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Aguilar-Lacasaña S, Cosin-Tomas M, Raimbault B, Gómez-Herrera L, Sánchez O, Zanini MJ, Capdevila RP, Foraster M, Gascon M, Rivas I, Llurba E, Gómez-Roig MD, Sunyer J, Bustamante M, Vrijheid M, Dadvand P. Epigenome-wide association study of pregnancy exposure to green space and placental DNA methylation. ENVIRONMENTAL RESEARCH 2025; 274:121286. [PMID: 40043929 DOI: 10.1016/j.envres.2025.121286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Revised: 02/28/2025] [Accepted: 03/02/2025] [Indexed: 05/04/2025]
Abstract
Green space exposure during pregnancy has been associated with lower risk of adverse birth outcomes, but the biological mechanisms remain unclear. Epigenetic changes, such as DNA methylation (DNAm), may contribute to this association. The placenta, crucial for foetal development, has been understudied in relation to prenatal green space exposure and DNAm on a genome-wide scale. Here, we aimed to investigate the association between green space exposure during pregnancy and epigenome-wide placental DNAm in 550 mother-child pairs from the Barcelona Life Study Cohort (BiSC) in Spain. Green space exposure was assessed as (i) residential surrounding greenness (satellite-based Normalized Difference Vegetation Index (NDVI) in buffers of 100 m, 300 m and 500 m), (ii) residential distance to the nearest major green space (meters), (iii) use of green space (hours/week), and (iv) visual access to greenery through the home window (≥half of the view). Placental DNAm was measured with the EPIC array. Differentially methylated positions (DMPs) were identified using robust linear regression models adjusted for covariates, while differentially methylated regions (DMRs) were identified using the dmrff method. After Bonferroni correction, cg14852540, annotated to SLC25A10 gene, showed an inverse association with residential greenness within 500 m buffer. Additionally, 101 DMPs were suggestively significant (p-values <1 × 10-5) and annotated to genes involved in glucocorticoid-related pathways, inflammatory response, oxidative stress response, and oocyte maturation. No DMRs were identified. Overall, we identified an association between residential greenness and DNAm levels at one CpG in the SLC25A10 gene. Larger studies are needed to validate these findings and understand the biological pathways.
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Affiliation(s)
- Sofía Aguilar-Lacasaña
- ISGlobal, Barcelona, Spain; Universitat de Barcelona (UB), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Instituto de Salud Carlos III, Spain.
| | - Marta Cosin-Tomas
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Instituto de Salud Carlos III, Spain
| | - Bruno Raimbault
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Instituto de Salud Carlos III, Spain
| | - Laura Gómez-Herrera
- ISGlobal, Barcelona, Spain; Universitat de Barcelona (UB), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Instituto de Salud Carlos III, Spain
| | - Olga Sánchez
- Primary Care Interventions to Prevent Maternal and Child Chronic Diseases of Perinatal and Developmental Origin Network (RICORS-SAMID) (RD21/0012/0001), Spain; Department of Obstetrics and Gynaecology. Hospital de la Santa Creu i Sant Pau, Institut de Recerca (IR SANT PAU), Barcelona, 08041, Spain
| | - Maria Julia Zanini
- Department of Obstetrics and Gynaecology. Hospital de la Santa Creu i Sant Pau, Institut de Recerca (IR SANT PAU), Barcelona, 08041, Spain
| | - Rosalia Pascal Capdevila
- Primary Care Interventions to Prevent Maternal and Child Chronic Diseases of Perinatal and Developmental Origin Network (RICORS-SAMID) (RD21/0012/0003), Spain; BCNatal. Barcelona Center for Maternal Foetal and Neonatal Medicine (Hospital Sant Joan de Déu and Hospital Clínic), University of Barcelona, Barcelona, Spain
| | - Maria Foraster
- PHAGEX Research Group, Blanquerna School of Health Science, Universitat Ramon Llull (URL), Barcelona, Spain
| | - Mireia Gascon
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Instituto de Salud Carlos III, Spain; Unitat de Suport a la Recerca de la Catalunya Central, Fundació Institut Universitari per a la Recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Manresa, Spain
| | - Ioar Rivas
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Instituto de Salud Carlos III, Spain
| | - Elisa Llurba
- Primary Care Interventions to Prevent Maternal and Child Chronic Diseases of Perinatal and Developmental Origin Network (RICORS-SAMID) (RD21/0012/0001), Spain; Department of Obstetrics and Gynaecology. Hospital de la Santa Creu i Sant Pau, Institut de Recerca (IR SANT PAU), Barcelona, 08041, Spain
| | - Maria Dolores Gómez-Roig
- Primary Care Interventions to Prevent Maternal and Child Chronic Diseases of Perinatal and Developmental Origin Network (RICORS-SAMID) (RD21/0012/0003), Spain; BCNatal. Barcelona Center for Maternal Foetal and Neonatal Medicine (Hospital Sant Joan de Déu and Hospital Clínic), University of Barcelona, Barcelona, Spain; Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Jordi Sunyer
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Instituto de Salud Carlos III, Spain
| | - Mariona Bustamante
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Instituto de Salud Carlos III, Spain.
| | - Martine Vrijheid
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Instituto de Salud Carlos III, Spain
| | - Payam Dadvand
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública, Instituto de Salud Carlos III, Spain
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Nyembwe A, Zhao Y, Caceres BA, Belsky DW, Ryan CP, Taylor B, Morrison MT, Prescott L, Potts-Thompson S, Aziz A, Aruleba F, Matute-Arcos E, Williams O, Crusto C, Taylor JY. Discrimination, Coping, and DNAm Accelerated Aging Among African American Mothers of the InterGEN Study. EPIGENOMES 2025; 9:14. [PMID: 40407423 PMCID: PMC12101303 DOI: 10.3390/epigenomes9020014] [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: 03/03/2025] [Revised: 04/23/2025] [Accepted: 04/28/2025] [Indexed: 05/26/2025] Open
Abstract
Background: Racial discrimination experiences are associated with the activation of stress biology pathways and signs of accelerated biological aging, including alterations in DNA methylation (DNAm). Coping strategies may mitigate stress from racial discrimination and protect against long-term adverse health outcomes. Methods: We conducted a secondary analysis of data from the Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure cohort, an all-African-American sample, to test the hypothesis that social support can protect against accelerated biological aging associated with experiences of racial discrimination. We measured biological aging from saliva DNAm using six epigenetic clocks. Clock values were residualized on participant age and the estimated proportion of epithelial cells contributing to the DNA sample and standardized to M = 0, SD = 1 within the analysis sample. The primary analysis was focused on the second-generation PhenoAge and GrimAge clocks and the third-generation DunedinPACE "speedometer," which previous studies have linked with racial discrimination. Results: In our sample (n = 234; mean age = 31.9 years; SD = 5.80), we found evidence consistent with our hypothesis in the case of the PhenoAge clock, but not the other clocks. Among mothers who did not seek social support, experiences of racial discrimination were associated with an older PhenoAge (b = 0.26, 95% CI = 0.02-0.50, p = 0.03). However, social-support seeking mitigated this risk; at the highest levels of social support, no adverse consequences of discrimination were observed (interaction b = -0.01, 95% CI = -0.02--0.00, p = 0.03). Conclusions: The replication of results is needed. Future research should also investigate additional adaptive and maladaptive coping strategies utilized by African American women and mothers to identify protective measures that influence health outcomes.
