins. METHODS A total of 15 pairs of monozygotic twins were included. Epigenetic age in peripheral blood cells was estimated by previously published algorithms, using the 450K Beadchip microarray. RESULTS We found that in twins with a diagnosis of a psychiatric disorder, the epigenetic clock could increase compared to their twin without a psychiatric disorder. DISCUSSION AND CONCLUSION The presence of some psychiatric disorder could accelerate the epigenetic clock in homozygous twins, but studies with larger samples are required to clarify this relationship.
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Affiliation(s)
- José Jaime Martínez-Magaña
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | - Alma Delia Genis-Mendoza
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica, Ciudad de México, México; Servicios de Atención Psiquiátrica, Hospital Psiquiátrico Infantil Juan N. Navarro, Ciudad de México, México
| | - Daniel Santana
- Clínica de Trastornos del Sueño, Universidad Nacional Autonóma de México, Ciudad de México, México
| | - Carlos Alfonso Tóvilla-Zárate
- División Académica Multidisciplinaria de Comalcalco, Universidad Juárez Autónoma de Tabasco, Comalcalco, Tabasco, México
| | - Nuria Lanzagorta
- División de Investigación, Departamento de Psiquiatría, Grupo de Estudios Médicos y Familiares Carracci, Ciudad de México, México
| | - Humberto Nicolini
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica, Ciudad de México, México; División de Investigación, Departamento de Psiquiatría, Grupo de Estudios Médicos y Familiares Carracci, Ciudad de México, México.
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41
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Joyce BT, Gao T, Koss K, Zheng Y, Cardenas A, Heiss J, Just A, Zhang K, van Horn L, Allen NB, Greenland P, Cohen S, Gordon-Larsen P, Mitchell C, McLanahan S, Schneper L, Notterman D, Rifas-Shiman SL, Oken E, Hivert MF, Wright R, Baccarelli A, Lloyd-Jones D, Hou L. Impact of paternal education on epigenetic ageing in adolescence and mid-adulthood: a multi-cohort study in the USA and Mexico. Int J Epidemiol 2021; 51:870-884. [PMID: 34534313 DOI: 10.1093/ije/dyab196] [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] [Accepted: 08/26/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Both parental and neighbourhood socio-economic status (SES) are linked to poorer health independently of personal SES measures, but the biological mechanisms are unclear. Our objective was to examine these influences via epigenetic age acceleration (EAA)-the discrepancy between chronological and epigenetic ages. METHODS We examined three USA-based [Coronary Artery Risk Disease in Adults (CARDIA) study, Fragile Families and Child Wellbeing Study (FFCWS) and Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS)] and one Mexico-based (Project Viva) cohort. DNA methylation was measured using Illumina arrays, personal/parental SES by questionnaire and neighbourhood disadvantage from geocoded address. In CARDIA, we examined the most strongly associated personal, parental and neighbourhood SES measures with EAA (Hannum's method) at study years 15 and 20 separately and combined using a generalized estimating equation (GEE) and compared with other EAA measures (Horvath's EAA, PhenoAge and GrimAge calculators, and DunedinPoAm). RESULTS EAA was associated with paternal education in CARDIA [GEEs: βsome college = -1.01 years (-1.91, -0.11) and β<high school = 1.05 (0.09, 2.01) vs college graduates] and FFCWS [GEEs: β<high school = 0.62 (0.00, 1.24)]. We found stronger associations for some paternal education categories among White adults (for GEE, βsome college = -1.39 (-2.41, -0.38)], men (βsome college = -1.76 (-3.16, -0.35)] and women [β<high school = 1.77 (0.42, 3.11)]. CONCLUSIONS These findings suggest that EAA captures epigenetic impacts of paternal education independently of personal SES later in life. Longitudinal studies should explore these associations at different life stages and link them to health outcomes. EAA could be a useful biomarker of SES-associated health and provide important insight into the pathogenesis and prevention of chronic disease.