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Affiliation(s)
- Alexandria Nyembwe
- Sue & Bill Gross School of Nursing, University of California, Irvine, 854 Health Sciences Rd., Irvine, CA 92697, USA
| | - Yihong Zhao
- Center for Research on People of Color, School of Nursing, Columbia University, 560 W 168th St, New York, NY 10032, USA; (Y.Z.); (B.A.C.); (M.T.M.); (L.P.); (S.P.-T.); (A.A.); (E.M.-A.); (J.Y.T.)
| | - Billy A. Caceres
- Center for Research on People of Color, School of Nursing, Columbia University, 560 W 168th St, New York, NY 10032, USA; (Y.Z.); (B.A.C.); (M.T.M.); (L.P.); (S.P.-T.); (A.A.); (E.M.-A.); (J.Y.T.)
| | - Daniel W. Belsky
- Robert N. Butler Columbia Aging Center, Columbia University, 722 West 168th Street, New York, NY 10032, USA; (D.W.B.); (C.P.R.)
| | - Calen Patrick Ryan
- Robert N. Butler Columbia Aging Center, Columbia University, 722 West 168th Street, New York, NY 10032, USA; (D.W.B.); (C.P.R.)
| | - Brittany Taylor
- School of Nursing, University of Pittsburgh, 3500 Victoria Street, Victoria Building, Pittsburgh, PA 15213, USA;
| | - Morgan T. Morrison
- Center for Research on People of Color, School of Nursing, Columbia University, 560 W 168th St, New York, NY 10032, USA; (Y.Z.); (B.A.C.); (M.T.M.); (L.P.); (S.P.-T.); (A.A.); (E.M.-A.); (J.Y.T.)
| | - Laura Prescott
- Center for Research on People of Color, School of Nursing, Columbia University, 560 W 168th St, New York, NY 10032, USA; (Y.Z.); (B.A.C.); (M.T.M.); (L.P.); (S.P.-T.); (A.A.); (E.M.-A.); (J.Y.T.)
| | - Stephanie Potts-Thompson
- Center for Research on People of Color, School of Nursing, Columbia University, 560 W 168th St, New York, NY 10032, USA; (Y.Z.); (B.A.C.); (M.T.M.); (L.P.); (S.P.-T.); (A.A.); (E.M.-A.); (J.Y.T.)
| | - Arezo Aziz
- Center for Research on People of Color, School of Nursing, Columbia University, 560 W 168th St, New York, NY 10032, USA; (Y.Z.); (B.A.C.); (M.T.M.); (L.P.); (S.P.-T.); (A.A.); (E.M.-A.); (J.Y.T.)
| | - Fisola Aruleba
- School of Medicine, The City College of New York (CUNY), Harris Hall, 160 Convent Avenue, New York, NY 10031, USA;
| | - Erica Matute-Arcos
- Center for Research on People of Color, School of Nursing, Columbia University, 560 W 168th St, New York, NY 10032, USA; (Y.Z.); (B.A.C.); (M.T.M.); (L.P.); (S.P.-T.); (A.A.); (E.M.-A.); (J.Y.T.)
| | - Olajide Williams
- Vagelos College of Physicians and Surgeons, Columbia University, 630 W 168th St, New York, NY 10032, USA;
| | - Cindy Crusto
- Keck School of Medicine, University of Southern California (USC), 1975 Zonal Ave, Los Angeles, CA 90033, USA;
| | - Jacquelyn Y. Taylor
- Center for Research on People of Color, School of Nursing, Columbia University, 560 W 168th St, New York, NY 10032, USA; (Y.Z.); (B.A.C.); (M.T.M.); (L.P.); (S.P.-T.); (A.A.); (E.M.-A.); (J.Y.T.)
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Douglas J, Wang Z, Zumpano F, Satagopan JM, Moye J, Arpadi SM, Marsit CJ, Barrett ES, Shiau S. Isolating the effects of HIV infection and HIV exposure on epigenetic profiles in infants using historical data from the Mothers and Infants Cohort Study. EBioMedicine 2025; 115:105696. [PMID: 40288238 PMCID: PMC12056770 DOI: 10.1016/j.ebiom.2025.105696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 03/27/2025] [Accepted: 03/28/2025] [Indexed: 04/29/2025] Open
Abstract
BACKGROUND Epigenetics offers insight into the mechanisms by which early life HIV infection and HIV exposure in utero affects offspring health. However, due to the widespread use of antiretroviral therapy (ART) during pregnancy/infancy, contemporary studies are unable to disentangle effects of HIV from ART exposure on epigenetic profiles. METHODS Using historical specimens collected before widespread use of ART (1985-1991), we compared DNA methylation (DNAm) profiles among infants with perinatally-acquired HIV (PHIV), HIV-exposed but uninfected (HEU), and HIV-unexposed uninfected (HUU). DNAm in peripheral blood mononuclear cells collected at 3 and 12 months of age (36 PHIV, 33 HEU, and 33 HUU) was profiled using the Illumina Infinium MethylationEPIC BeadChip. We tested for differentially methylated (DM) CpG sites between groups at 3 and 12 months, adjusting for sex, race/ethnicity, and cell type proportions. Biological pathway enrichment analyses were conducted. FINDINGS Comparing PHIV to HEU, there were 2 DM sites at 3 months and 11 at 12 months. Comparing PHIV to HUU, there was 1 DM CpG site at 3 months and 6 at 12 months. Immune-related pathways, including interferon-mediated signalling pathways were enriched. HIV exposure was not associated with any variation in DNA methylation, as no differences were detected between HEU vs. HUU at 3 or 12 months. INTERPRETATION HIV infection (in the absence of ART during pregnancy/infancy) was associated with DNA methylation changes at 3 and 12 months of life in infants. Differential methylation in PHIV is related to immune processes and HIV exposure in the absence of infection does not contribute to differential methylation. FUNDING This study was supported by funding from the National Institutes of Health (R21HD104558 to SS, K01DA053157 to SS, P30ES019776 to CJM, and P30ES005022 to ESB.
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Affiliation(s)
- Jasmine Douglas
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ, USA
| | - Ziyi Wang
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ, USA
| | - Francesca Zumpano
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ, USA
| | - Jaya M Satagopan
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ, USA
| | - Jack Moye
- Maternal and Pediatric Infectious Disease Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Stephen M Arpadi
- Gertrude H. Sergievsky Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Emily S Barrett
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ, USA; Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ, USA
| | - Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ, USA.
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Zarandooz S, Raffington L. Applying blood-derived epigenetic algorithms to saliva: cross-tissue similarity of DNA-methylation indices of aging, physiology, and cognition. Clin Epigenetics 2025; 17:61. [PMID: 40270051 PMCID: PMC12016411 DOI: 10.1186/s13148-025-01868-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2024] [Accepted: 03/29/2025] [Indexed: 04/25/2025] Open
Abstract
BACKGROUND Epigenetic algorithms of aging, health, and cognition, based on DNA-methylation (DNAm) patterns, are prominent tools for measuring biological age and have been linked to age-related diseases, cognitive decline, and mortality. While most of these methylation profile scores (MPSs) are developed in blood tissue, there is growing interest in using less invasive tissues like saliva. The aim of the current study is to probe the cross-tissue intraclass correlation coefficients (ICCs) of MPSs developed in blood applied to saliva DNAm from the same people. While our primary focus is on MPSs that were previously found to be robustly correlated with social determinants of health, including second- and third-generation clocks and MPSs of physiology and cognition, we also report ICC values for first-generation clocks to enable comparison across metrics. We pooled three publicly available datasets that had both saliva and blood DNAm from the same individuals (total n = 107, aged 5-74 years), corrected MPSs for cell composition within each tissue, and computed the cross-tissue ICCs. RESULTS We found that after correcting for cell composition, saliva-blood cross-tissue ICCs were moderate for second- and third-generation indices of aging and MPSs of physiology and cognition. Specifically, PCGrimAge had the highest ICC (0.76), followed by PCPhenoAge (0.72), a measure of cognitive performance (Epigenetic-g, 0.69), DunedinPACE (0.68), PCGrimAge Acceleration (0.67), PCPhenoAge Acceleration (0.66), an MPS of hs-CRP (0.58), and BMI (0.54). These ICCs appear lower than previous reports on within-tissue ICCs (saliva ICCs range from 0.67 to 0.85, blood ICCs range from 0.73 to 0.93). Cross-tissue ICCs values for first-generation biological age acceleration measures were poor, ranging from 0.19 to 0.25. CONCLUSIONS Our findings suggest that applying second- and third-generation MPSs of biological age acceleration and related phenotypes developed in blood to saliva DNAm results in moderate cross-tissue similarity and the precise cross-tissue correspondence differs by measure. While the degree of cross-tissue similarity of several MPSs may suffice for some research settings, it may not be suitable in clinical or commercial applications. Collection of both blood and saliva DNAm samples is necessary to validate existing algorithms and to customize MPSs in saliva DNAm.
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Affiliation(s)
- Sepideh Zarandooz
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Berlin, Germany
| | - Laurel Raffington
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Berlin, Germany.
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Newman BT, Danoff JS, Lynch ME, Giamberardino SN, Gregory SG, Connelly JJ, Druzgal TJ, Morris JP. Epigenetic age acceleration predicts subject-specific white matter degeneration in the human brain. Aging Cell 2025; 24:e14426. [PMID: 39605173 PMCID: PMC11984680 DOI: 10.1111/acel.14426] [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: 09/18/2023] [Revised: 11/10/2024] [Accepted: 11/13/2024] [Indexed: 11/29/2024] Open
Abstract
Epigenetic clocks provide powerful tools for estimating health and lifespan but their ability to predict brain degeneration and neuronal damage during the aging process is unknown. In this study, we use GrimAge, an epigenetic clock correlated to several blood plasma proteins, to longitudinally investigate brain cellular microstructure in axonal white matter from a cohort of healthy aging individuals. A specific focus was made on white matter hyperintensities, a visible neurological manifestation of small vessel disease, and the axonal pathways throughout each individual's brain affected by their unique white matter hyperintensity location and volume. 98 subjects over 55 years of age were scanned at baseline with 41 returning for a follow-up scan 2 years later. Using diffusion MRI lesionometry, we reconstructed subject-specific networks of affected axonal tracts and examined the diffusion cellular microstructure composition of these areas, both at baseline and longitudinally, for evidence of cellular degeneration. A chronological age-adjusted version of GrimAge was significantly correlated with baseline WMH volume and markers of neuronal decline, indicated by increased extracellular free water, increased intracellular signal, and decreased axonal signal within WMH. By isolating subject-specific axonal regions "lesioned" by crossing through a WMH, age-adjusted GrimAge was also able to predict longitudinal development of similar patterns of neuronal decline throughout the brain. This study is the first to demonstrate WMH lesionometry as a subject-specific precision imaging technique to study degeneration in aging and the first to establish a relationship between accelerated epigenetic GrimAge and brain cellular microstructure in humans.
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Affiliation(s)
- Benjamin T. Newman
- Department of PsychologyUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Radiology and Medical Imaging, School of MedicineUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Joshua S. Danoff
- Department of PsychologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Morgan E. Lynch
- Department of PsychologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | | | - Simon G. Gregory
- Duke Molecular Physiology InstituteDuke UniversityDurhamNorth CarolinaUSA
- Department of NeurologyDuke UniversityDurhamNorth CarolinaUSA
| | | | - T. Jason Druzgal
- Department of Radiology and Medical Imaging, School of MedicineUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - James P. Morris
- Department of PsychologyUniversity of VirginiaCharlottesvilleVirginiaUSA
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Comendul A, Ruf-Zamojski F, Ford CT, Agarwal P, Zaslavsky E, Nudelman G, Hariharan M, Rubenstein A, Pincas H, Nair VD, Michaleas AM, Fremont-Smith PD, Ricke DO, Sealfon SC, Woods CW, Claypool KT, Jaimes R. Comprehensive guide for epigenetics and transcriptomics data quality control. STAR Protoc 2025; 6:103607. [PMID: 39869481 PMCID: PMC11799959 DOI: 10.1016/j.xpro.2025.103607] [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: 08/07/2024] [Revised: 09/27/2024] [Accepted: 01/07/2025] [Indexed: 01/29/2025] Open
Abstract
Host response to environmental exposures such as pathogens and chemicals can include modifications to the epigenome and transcriptome. Improved signature discovery, including the identification of the agent and timing of exposure, has been enabled by advancements in assaying techniques to detect RNA expression, DNA base modifications, histone modifications, and chromatin accessibility. The interrogation of the epigenome and transcriptome cascade requires analyzing disparate datasets from multiple assay types, often at single-cell resolution, derived from the same biospecimen. However, there remains a paucity of rigorous quality control standards of those datasets that reflect quality assurance of the underlying assay. This guide outlines a comprehensive suite of metrics that can be used to ensure quality from 11 different epigenetics and transcriptomics assays. Recommended mitigative actions to address failed metrics are provided. The workflow presented aims to improve benchwork protocols and dataset quality to enable accurate discovery of exposure signatures.
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Affiliation(s)
- Arianna Comendul
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, USA
| | - Frederique Ruf-Zamojski
- Cedars-Sinai Medical Center, Department of Medicine, Los Angeles, CA, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Colby T Ford
- Tuple LLC, Charlotte, NC, USA; University of North Carolina at Charlotte, Department of Bioinformatics and Genomics, Charlotte, NC, USA; University of North Carolina at Charlotte, Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Charlotte, NC, USA
| | | | | | | | - Manoj Hariharan
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA, USA
| | | | - Hanna Pincas
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Adam M Michaleas
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, USA
| | | | - Darrell O Ricke
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, USA
| | | | | | - Kajal T Claypool
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, USA
| | - Rafael Jaimes
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA, USA.
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León I, Góngora D, Rodrigo MJ, Herrero-Roldán S, López Rodríguez M, Mitchell C, Fisher J, Iturria-Medina Y. Maternal epigenetic index links early neglect to later neglectful care and other psychopathological, cognitive, and bonding effects. Clin Epigenetics 2025; 17:46. [PMID: 40057810 PMCID: PMC11890505 DOI: 10.1186/s13148-025-01839-7] [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: 09/28/2024] [Accepted: 02/09/2025] [Indexed: 05/13/2025] Open
Abstract
BACKGROUND Past experiences of maltreatment and life adversity induce DNA methylation changes in adults, but less is known about their impact on mothers' maladaptive neglectful parenting and its negative effects. We performed an epigenome-wide association study to investigate the role of DNA methylation levels in mothers with neglectful care, who were exposed to childhood maltreatment and neglect, and their current negative effects. Saliva DNA methylation was determined with the Illumina Human Methylation EPIC BeadChip v1. The individual epigenome was the input to a machine learning algorithm for trajectory inference, which assigned a specific state to each mother in the progression from healthy controls to the extreme neglect condition. A compound epigenetic maternal neglect score (EMN) was derived from 138 mothers (n = 51 in the neglectful group; n = 87 in the control non-neglectful group) having young children. Differential methylation between groups was utilized to derive the EMNs adjusted for education level, age, experimental variables, and blood cell types in saliva samples. RESULTS Structural equation modeling: X2 (29) = 37.81; p = 0.127; RMSEA = 0.048, confirmed that EMNs link their early experience of physical neglect to current reports of psychopathological symptoms, lower cognitive status, and observed poor mother-child emotional availability. A third of the genes annotated to the CpGs that affect EMNs are related to cognitive impairment and neurodegenerative and psychopathological disorders. CONCLUSIONS EMNs are a novel index to assess the contribution of DNA methylations as a neglected girl to later neglectful caregiving behavior and other negative effects. The evidence provided expands the possibilities for earlier interventions on the neglect condition to prevent and ameliorate the direct or indirect epigenetic impact of maternal adversities on mother-child care, helping to break the cycle of maltreatment.
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Affiliation(s)
- Inmaculada León
- Instituto Universitario de Neurociencia, Universidad de La Laguna, Campus de Guajara, 38201, San Cristóbal de La Laguna, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Daylín Góngora
- Department of Microeconomics and Public Economics, Maastricht University School of Business and Economics, Maastricht University - Center of Neuroeconomics, Maastricht, The Netherlands
- Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - María José Rodrigo
- Instituto Universitario de Neurociencia, Universidad de La Laguna, Campus de Guajara, 38201, San Cristóbal de La Laguna, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Silvia Herrero-Roldán
- Instituto Universitario de Neurociencia, Universidad de La Laguna, Campus de Guajara, 38201, San Cristóbal de La Laguna, Spain.