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Affiliation(s)
- Brian T Joyce
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tao Gao
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kalsea Koss
- Department of Human Development and Family Science, University of Georgia, Athens, GA, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Jonathan Heiss
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - Allan Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - Kai Zhang
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Linda van Horn
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Norrina Bai Allen
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Philip Greenland
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sheldon Cohen
- Department of Psychology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colter Mitchell
- Center for Human Growth and Development, University of Michigan, Ann Arbor, MI, USA
| | - Sara McLanahan
- Department of Sociology, Princeton University, Princeton, NJ, USA
| | - Lisa Schneper
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Daniel Notterman
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA.,Department of Endocrinology, Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Robert Wright
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - Andrea Baccarelli
- Department of Environmental Health Sciences, Columbia University, New York, NY, USA
| | - Donald Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Freeland J, Crowell PD, Giafaglione JM, Boutros PC, Goldstein AS. Aging of the progenitor cells that initiate prostate cancer. Cancer Lett 2021; 515:28-35. [PMID: 34052326 PMCID: PMC8494000 DOI: 10.1016/j.canlet.2021.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/18/2022]
Abstract
Many organs experience a loss of tissue mass and a decline in regenerative capacity during aging. In contrast, the prostate continues to grow in volume. In fact, age is the most important risk factor for prostate cancer. However, the age-related factors that influence the composition, morphology and molecular features of prostate epithelial progenitor cells, the cells-of-origin for prostate cancer, are poorly understood. Here, we review the evidence that prostate luminal progenitor cells are expanded with age. We explore the age-related changes to the microenvironment that may influence prostate epithelial cells and risk of transformation. Finally, we raise a series of questions about models of aging and regulators of prostate aging which need to be addressed. A fundamental understanding of aging in the prostate will yield critical insights into mechanisms that promote the development of age-related prostatic disease.
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Affiliation(s)
- Jack Freeland
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, USA
| | - Preston D Crowell
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, USA
| | - Jenna M Giafaglione
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, USA
| | - Paul C Boutros
- Departments of Human Genetics & Urology, Jonsson Comprehensive Cancer Center and Institute for Precision Health, University of California, Los Angeles, USA
| | - Andrew S Goldstein
- Departments of Molecular, Cell and Developmental Biology & Urology, Broad Stem Cell Research Center and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA.
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43
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Joyce BT, Gao T, Zheng Y, Ma J, Hwang SJ, Liu L, Nannini D, Horvath S, Lu AT, Bai Allen N, Jacobs DR, Gross M, Krefman A, Ning H, Liu K, Lewis CE, Schreiner PJ, Sidney S, Shikany JM, Levy D, Greenland P, Hou L, Lloyd-Jones D. Epigenetic Age Acceleration Reflects Long-Term Cardiovascular Health. Circ Res 2021; 129:770-781. [PMID: 34428927 DOI: 10.1161/circresaha.121.318965] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Brian T Joyce
- Center for Global Oncology, Institute for Global Health (B.T.J., T.G., Y.Z., D.N., L.H.), Feinberg School of Medicine, Northwestern University, Chicago, IL.,Department of Preventive Medicine (B.T.J., T.G., Y.Z., D.N., N.B.A., A.K., H.N., K.L., P.G., L.H., D.L.-J.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Tao Gao
- Center for Global Oncology, Institute for Global Health (B.T.J., T.G., Y.Z., D.N., L.H.), Feinberg School of Medicine, Northwestern University, Chicago, IL.,Department of Preventive Medicine (B.T.J., T.G., Y.Z., D.N., N.B.A., A.K., H.N., K.L., P.G., L.H., D.L.-J.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Yinan Zheng
- Center for Global Oncology, Institute for Global Health (B.T.J., T.G., Y.Z., D.N., L.H.), Feinberg School of Medicine, Northwestern University, Chicago, IL.,Department of Preventive Medicine (B.T.J., T.G., Y.Z., D.N., N.B.A., A.K., H.N., K.L., P.G., L.H., D.L.-J.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Jiantao Ma
- The Framingham Heart Study, Framingham, MA; (J.M., S.-J.H., D.L.).,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (J.M., S.-J.H., D.L.)
| | - Shih-Jen Hwang
- The Framingham Heart Study, Framingham, MA; (J.M., S.-J.H., D.L.).,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (J.M., S.-J.H., D.L.)
| | - Lei Liu
- Division of Biostatistics, Washington University, St. Louis, MO (L.L.)