- Facultad de Ciencias Sociales Aplicadas y de La Comunicación, UNIE Universidad, Madrid, Spain.
| | - Maykel López Rodríguez
- Department of Pathology and Laboratory Medicine at the David Geffen School of Medicine, UCLA, Los Angeles, USA
| | - Colter Mitchell
- Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Jonah Fisher
- Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Yasser Iturria-Medina
- Neurology and Neurosurgery Department, Montreal Neurological Institute, Montreal, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, Montreal, Canada
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Everson TM, Sehgal N, Campbell K, Barr DB, Panuwet P, Yakimavets V, Chen K, Perez C, Shankar K, Eick SM, Pearson KJ, Andres A. Placental PFAS concentrations are associated with perturbations of placental DNA methylation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2025; 368:125737. [PMID: 39862910 DOI: 10.1016/j.envpol.2025.125737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 01/12/2025] [Accepted: 01/21/2025] [Indexed: 01/27/2025]
Abstract
The placenta is crucial for fetal development, is affected by PFAS toxicity, and evidence is accumulating that gestational PFAS perturb the epigenetic activity of the placenta. Gestational PFAS exposure can adversely affect offspring, yet individual and cumulative impacts of PFAS on the placental epigenome remain underexplored. Here, we conducted an epigenome-wide association study (EWAS) to examine the relationships between placental PFAS levels and DNA methylation in a cohort of mother-infant dyads in Arkansas (N = 151). We measured 17 PFAS in human placental tissues and quantified placental DNA methylation levels via the Illumina EPIC Microarray. We tested for differential DNA methylation with individual PFAS, and with mixtures of multiple PFAS. Our results demonstrated that numerous epigenetic loci were perturbed by PFAS, with PFHxS exhibiting the most abundant effects. Mixture analyses suggested cumulative effects of PFOA and PFOS, while PFHxS may act more independently. We additionally explored whether sex-specific effects may be present and concluded that future large studies should explicitly test for sex-specific effects. The genes that are annotated to our PFAS-associated epigenetic loci are primarily involved in growth processes and cardiometabolic health, while some genes are involved in neurodevelopment. These findings shed light on how prenatal PFAS exposures affect birth outcomes and children's health, emphasizing the importance of understanding PFAS mechanisms in the in-utero environment.
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Affiliation(s)
- Todd M Everson
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA; Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA.
| | - Neha Sehgal
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Kyle Campbell
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Dana Boyd Barr
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Parinya Panuwet
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Volha Yakimavets
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Kelsey Chen
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Cynthia Perez
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Kartik Shankar
- USDA Agricultural Research Service, Responsive Agricultural Food Systems Research Unit, College Station, TX, USA
| | - Stephanie M Eick
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA; Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Kevin J Pearson
- Department of Pharmacology & Nutritional Sciences, University of Kentucky College of Medicine, USA
| | - Aline Andres
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Arkansas Children's Nutrition Center, Little Rock, AR, USA
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Mulligan CJ, Quinn EB, Hamadmad D, Dutton CL, Nevell L, Binder AM, Panter-Brick C, Dajani R. Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees. Sci Rep 2025; 15:5945. [PMID: 40016245 PMCID: PMC11868390 DOI: 10.1038/s41598-025-89818-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 02/07/2025] [Indexed: 03/01/2025] Open
Abstract
Maternal trauma influences infant and adult health outcomes and may impact future generations through epigenetic modifications such as DNA methylation (DNAm). Research in humans on the intergenerational epigenetic transmission of trauma effects is limited. In this study, we assessed DNAm signatures of war-related violence by comparing germline, prenatal, and direct exposures to violence across three generations of Syrian refugees. We compared families in which a pregnant grandmother versus a pregnant mother was exposed to violence and included a control group with no exposure to war. We collected buccal swab samples and survey data from mothers and 1-2 children in each of 48 families (n = 131 participants). Based on an epigenome-wide association study (EWAS), we identified differentially methylated regions (DMPs): 14 were associated with germline and 21 with direct exposure to violence. Most DMPs showed the same directionality in DNAm change across germline, prenatal, and direct exposures, suggesting a common epigenetic response to violence. Additionally, we identified epigenetic age acceleration in association with prenatal exposure to violence in children, highlighting the critical period of in utero development. This is the first report of an intergenerational epigenetic signature of violence, which has important implications for understanding the inheritance of trauma.
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Affiliation(s)
- Connie J Mulligan
- Department of Anthropology, University of Florida, Gainesville, FL, USA.
- Genetics Institute, University of Florida, Gainesville, FL, USA.
| | - Edward B Quinn
- Department of Anthropology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Baltimore City Department of Social Services, Baltimore, MD, USA
| | | | - Christopher L Dutton
- Department of Anthropology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Lisa Nevell
- Department of Anthropology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Alexandra M Binder
- Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA
- Department of Epidemiology, University of California, Los Angeles, CA, USA
| | - Catherine Panter-Brick
- Department of Anthropology, Yale University, New Haven, CT, USA
- Jackson School of Global Affairs, Yale University, New Haven, CT, USA
| | - Rana Dajani
- Department of Biology and Biotechnology, The Hashemite University, Zarqa, Jordan
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10
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Hüls A, Liu J, Konwar C, Conneely KN, Levey AI, Lah JJ, Wingo AP, Wingo TS. Epigenome-wide association study of cerebrospinal fluid-based biomarkers of Alzheimer's disease in cognitively normal individuals. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.02.04.25321657. [PMID: 39974053 PMCID: PMC11838696 DOI: 10.1101/2025.02.04.25321657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
INTRODUCTION Cerebrospinal fluid (CSF) biomarkers of Alzheimer's disease (AD) are reliable predictors of future AD risk. We investigated whether pre-clinical changes in AD CSF biomarkers are reflected in blood DNA methylation (DNAm) levels in cognitively normal participants. METHODS We profiled blood-based DNAm with the EPIC array in participants without a diagnosis of cognitive impairment in the Emory Healthy Brain Study (EHBS; N=495) and ADNI (N=122). Their CSF Aβ42, tTau, and pTau levels were quantified using Elecsys immunoassays. We conducted epigenome-wide association studies to assess associations between DNAm and CSF biomarkers of AD. RESULTS In EHBS, no loci were Bonferroni-significant after adjusting for confounding factors. In ADNI, two loci were significant, but they were not replicated in EHBS. There was little agreement between the top loci from EHBS and ADNI. DISCUSSION Our study showed little evidence of an association between differential blood-based DNAm and pre-clinical AD CSF biomarkers.