| | - Drew Nannini
- Center for Global Oncology, Institute for Global Health (B.T.J., T.G., Y.Z., D.N., L.H.), Feinberg School of Medicine, Northwestern University, Chicago, IL.,Department of Preventive Medicine (B.T.J., T.G., Y.Z., D.N., N.B.A., A.K., H.N., K.L., P.G., L.H., D.L.-J.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Steve Horvath
- Department of Human Genetics, UCLA David Geffen School of Medicine, Los Angeles, CA (S.H., A.T.L.)
| | - Ake T Lu
- Department of Human Genetics, UCLA David Geffen School of Medicine, Los Angeles, CA (S.H., A.T.L.)
| | - Norrina Bai Allen
- Department of Preventive Medicine (B.T.J., T.G., Y.Z., D.N., N.B.A., A.K., H.N., K.L., P.G., L.H., D.L.-J.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - David R Jacobs
- Division of Epidemiology and Community Health, School of Public Health (D.R.J., M.G.), University of Minnesota, Minneapolis
| | - Myron Gross
- Division of Epidemiology and Community Health, School of Public Health (D.R.J., M.G.), University of Minnesota, Minneapolis
| | - Amy Krefman
- Department of Preventive Medicine (B.T.J., T.G., Y.Z., D.N., N.B.A., A.K., H.N., K.L., P.G., L.H., D.L.-J.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Hongyan Ning
- Department of Preventive Medicine (B.T.J., T.G., Y.Z., D.N., N.B.A., A.K., H.N., K.L., P.G., L.H., D.L.-J.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Kiang Liu
- Department of Preventive Medicine (B.T.J., T.G., Y.Z., D.N., N.B.A., A.K., H.N., K.L., P.G., L.H., D.L.-J.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Cora E Lewis
- Division of Preventive Medicine, School of Medicine, University of Alabama at Birmingham (C.E.L., J.M.S.)
| | | | - Stephen Sidney
- Division of Research, Kaiser Permanente, Oakland, CA (S.S.)
| | - James M Shikany
- Division of Preventive Medicine, School of Medicine, University of Alabama at Birmingham (C.E.L., J.M.S.)
| | - Daniel Levy
- The Framingham Heart Study, Framingham, MA; (J.M., S.-J.H., D.L.).,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (J.M., S.-J.H., D.L.)
| | - Philip Greenland
- Department of Preventive Medicine (B.T.J., T.G., Y.Z., D.N., N.B.A., A.K., H.N., K.L., P.G., L.H., D.L.-J.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Lifang Hou
- Center for Global Oncology, Institute for Global Health (B.T.J., T.G., Y.Z., D.N., L.H.), Feinberg School of Medicine, Northwestern University, Chicago, IL.,Department of Preventive Medicine (B.T.J., T.G., Y.Z., D.N., N.B.A., A.K., H.N., K.L., P.G., L.H., D.L.-J.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Donald Lloyd-Jones
- Department of Preventive Medicine (B.T.J., T.G., Y.Z., D.N., N.B.A., A.K., H.N., K.L., P.G., L.H., D.L.-J.), Feinberg School of Medicine, Northwestern University, Chicago, IL
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44
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Shiau S, Cantos A, Ramon CV, Shen Y, Shah J, Jang G, Baccarelli AA, Arpadi SM, Yin MT. Epigenetic Age in Young African American Adults With Perinatally Acquired HIV. J Acquir Immune Defic Syndr 2021; 87:1102-1109. [PMID: 33765682 PMCID: PMC8217147 DOI: 10.1097/qai.0000000000002687] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/01/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Prior studies have measured accelerated aging in people with HIV using a DNA methylation (DNAm)-based biomarker of aging, "epigenetic age," but data are limited in African American (AA) young adults with perinatally acquired HIV infection (PHIV). METHODS We performed a cross-sectional study of AA young adults aged 20-35 years with PHIV (N = 31) and seronegative controls (N = 30) using DNAm measured in whole blood and cognitive function measured by the NIH Toolbox. Illumina EPIC array was used to measure DNAm age and accelerated aging markers including epigenetic age acceleration (EAA), as well as extrinsic (EEAA) and intrinsic (IEAA) EAA. RESULTS PHIV and controls did not differ by sex (45 vs. 43% male), chronological age (26.2 vs. 28.0 years), or ethnicity. Chronological age and DNAm age were correlated (r = 0.56, P < 0.01). PHIV had a higher mean EAA (2.86 ± 6.5 vs. -2.96 ± 3.9, P < 0.01) and EEAA (4.57 ± 13.0 vs. -4.72 ± 6.0, P < 0.01) than controls; however, IEAA was not different between groups. Among PHIV, EAA and EEAA were higher in those with HIV viral load ≥50 copies/mL than <50 copies/mL (EEA: 8.1 ± 5.2 vs. 0.11 ± 5.5, P = 0 < 0.01 and EEAA: 16.1 ± 10.6 vs. -1.83 ± 9.7, P < 0.01). We observed negative correlations (r = -0.36 to -0.31) between EEAA and executive function, attention, and language scores. CONCLUSIONS In conclusion, EAA in blood was observed in AA young adults with PHIV on ART using 2 measures, including EEAA which upweights the contribution of immunosenescent cell types. However, there was no evidence of age acceleration with a measure independent of cell type composition.