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Affiliation(s)
- Anke Hüls
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA, 30322
- Ganagarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA, 30322
| | - Jiaqi Liu
- Department of Psychiatry, University of California, Davis, Sacramento, CA USA, 95816
| | - Chaini Konwar
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver BC V5Z 4H4, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC Canada V5Z 4H4
| | - Karen N. Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA, 95816
| | - Allan I. Levey
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA USA, 30322
- Department of Neurology, Emory University School of Medicine, Atlanta, GA USA, 30322
| | - James J. Lah
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA USA, 30322
- Department of Neurology, Emory University School of Medicine, Atlanta, GA USA, 30322
| | - Aliza P. Wingo
- Department of Psychiatry, University of California, Davis, Sacramento, CA USA, 95816
- Division of Mental Health, Northern California VA, Sacramento, CA USA, 95816
| | - Thomas S. Wingo
- Department of Neurology, University of California, Davis, Sacramento, CA USA, 95816
- Alzheimer’s Disease Research Center, University of California, Davis, Sacramento, USA, 95816
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11
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Campbell KA, Colacino JA, Dou J, Dolinoy DC, Park SK, Loch-Caruso R, Padmanabhan V, Bakulski KM. Placental and immune cell DNA methylation reference panel for bulk tissue cell composition estimation in epidemiological studies. Epigenetics 2024; 19:2437275. [PMID: 39648517 PMCID: PMC11633140 DOI: 10.1080/15592294.2024.2437275] [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: 07/17/2024] [Revised: 11/03/2024] [Accepted: 11/27/2024] [Indexed: 12/10/2024] Open
Abstract
To distinguish DNA methylation (DNAm) from cell proportion changes in whole placental villous tissue research, we developed a robust cell type-specific DNAm reference to estimate cell composition. We collated new and existing cell type DNAm profiles quantified via Illumina EPIC or 450k microarrays. To estimate cell composition, we deconvoluted whole placental samples (n = 36) with robust partial correlation based on the top 30 hyper- and hypomethylated sites identified per cell type. To test deconvolution performance, we evaluated root mean square error in predicting principal components of DNAm variation in 204 external placental samples. We analyzed DNAm profiles (n = 368,435 sites) from 12 cell types: cytotrophoblasts (n = 18), endothelial cells (n = 19), Hofbauer cells (n = 26), stromal cells (n = 21), syncytiotrophoblasts (n = 4), six lymphocyte types (n = 36), and nucleated red blood cells (n = 11). Median cell composition was consistent with placental biology: 60.9% syncytiotrophoblast, 17.3% stromal, 8.8% endothelial, 3.7% cytotrophoblast, 3.7% Hofbauer, 1.7% nucleated red blood cells, and 1.2% neutrophils. Our expanded reference outperformed an existing reference in predicting DNAm variation (PC1, 15.4% variance explained, IQR = 21.61) with cell composition estimates (mean square error of prediction: 8.62 vs. 10.79, p-value < 0.001). This cell type reference can robustly estimate cell composition from whole placental DNAm data to detect important cell types, reveal biological mechanisms, and improve causal inference.
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Affiliation(s)
- Kyle A. Campbell
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Justin A. Colacino
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - John Dou
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Dana C. Dolinoy
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Sung Kyun Park
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Rita Loch-Caruso
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Vasantha Padmanabhan
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Obstetrics and Gynecology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kelly M. Bakulski
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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12
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Tindula G, Mukherjee SK, Ekramullah SM, Arman DM, Islam J, Biswas SK, Warf BC, Christiani DC, Lemos B, Liang L, Cardenas A, Mazumdar M. Parental arsenic exposure and tissue-specific DNA methylation in Bangladeshi infants with spina bifida. Epigenetics 2024; 19:2416345. [PMID: 39425535 PMCID: PMC11492674 DOI: 10.1080/15592294.2024.2416345] [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: 06/14/2024] [Revised: 08/31/2024] [Accepted: 10/09/2024] [Indexed: 10/21/2024] Open
Abstract
An emerging hypothesis linking arsenic toxicity involves altered epigenetic mechanisms, such as DNA methylation. In this study, we examined the relationship between parents' arsenic exposure and DNA methylation in tissues obtained from 28 infants with spina bifida from Bangladesh. We analyzed arsenic in parents' toenails using inductively coupled plasma mass spectrometry (ICP-MS). DNA methylation was measured in infants' dural tissue, buccal swabs, and whole blood using the Illumina Infinium MethylationEPIC BeadChip. We performed epigenome-wide association analyses (EWAS) and tested differentially methylated regions (DMRs). In EWAS, DNA methylation at cg24039697 in dural tissue was positively associated (β = 0.59, p = 7.6 × 10-9) with father's toenail arsenic concentrations, adjusting for covariates. We did not identify any CpG sites related to father's arsenic exposure in the other tissues, or any CpG sites related to mother's arsenic exposure. Gene ontology analysis identified many biological pathways of interest, including the Wnt signaling pathways. We identified several DMRs across the tissues related to arsenic exposure that included probes mapping to genes that have previously been identified in studies of neural tube defects. This study emphasizes the potential impact of arsenic exposure in fathers, often understudied in epidemiological studies, on DNA methylation in a unique neurological tissue specific to spina bifida.
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Affiliation(s)
- Gwen Tindula
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Sudipta Kumer Mukherjee
- Department of Paediatric Neurosurgery, National Institute of Neurosciences and Hospital (NINS&H), Dhaka, Bangladesh
| | - Sheikh Muhammad Ekramullah
- Department of Paediatric Neurosurgery, National Institute of Neurosciences and Hospital (NINS&H), Dhaka, Bangladesh
| | - DM Arman
- Department of Paediatric Neurosurgery, National Institute of Neurosciences and Hospital (NINS&H), Dhaka, Bangladesh
| | - Joynul Islam
- Department of Clinical Neurosurgery, National Institute of Neurosciences and Hospital (NINS&H), Dhaka, Bangladesh
| | - Subrata Kumar Biswas
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Benjamin C. Warf
- Department of Neurosurgery, Boston Children’s Hospital, Boston, MA, USA
| | - David C. Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Bernardo Lemos
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
- Coit Center for Longevity and Neurotherapeutics, The University of Arizona, Tucson, AZ, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Maitreyi Mazumdar
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
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13
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Lussier AA, Schuurmans IK, Großbach A, Maclsaac J, Dever K, Koen N, Zar HJ, Stein DJ, Kobor MS, Dunn EC. Technical variability across the 450K, EPICv1, and EPICv2 DNA methylation arrays: lessons learned for clinical and longitudinal studies. Clin Epigenetics 2024; 16:166. [PMID: 39578866 PMCID: PMC11583407 DOI: 10.1186/s13148-024-01761-4] [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: 08/07/2024] [Accepted: 10/11/2024] [Indexed: 11/24/2024] Open
Abstract
DNA methylation (DNAm) is the most commonly measured epigenetic mechanism in human populations, with most studies using Illumina arrays to assess DNAm levels. In 2023, Illumina updated their DNAm arrays to the EPIC version 2 (EPICv2), building on prior iterations, namely the EPIC version 1 (EPICv1) and 450K arrays. Whether DNAm measurements are stable across these three generations of arrays has yet not been investigated, limiting the ability of researchers-especially those with longitudinal data-to compare and replicate results across arrays. Here, we present results from a study of 30 child participants (15 male; 15 female) from the Drakenstein Child Health Study, who had DNAm measured on all three of the latest arrays: 450K, EPICv1, and EPICv2. Using these data, we created an annotation of probe quality across arrays, which includes the intraclass correlations, interquartile ranges, correlations, and array bias (i.e., the extent to which DNAm levels were explained by array type) of all CpGs. We also present results from an analysis of sex differences, where we found that CpGs with lower replicability across arrays had higher array-based variance, suggesting this variance metric help guide replication efforts. We also showed that epigenetic age estimates across arrays were more stable when using the principal component versions of epigenetic clocks. Ultimately, this collection of results provides a framework for investigating the replicability and longitudinal stability of epigenetic changes across multiple versions of Illumina DNAm arrays.
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Affiliation(s)
- Alexandre A Lussier
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Isabel K Schuurmans
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Anna Großbach
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland
- The SFI Centre for Research Training in Genomics Data Science, Dublin, Ireland
| | - Julie Maclsaac
- 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
| | - Kristy Dever
- 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
| | - Nastassja Koen
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Pediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Dan J Stein
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - 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 Centre for Healthy Aging, University of British Columbia, Vancouver, BC, Canada
| | - Erin C Dunn
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Sociology, College of Liberal Arts, Purdue University, West Lafayette, IN, USA.
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14
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Liu S, Liu D, Bender CM, Erickson KI, Sereika SM, Shaffer JR, Weeks DE, Conley YP. Associations between DNA methylation and cognitive function in early-stage hormone receptor-positive breast cancer patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.11.17.24317299. [PMID: 39606386 PMCID: PMC11601744 DOI: 10.1101/2024.11.17.24317299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Background Approximately one-third of breast cancer (BC) patients show poorer cognitive function (CF) before receiving adjuvant therapy compared with age-matched healthy controls. However, the biological mechanisms driving CF variation in the context of BC remain unclear. In this study, we aimed to identify genes and biological pathways associated with CF in postmenopausal women with early-stage hormone receptor-positive (HR+) BC using DNA methylation (DNAm) data, a dynamic regulator of gene activity. Methods Epigenome-wide association studies (EWAS) and differentially methylated region analyses were performed for each CF phenotype (seven objective domains and one subjective phenotype) using DNAm data from whole blood samples (n=109) taken at time of enrollment. Post-EWAS functional analyses were performed to enhance the understanding of the CF-related cytosine-phosphate-guanine (CpG) sites. Results When adjusting for age, verbal IQ scores, and global DNAm signature, cg10331779 near CTNND2 (p-value= 9.65 × 10 -9 ) and cg25906741 in MLIP (p-value= 2.01 × 10 -8 ) were associated with processing speed and subjective CF, respectively, while regions in/near SLC6A11 , PRKG1/CSTF2T , and FAM3B for processing speed, and regions in/near PI4KB and SGCE/PEG10 for mental flexibility were differentially methylated. In addition, beta-estradiol was identified as a common upstream regulator for all the CF phenotypes, suggesting an essential role of estrogen in explaining variation in CF of HR+ BC patients. Conclusions In our EWAS of 8 CF phenotypes, we found two epigenome-wide significant signals, one at cg10331779 near CTNND2 with processing speed and the other at cg25906741 in MLIP with subjective CF. We also found three differentially methylated regions associated with processing speed and two associated with mental flexibility. These findings need replication in larger cohorts.
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15
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Diez-Ahijado L, Cilleros-Portet A, Fernández-Jimenez N, Fernández MF, Guxens M, Julvez J, Llop S, Lopez-Espinosa MJ, Subiza-Pérez M, Lozano M, Ibarluzea J, Sunyer J, Bustamante M, Cosin-Tomas M. Evaluating the association between placenta DNA methylation and cognitive functions in the offspring. Transl Psychiatry 2024; 14:383. [PMID: 39304652 DOI: 10.1038/s41398-024-03094-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/31/2024] [Accepted: 09/04/2024] [Indexed: 09/22/2024] Open
Abstract
The placenta plays a crucial role in protecting the fetus from environmental harm and supports the development of its brain. In fact, compromised placental function could predispose an individual to neurodevelopmental disorders. Placental epigenetic modifications, including DNA methylation, could be considered a proxy of placental function and thus plausible mediators of the association between intrauterine environmental exposures and genetics, and childhood and adult mental health. Although neurodevelopmental disorders such as autism spectrum disorder have been investigated in relation to placenta DNA methylation, no studies have addressed the association between placenta DNA methylation and child's cognitive functions. Thus, our goal here was to investigate whether the placental DNA methylation profile measured using the Illumina EPIC array is associated with three different cognitive domains (namely verbal score, perceptive performance score, and general cognitive score) assessed by the McCarthy Scales of Children's functions in childhood at age 4. To this end, we conducted epigenome-wide association analyses, including data from 255 mother-child pairs within the INMA project, and performed a follow-up functional analysis to help the interpretation of the findings. After multiple-testing correction, we found that methylation at 4 CpGs (cg1548200, cg02986379, cg00866476, and cg14113931) was significantly associated with the general cognitive score, and 2 distinct differentially methylated regions (DMRs) (including 27 CpGs) were significantly associated with each cognitive dimension. Interestingly, the genes annotated to these CpGs, such as DAB2, CEP76, PSMG2, or MECOM, are involved in placenta, fetal, and brain development. Moreover, functional enrichment analyses of suggestive CpGs (p < 1 × 10-4) revealed gene sets involved in placenta development, fetus formation, and brain growth. These findings suggest that placental DNA methylation could be a mechanism contributing to the alteration of important pathways in the placenta that have a consequence on the offspring's brain development and cognitive function.
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Affiliation(s)
- Laia Diez-Ahijado
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Basque Country, Spain
| | - Nora Fernández-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Basque Country, Spain
| | - Mariana F Fernández
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- University of Granada, Biomedical Research Centre, Instituto de Investigación Biosanitaria (ibs.GRANADA), Granada, Spain
| | - Monica Guxens
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jordi Julvez
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Clinical and Epidemiological Neuroscience, Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
| | - Sabrina Llop
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Public Health, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
| | - Maria-Jose Lopez-Espinosa
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Public Health, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
- Faculty of Nursing and Chiropody, University of Valencia, Valencia, Spain
| | - Mikel Subiza-Pérez
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Department of Clinical and Health Psychology and Research Methods, University of the Basque Country UPV/EHU, Avenida Tolosa 70, 20018, Donostia-San Sebastián, Spain
- Bradford Institute for Health Research, Temple Bank House, Bradford Royal Infirmary, Duckworth Lane, BD9 6RJ, Bradford, UK
- Biodonostia Health Research Institute, Group of Environmental Epidemiology and Child Development, Paseo Doctor Begiristain s/n, 20014, Donostia- San Sebastián, Spain
| | - Manuel Lozano
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Public Health, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
- Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine Department, Universitat de València, Valencia, Spain
| | - Jesus Ibarluzea
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Biodonostia Health Research Institute, Group of Environmental Epidemiology and Child Development, Paseo Doctor Begiristain s/n, 20014, Donostia- San Sebastián, Spain
- Ministry of Health of the Basque Government, Sub-Directorate for Public Health and Addictions of Gipuzkoa, San Sebastian, Spain
| | - Jordi Sunyer
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Mariona Bustamante
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Marta Cosin-Tomas
- ISGlobal, Institute for Global Health, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- CIBER Epidemiología y Salud Pública, Madrid, Spain.
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16
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Jiang Y, Qu M, Jiang M, Jiang X, Fernandez S, Porter T, Laws SM, Masters CL, Guo H, Cheng S, Wang C. MethylGenotyper: Accurate Estimation of SNP Genotypes and Genetic Relatedness from DNA Methylation Data. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae044. [PMID: 39353864 PMCID: PMC12016561 DOI: 10.1093/gpbjnl/qzae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/26/2024] [Accepted: 06/06/2024] [Indexed: 10/04/2024]
Abstract
Epigenome-wide association studies (EWAS) are susceptible to widespread confounding caused by population structure and genetic relatedness. Nevertheless, kinship estimation is challenging in EWAS without genotyping data. Here, we proposed MethylGenotyper, a method that for the first time enables accurate genotyping at thousands of single nucleotide polymorphisms (SNPs) directly from commercial DNA methylation microarrays. We modeled the intensities of methylation probes near SNPs with a mixture of three beta distributions corresponding to different genotypes and estimated parameters with an expectation-maximization algorithm. We conducted extensive simulations to demonstrate the performance of the method. When applying MethylGenotyper to the Infinium EPIC array data of 4662 Chinese samples, we obtained genotypes at 4319 SNPs with a concordance rate of 98.26%, enabling the identification of 255 pairs of close relatedness. Furthermore, we showed that MethylGenotyper allows for the estimation of both population structure and cryptic relatedness among 702 Australians of diverse ancestry. We also implemented MethylGenotyper in a publicly available R package (https://github.com/Yi-Jiang/MethylGenotyper) to facilitate future large-scale EWAS.