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Affiliation(s)
- Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ
| | - Anyelina Cantos
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Christian V Ramon
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Yanhan Shen
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Jayesh Shah
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Grace Jang
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Stephen M Arpadi
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY; and
- ICAP at Columbia, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Michael T Yin
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
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DNA methylation of decedent blood samples to estimate the chronological age of human remains. Int J Legal Med 2021; 135:2163-2173. [PMID: 34245337 DOI: 10.1007/s00414-021-02650-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/24/2021] [Indexed: 01/21/2023]
Abstract
Chronological age estimation may offer valuable investigative leads in human identification cases. Bisulfite pyrosequencing analysis of single CpG sites on five genes (KLF14, ELOVL2, C1orf132, TRIM59, and FHL2) was performed on 264 postmortem blood samples from individuals aged 3 months to 93 years. The goals were to develop age prediction models based on the correlation between the methylation profile and chronological age and to assess the accuracy of the prediction. Linear regression between methylation levels and age at each CpG site revealed that the five markers show a statistically significant correlation with age. The methylation data from a training set of 160 postmortem blood samples were used to develop an age prediction model with a correlation coefficient of 0.65, explaining 73.1% of age variation, with a mean absolute deviation from the chronological age of 7.60 years. The accuracy of the model was evaluated with a test set of 72 samples producing a mean absolute deviation of 7.42 years. The training and test sets were also categorized by specific age groups to assess accuracy and deviation from chronological age. The data for both sets revealed a lower prediction potential as an individual increases in age, particularly for the age categories above 50 years.
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46
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Xiao C, Yi S, Huang D. Genome-wide identification of age-related CpG sites for age estimation from blood DNA of Han Chinese individuals. Electrophoresis 2021; 42:1488-1496. [PMID: 33978960 DOI: 10.1002/elps.202000367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/07/2021] [Accepted: 05/05/2021] [Indexed: 11/11/2022]
Abstract
Age-related CpG (AR-CpG) sites are currently the most promising molecular markers for forensic age estimation. However, the AR-CpG sites of Han Chinese population remains to be systematically characterized. In this study, we performed genome-wide methylation analyses on 42 whole blood DNA from healthy Han Chinese volunteers (aged from 18 to 62 years) using the Illumina MethylationEPIC BeadChip microarray. As expected, both known and novel AR-CpG sites were identified. Considering the sex difference in aging rate, we then separately selected AR-CpG candidates and built pyrosequencing-based multiple linear regression models for age estimation of males and females. The model constructed from the male sample group (n = 167, aged from 1.50 to 85.71 years) explained 95.22% of variation in age using five AR-CpG sites (chr6:11044864 ELOVL2, chr1:207997068 C1orf132, cg19283806 CCDC102B, cg17740900, and chr10:73740306 CHST3) and yielded a mean absolute error (MAE) of 2.79 years. The model constructed from the female sample group (n = 141, aged from 3.33 to 80.38 years) explained 94.90% of variation in age with six AR-CpG sites (chr6:11044867 ELOVL2, chr1:207997060 C1orf132, chr2:106015757 FHL2, cg26947034, chr16: 67184108 B3GNT9, and chr20:44658203 SLC12A5) and yielded an MAE of 2.53 years. Besides, the estimated age was highly correlated with the actual age (R > 0.97). The robustness of these AR-CpG markers was demonstrated by 10-fold cross-validations. In conclusion, we updated the AR-CpG sites of Han Chinese population and provided two sets of AR-CpG sites for accurate age estimation.