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Affiliation(s)
- Yi Jiang
- Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Minghan Qu
- Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Minghui Jiang
- Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xuan Jiang
- Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shane Fernandez
- Centre for Precision Health, Edith Cowan University, Perth, WA 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Perth, WA 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia
- Curtin Medical School, Bentley, WA 6102, Australia
| | - Simon M Laws
- Centre for Precision Health, Edith Cowan University, Perth, WA 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia
- Curtin Medical School, Bentley, WA 6102, Australia
| | - Colin L Masters
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Huan Guo
- Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shanshan Cheng
- Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chaolong Wang
- Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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17
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Eisenberg DTA, Ryan CP, Lee NR, Carba DB, MacIsaac JL, Dever K, Atashzay P, Kobor MS, Kuzawa C. DNA methylation-based estimators of telomere length show low correspondence with paternal age at conception and other measures of external validity of telomere length. GeroScience 2024; 46:3957-3969. [PMID: 38466455 PMCID: PMC11226585 DOI: 10.1007/s11357-024-01114-2] [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: 03/27/2023] [Accepted: 02/09/2024] [Indexed: 03/13/2024] Open
Abstract
In humans, DNA methylation (DNAm) based estimators of telomere length (TL) have been shown to better predict TL-associated variables (e.g., age, sex, and mortality) than TL itself. The biological significance of DNAm-based estimators of TL (DNAmTL) is unclear. In vitro DNAmTL shortens with cell replications, even when telomerase is maintaining TL. Telomerase is typically suppressed in humans, except in testes. Accordingly, sperm TL increases with age, and offspring with greater paternal age at conception (PAC) have longer TL. Thus, we expect that PAC associations with DNAmTL can shed light on whether in vivo cell replications in the presence of high telomerase activity (production of sperm) shorten DNAmTL or if PAC-lengthened TL causes lengthened DNAmTL. In a pre-registered analysis, using data from 1733 blood samples from the Philippines, we examined the association between paternal age at conception (PAC) and offspring DNAmTL. We did not find an association between PAC and DNAmTL but found a positive association of paternal grandfather's age at father's conception predicting grandchild's DNAmTL. In post hoc analyses, we examined how DNAmTL versus qPCR-measured TL (qPCR-TL) correlated with measures typically associated with TL. Contrary to previous findings, on almost all measures of external validity (correlations with parental TLs, southern blot TL, and age), qPCR-TL outperformed DNAmTL. The "kilobase" units of DNAm-based estimators of TL showed considerable deviations from southern blot-derived kilobase measures. Our findings suggest that DNAmTL is not a reliable index of inherited aspects of TL and underscores uncertainty about the biological meaning of DNAmTL.
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Affiliation(s)
- Dan T A Eisenberg
- Department of Anthropology, University of Washington, Seattle, WA, USA.
- Center for Studies in Demography and Ecology, University of Washington, Seattle, WA, USA.
| | - Calen P Ryan
- Columbia Aging Center GeroScience Computational Core, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Nanette R Lee
- USC-Office of Population Studies Foundation, Inc., University of San Carlos, Cebu City, Philippines
| | - Delia B Carba
- USC-Office of Population Studies Foundation, Inc., University of San Carlos, Cebu City, Philippines
| | - Julie L MacIsaac
- Edwin S.H. Leong Healthy Aging Program, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Kristy Dever
- Edwin S.H. Leong Healthy Aging Program, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Parmida Atashzay
- Edwin S.H. Leong Healthy Aging Program, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Michael S Kobor
- Edwin S.H. Leong Healthy Aging Program, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Christopher Kuzawa
- Department of Anthropology, Northwestern University; Institute for Policy Research, Northwestern University, Evanston, IL, USA
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18
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Seo S, Kim YA, Lee Y, Kim YJ, Kim BJ, An JH, Jin H, Do AR, Park K, Won S, Seo JH. Epigenetic link between Agent Orange exposure and type 2 diabetes in Korean veterans. Front Endocrinol (Lausanne) 2024; 15:1375459. [PMID: 39072272 PMCID: PMC11272593 DOI: 10.3389/fendo.2024.1375459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/24/2024] [Indexed: 07/30/2024] Open
Abstract
Conflicting findings have been reported regarding the association between Agent Orange (AO) exposure and type 2 diabetes. This study aimed to examine whether AO exposure is associated with the development of type 2 diabetes and to verify the causal relationship between AO exposure and type 2 diabetes by combining DNA methylation with DNA genotype analyses. An epigenome-wide association study and DNA genotype analyses of the blood of AO-exposed and AO-unexposed individuals with type 2 diabetes and that of healthy controls were performed. Methylation quantitative trait locus and Mendelian randomisation analyses were performed to evaluate the causal effect of AO-exposure-identified CpGs on type 2 diabetes. AO-exposed individuals with type 2 diabetes were associated with six hypermethylated CpG sites (cg20075319, cg21757266, cg05203217, cg20102280, cg26081717, and cg21878650) and one hypo-methylated CpG site (cg07553761). Methylation quantitative trait locus analysis showed the methylation levels of some CpG sites (cg20075319, cg20102280, and cg26081717) to be significantly different. Mendelian randomisation analysis showed that CpG sites that were differentially methylated in AO-exposed individuals were causally associated with type 2 diabetes; the reverse causal effect was not significant. These findings reflect the need for further epigenetic studies on the causal relationship between AO exposure and type 2 diabetes.
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Affiliation(s)
- Sujin Seo
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Ye An Kim
- Division of Endocrinology, Department of Internal Medicine, Veterans Health Service Medical Center, Seoul, Republic of Korea
| | - Young Lee
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul, Republic of Korea
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Republic of Korea
| | - Bong-Jo Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Republic of Korea
| | - Jae Hoon An
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
| | - Heejin Jin
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
| | - Ah Ra Do
- Interdisciplinary Program of Bioinformatics, College of National Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kyungtaek Park
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
| | - Sungho Won
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program of Bioinformatics, College of National Sciences, Seoul National University, Seoul, Republic of Korea
| | - Je Hyun Seo
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul, Republic of Korea
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19
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Liang X, Aouizerat BE, So‐Armah K, Cohen MH, Marconi VC, Xu K, Justice AC. DNA methylation-based telomere length is associated with HIV infection, physical frailty, cancer, and all-cause mortality. Aging Cell 2024; 23:e14174. [PMID: 38629454 PMCID: PMC11258465 DOI: 10.1111/acel.14174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 07/21/2024] Open
Abstract
Telomere length (TL) is an important indicator of cellular aging. Shorter TL is associated with several age-related diseases including coronary heart disease, heart failure, diabetes, osteoporosis, and cancer. Recently, a DNA methylation-based TL (DNAmTL) estimator has been developed as an alternative method for directly measuring TL. In this study, we examined the association of DNAmTL with cancer prevalence and mortality risk among people with and without HIV in the Veterans Aging Cohort Study Biomarker Cohort (VACS, N = 1917) and Women's Interagency HIV Study Cohort (WIHS, N = 481). We profiled DNAm in whole blood (VACS) or in peripheral blood mononuclear cells (WIHS) using an array-based method. Cancer prevalence was estimated from electronic medical records and cancer registry data. The VACS Index was used as a measure of physiologic frailty. Models were adjusted for self-reported race and ethnicity, batch, smoking status, alcohol consumption, and five cell types (CD4, CD8, NK, B cell, and monocyte). We found that people with HIV had shorter average DNAmTL than those without HIV infection [beta = -0.25, 95% confidence interval (-0.32, -0.18), p = 1.48E-12]. Greater value of VACS Index [beta = -0.002 (-0.003, -0.001), p = 2.82E-05] and higher cancer prevalence [beta = -0.07 (-0.10, -0.03), p = 1.37E-04 without adjusting age] were associated with shortened DNAmTL. In addition, one kilobase decrease in DNAmTL was associated with a 40% increase in mortality risk [hazard ratio: 0.60 (0.44, 0.82), p = 1.42E-03]. In summary, HIV infection, physiologic frailty, and cancer are associated with shortening DNAmTL, contributing to an increased risk of all-cause mortality.