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Affiliation(s)
- Chao Xiao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, P. R. China
| | - Shaohua Yi
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, P. R. China
| | - Daixin Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, P. R. China
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Benincasa G, DeMeo DL, Glass K, Silverman EK, Napoli C. Epigenetics and pulmonary diseases in the horizon of precision medicine: a review. Eur Respir J 2021; 57:13993003.03406-2020. [PMID: 33214212 DOI: 10.1183/13993003.03406-2020] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
Epigenetic mechanisms represent potential molecular routes which could bridge the gap between genetic background and environmental risk factors contributing to the pathogenesis of pulmonary diseases. In patients with COPD, asthma and pulmonary arterial hypertension (PAH), there is emerging evidence of aberrant epigenetic marks, mainly including DNA methylation and histone modifications which directly mediate reversible modifications to the DNA without affecting the genomic sequence. Post-translational events and microRNAs can be also regulated epigenetically and potentially participate in disease pathogenesis. Thus, novel pathogenic mechanisms and putative biomarkers may be detectable in peripheral blood, sputum, nasal and buccal swabs or lung tissue. Besides, DNA methylation plays an important role during the early phases of fetal development and may be impacted by environmental exposures, ultimately influencing an individual's susceptibility to COPD, asthma and PAH later in life. With the advances in omics platforms and the application of computational biology tools, modelling the epigenetic variability in a network framework, rather than as single molecular defects, provides insights into the possible molecular pathways underlying the pathogenesis of COPD, asthma and PAH. Epigenetic modifications may have clinical applications as noninvasive biomarkers of pulmonary diseases. Moreover, combining molecular assays with network analysis of epigenomic data may aid in clarifying the multistage transition from a "pre-disease" to "disease" state, with the goal of improving primary prevention of lung diseases and its subsequent clinical management.We describe epigenetic mechanisms known to be associated with pulmonary diseases and discuss how network analysis could improve our understanding of lung diseases.
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Affiliation(s)
- Giuditta Benincasa
- Dept of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Dawn L DeMeo
- Channing Division of Network Medicine and the Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine and the Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine and the Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Claudio Napoli
- Dept of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy .,Clinical Dept of Internal and Specialty Medicine (DAI), University Hospital (AOU), University of Campania "Luigi Vanvitelli", Naples, Italy
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48
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Hanson BM, Tao X, Zhan Y, Jenkins TG, Morin SJ, Scott RT, Seli EU. Young women with poor ovarian response exhibit epigenetic age acceleration based on evaluation of white blood cells using a DNA methylation-derived age prediction model. Hum Reprod 2021; 35:2579-2588. [PMID: 33049778 DOI: 10.1093/humrep/deaa206] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/22/2020] [Indexed: 12/14/2022] Open
Abstract
STUDY QUESTION Is poor ovarian response associated with a change in predicted age based on a DNA methylation-derived age prediction model (the Horvath algorithm) in white blood cells (WBCs) or cumulus cells (CCs)? SUMMARY ANSWER In young women, poor ovarian response is associated with epigenetic age acceleration within WBC samples but is not associated with age-related changes in CC. WHAT IS KNOWN ALREADY The majority of human tissues follow predictable patterns of methylation which can be assessed throughout a person's lifetime. DNA methylation patterns may serve as informative biomarkers of aging within various tissues. Horvath's 'epigenetic clock', which is a DNA methylation-derived age prediction model, accurately predicts a subject's true chronologic age when applied to WBC but not to CC. STUDY DESIGN, SIZE, DURATION A prospective cohort study was carried out involving 175 women undergoing ovarian stimulation between February 2017 and December 2018. Women were grouped according to a poor (≤5 oocytes retrieved) or good (>5 oocytes) response to ovarian stimulation. Those with polycystic ovary syndrome (PCOS) (n = 35) were placed in the good responder group. PARTICIPANTS/MATERIALS, SETTING, METHODS DNA methylation patterns from WBC and CC were assessed for infertile patients undergoing ovarian stimulation at a university-affiliated private practice. DNA was isolated from peripheral blood samples and CC. Bisulfite conversion was then performed and a DNA methylation array was utilized to measure DNA methylation levels throughout the genome. Likelihood ratio tests were utilized to assess the relationship between predicted age, chronologic age and ovarian response. MAIN RESULTS AND THE ROLE OF CHANCE The Horvath-predicted age for WBC samples was consistent with patients' chronologic age. However, predicted age from analysis of CC was younger than chronologic age. In subgroup analysis of women less than 38 years of age, poor ovarian response was associated with an accelerated predicted age in WBC (P = 0.017). Poor ovarian response did not affect the Horvath-predicted age based on CC samples (P = 0.502). No alternative methylation-based calculation was identified to be predictive of age for CC. LIMITATIONS, REASONS FOR CAUTION To date, analyses of CC have failed to identify epigenetic changes that are predictive of the aging process within the ovary. Despite the poor predictive nature of both the Horvath model and the novel methylation-based age prediction model described here, it is possible that our efforts failed to identify appropriate sites which would result in a successful age-prediction model derived from the CC epigenome. Additionally, lower DNA input for CC samples compared to WBC samples was a methodological limitation. We acknowledge that a universally accepted definition of poor ovarian response is lacking. Furthermore, women with PCOS were included and therefore the group of good responders in the current study may not represent a population with entirely normal methylation profiles. WIDER IMPLICATIONS OF THE FINDINGS The process of ovarian and CC aging continues to be poorly understood. Women who demonstrate poor ovarian response to stimulation represent a common clinical challenge, so clarifying the exact biological changes that occur within the ovary over time is a worthwhile endeavor. The data from CC support a view that hormonally responsive tissues may possess distinct epigenetic aging patterns when compared with other tissue types. Future studies may be able to determine whether alternative DNA methylation sites can accurately predict chronologic age or ovarian response to stimulation from CC samples. Going forward, associations between epigenetic age acceleration and reproductive and general health consequences must also be clearly defined. STUDY FUNDING/COMPETING INTEREST(S) No external funding was obtained for the study and there are no conflicts of interest. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Brent M Hanson
- IVI-Reproductive Medicine Associates of New Jersey, Basking Ridge, NJ, USA
- Department of Obstetrics & Gynecology, Division of Reproductive Endocrinology and Infertility Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Xin Tao
- Foundation for Embryonic Competence, Basking Ridge, NJ, USA
| | - Yiping Zhan
- Foundation for Embryonic Competence, Basking Ridge, NJ, USA
| | - Timothy G Jenkins
- Department of Surgery, Division of Urology University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Physiology & Developmental Biology, Brigham Young University, Provo, UT, USA
| | - Scott J Morin
- IVI-Reproductive Medicine Associations of Northern California, San Francisco, CA, USA
| | - Richard T Scott
- IVI-Reproductive Medicine Associates of New Jersey, Basking Ridge, NJ, USA
- Department of Obstetrics & Gynecology, Division of Reproductive Endocrinology and Infertility Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Emre U Seli
- IVI-Reproductive Medicine Associates of New Jersey, Basking Ridge, NJ, USA
- Department of Obstetrics & Gynecology, Division of Reproductive Endocrinology & Infertility Yale University School of Medicine, New Haven, CT, USA
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49
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Nwanaji-Enwerem JC, Jackson CL, Ottinger MA, Cardenas A, James KA, Malecki KM, Chen JC, Geller AM, Mitchell UA. Adopting a "Compound" Exposome Approach in Environmental Aging Biomarker Research: A Call to Action for Advancing Racial Health Equity. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:45001. [PMID: 33822649 PMCID: PMC8043128 DOI: 10.1289/ehp8392] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/24/2021] [Accepted: 03/15/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND In June 2020, the National Academies of Sciences, Engineering, and Medicine hosted a virtual workshop focused on integrating the science of aging and environmental health research. The concurrent COVID-19 pandemic and national attention on racism exposed shortcomings in the environmental research field's conceptualization and methodological use of race, which have subsequently hindered the ability of research to address racial health disparities. By the workshop's conclusion, the authors deduced that the utility of environmental aging biomarkers-aging biomarkers shown to be specifically influenced by environmental exposures-would be greatly diminished if these biomarkers are developed absent of considerations of broader societal factors-like structural racism-that impinge on racial health equity. OBJECTIVES The authors reached a post-workshop consensus recommendation: To advance racial health equity, a "compound" exposome approach should be widely adopted in environmental aging biomarker research. We present this recommendation here. DISCUSSION The authors believe that without explicit considerations of racial health equity, people in most need of the benefits afforded by a better understanding of the relationships between exposures and aging will be the least likely to receive them because biomarkers may not encompass cumulative impacts from their unique social and environmental stressors. Employing an exposome approach that allows for more comprehensive exposure-disease pathway characterization across broad domains, including the social exposome and neighborhood factors, is the first step. Exposome-centered study designs must then be supported with efforts aimed at increasing the recruitment and retention of racially diverse study populations and researchers and further "compounded" with strategies directed at improving the use and interpretation of race throughout the publication and dissemination process. This compound exposome approach maximizes the ability of our science to identify environmental aging biomarkers that explicate racial disparities in health and best positions the environmental research community to contribute to the elimination of racial health disparities. https://doi.org/10.1289/EHP8392.
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Affiliation(s)
- Jamaji C. Nwanaji-Enwerem
- Department of Environmental Health, Harvard T.H. Chan School of Public Health and MD/PhD Program, Harvard Medical School, Boston, Massachusetts, USA
- Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, Berkeley, California, USA
| | - Chandra L. Jackson
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health (NIH), U.S. Department of Health and Human Services (U.S. HHS), Research Triangle Park, North Carolina, USA
- Intramural Program, National Institute on Minority Health and Health Disparities, NIH, U.S. HHS, Bethesda, Maryland, USA
| | - Mary Ann Ottinger
- Department of Biology and Biochemistry, University of Houston, Houston, Texas USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, Berkeley, California, USA
| | - Katherine A. James
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kristen M.C. Malecki
- Department of Population Health Sciences, University of Wisconsin Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Jiu-Chiuan Chen
- Departments of Preventive Medicine and Neurology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Andrew M. Geller
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Uchechi A. Mitchell
- Division of Community Health Sciences, School of Public Health, University of Illinois at Chicago, Chicago, Illinois, USA
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50
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Pellegrini C, Pirazzini C, Sala C, Sambati L, Yusipov I, Kalyakulina A, Ravaioli F, Kwiatkowska KM, Durso DF, Ivanchenko M, Monti D, Lodi R, Franceschi C, Cortelli P, Garagnani P, Bacalini MG. A Meta-Analysis of Brain DNA Methylation Across Sex, Age, and Alzheimer's Disease Points for Accelerated Epigenetic Aging in Neurodegeneration. Front Aging Neurosci 2021; 13:639428. [PMID: 33790779 PMCID: PMC8006465 DOI: 10.3389/fnagi.2021.639428] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/05/2021] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by specific alterations of brain DNA methylation (DNAm) patterns. Age and sex, two major risk factors for AD, are also known to largely affect the epigenetic profiles in brain, but their contribution to AD-associated DNAm changes has been poorly investigated. In this study we considered publicly available DNAm datasets of four brain regions (temporal, frontal, entorhinal cortex, and cerebellum) from healthy adult subjects and AD patients, and performed a meta-analysis to identify sex-, age-, and AD-associated epigenetic profiles. In one of these datasets it was also possible to distinguish 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) profiles. We showed that DNAm differences between males and females tend to be shared between the four brain regions, while aging differently affects cortical regions compared to cerebellum. We found that the proportion of sex-dependent probes whose methylation is modified also during aging is higher than expected, but that differences between males and females tend to be maintained, with only a few probes showing age-by-sex interaction. We did not find significant overlaps between AD- and sex-associated probes, nor disease-by-sex interaction effects. On the contrary, we found that AD-related epigenetic modifications are significantly enriched in probes whose DNAm varies with age and that there is a high concordance between the direction of changes (hyper or hypo-methylation) in aging and AD, supporting accelerated epigenetic aging in the disease. In summary, our results suggest that age-associated DNAm patterns concur to the epigenetic deregulation observed in AD, providing new insights on how advanced age enables neurodegeneration.
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Affiliation(s)
- Camilla Pellegrini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Luisa Sambati
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Katarzyna M. Kwiatkowska
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Danielle F. Durso
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Raffaele Lodi
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Pietro Cortelli
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Applied Biomedical Research Center, Policlinico S.Orsola-Malpighi Polyclinic, Bologna, Italy
- National Research Council of Italy Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza,” Unit of Bologna, Bologna, Italy
| | - Maria Giulia Bacalini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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