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Affiliation(s)
- Xiaoyu Liang
- Department of Epidemiology and BiostatisticsMichigan State UniversityEast LansingMichiganUSA
| | - Bradley E. Aouizerat
- Translational Research Center, College of DentistryNew York UniversityNew YorkNew YorkUSA
- Department of Oral and Maxillofacial Surgery, College of DentistryNew York UniversityNew YorkNew YorkUSA
| | - Kaku So‐Armah
- Boston University School of MedicineBostonMassachusettsUSA
| | - Mardge H. Cohen
- Department of MedicineStroger Hospital of Cook CountyChicagoIllinoisUSA
| | - Vincent C. Marconi
- Emory University School of Medicine and Rollins School of Public HealthThe Atlanta Veterans Affairs Medical CenterAtlantaGeorgiaUSA
| | - Ke Xu
- Department of PsychiatryYale School of MedicineNew HavenConnecticutUSA
- VA Connecticut Healthcare SystemWest HavenConnecticutUSA
| | - Amy C. Justice
- VA Connecticut Healthcare SystemWest HavenConnecticutUSA
- Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
- Yale School of Public HealthNew HavenConnecticutUSA
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20
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Shiau S, Zumpano F, Wang Z, Shah J, Tien PC, Ross RD, Sharma A, Yin MT. Epigenetic Aging and Musculoskeletal Outcomes in a Cohort of Women Living With HIV. J Infect Dis 2024; 229:1803-1811. [PMID: 38366369 PMCID: PMC11175700 DOI: 10.1093/infdis/jiae016] [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: 09/07/2023] [Accepted: 01/19/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND The relationship between accelerated epigenetic aging and musculoskeletal outcomes in women with HIV (WWH) has not been studied. METHODS We measured DNA methylation age using the Infinium MethylationEPIC BeadChip in a cohort from the Women's Interagency HIV Study (n = 190) with measures of bone mineral density (BMD) and physical function. We estimated 6 biomarkers of epigenetic aging-epigenetic age acceleration (EAA), extrinsic EAA, intrinsic EAA, GrimAge, PhenoAge, and DNA methylation-estimated telomere length-and evaluated associations of epigenetic aging measures with BMD and physical function. We also performed epigenome-wide association studies to examine associations of DNA methylation signatures with BMD and physical function. RESULTS This study included 118 WWH (mean age, 49.7 years; 69% Black) and 72 without HIV (mean age, 48.9 years; 69% Black). WWH had higher EAA (mean ± SD, 1.44 ± 5.36 vs -1.88 ± 5.07; P < .001) and lower DNA methylation-estimated telomere length (7.13 ± 0.31 vs 7.34 ± 0.23, P < .001) than women without HIV. There were no significant associations between accelerated epigenetic aging and BMD. Rather, measures of accelerated epigenetic aging were associated with lower physical function. CONCLUSIONS Accelerated epigenetic aging was observed in WWH as compared with women without HIV and was associated with lower physical function in both groups.
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Affiliation(s)
- Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey
| | - Francesca Zumpano
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey
| | - Ziyi Wang
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey
| | - Jayesh Shah
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Phyllis C Tien
- Department of Medicine, Veterans Affairs Medical Center
- Department of Medicine, University of California San Francisco
| | - Ryan D Ross
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, Illinois
| | - Anjali Sharma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Michael T Yin
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York
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21
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Leung ML, Abdullaev Z, Santana-Santos L, Skaugen JM, Moore S, Ji J. Microarray-Based DNA Methylation Profiling: Validation Considerations for Clinical Testing. J Mol Diagn 2024; 26:447-455. [PMID: 38378079 PMCID: PMC11238273 DOI: 10.1016/j.jmoldx.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/22/2024] Open
Abstract
Microarray-based methylation profiling has emerged as a valuable tool for refining diagnoses and revealing novel tumor subtypes, particularly in central nervous system tumors. Despite the increasing adoption of this technique in clinical genomic laboratories, no technical standards have been published in establishing minimum criteria for test validation. A working group with experience and expertise in DNA-based methylation profiling tests on central nervous system tumors collaborated to develop practical discussion points and focus on important considerations for validating this test in clinical laboratory settings. The experience in validating this methodology in a clinical setting is summarized. Specifically, the advantages and challenges associated with utilizing an in-house classifier compared with a third-party classifier are highlighted. Additionally, experiences in demonstrating the assay's sensitivity and specificity, establishing minimum sample criteria, and implementing quality control metrics are described. As methylation profiling for tumor classification expands to other tumor types and continues to evolve for various other applications, the critical considerations described here are expected to serve as a guidance for future efforts in establishing professional guidelines for this assay.
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Affiliation(s)
- Marco L Leung
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio; Departments of Pathology and Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio.
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lucas Santana-Santos
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - John M Skaugen
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Stephen Moore
- Department of Molecular and Medical Genetics and Knight Diagnostic Laboratory, Oregon Health & Science University, Portland, Oregon
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
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22
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Hahn G, Prokopenko D, Hecker J, Lutz SM, Mullin K, Sejour L, Hide W, Vlachos I, DeSantis S, Tanzi RE, Lange C. Prediction of disease-free survival for precision medicine using cooperative learning on multi-omic data. Brief Bioinform 2024; 25:bbae267. [PMID: 38836403 PMCID: PMC11151121 DOI: 10.1093/bib/bbae267] [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: 10/17/2023] [Revised: 04/17/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
In precision medicine, both predicting the disease susceptibility of an individual and forecasting its disease-free survival are areas of key research. Besides the classical epidemiological predictor variables, data from multiple (omic) platforms are increasingly available. To integrate this wealth of information, we propose new methodology to combine both cooperative learning, a recent approach to leverage the predictive power of several datasets, and polygenic hazard score models. Polygenic hazard score models provide a practitioner with a more differentiated view of the predicted disease-free survival than the one given by merely a point estimate, for instance computed with a polygenic risk score. Our aim is to leverage the advantages of cooperative learning for the computation of polygenic hazard score models via Cox's proportional hazard model, thereby improving the prediction of the disease-free survival. In our experimental study, we apply our methodology to forecast the disease-free survival for Alzheimer's disease (AD) using three layers of data. One layer contains epidemiological variables such as sex, APOE (apolipoprotein E, a genetic risk factor for AD) status and 10 leading principal components. Another layer contains selected genomic loci, and the last layer contains methylation data for selected CpG sites. We demonstrate that the survival curves computed via cooperative learning yield an AUC of around $0.7$, above the state-of-the-art performance of its competitors. Importantly, the proposed methodology returns (1) a linear score that can be easily interpreted (in contrast to machine learning approaches), and (2) a weighting of the predictive power of the involved data layers, allowing for an assessment of the importance of each omic (or other) platform. Similarly to polygenic hazard score models, our methodology also allows one to compute individual survival curves for each patient.
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Affiliation(s)
- Georg Hahn
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, 02115, Boston, MA, USA
| | - Dmitry Prokopenko
- Department of Neurology, Genetics and Aging Research Unit, McCance Center for Brain Health, Massachusetts General Hospital, 55 Fruit Street, 02114, Boston, MA, USA
| | - Julian Hecker
- Channing Divsion of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, 02115, Boston, MA, USA
| | - Sharon M Lutz
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, 02115, Boston, MA, USA
| | - Kristina Mullin
- Department of Neurology, Genetics and Aging Research Unit, McCance Center for Brain Health, Massachusetts General Hospital, 55 Fruit Street, 02114, Boston, MA, USA
| | - Leinal Sejour
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, 02215, Boston, MA, USA
| | - Winston Hide
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, 02215, Boston, MA, USA
| | - Ioannis Vlachos
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, 02215, Boston, MA, USA
| | - Stacia DeSantis
- Houston Campus, The University of Texas Health Science Center, 1200 Pressler Street, 77030, Houston, TX, USA
| | - Rudolph E Tanzi
- Department of Neurology, Genetics and Aging Research Unit, McCance Center for Brain Health, Massachusetts General Hospital, 55 Fruit Street, 02114, Boston, MA, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, 02115, Boston, MA, USA
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23
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Campbell KA, Colacino JA, Dou J, Dolinoy DC, Park SK, Loch-Caruso R, Padmanabhan V, Bakulski KM. Placental and Immune Cell DNA Methylation Reference Panel for Bulk Tissue Cell Composition Estimation in Epidemiological Studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.588886. [PMID: 38766167 PMCID: PMC11100803 DOI: 10.1101/2024.05.06.588886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
To distinguish DNA methylation (DNAm) from cell proportion changes in whole placental tissue research, we developed a robust cell type-specific DNAm reference to estimate cell composition. We collated newly collected and existing cell type DNAm profiles quantified via Illumina EPIC or 450k microarrays. To estimate cell composition, we deconvoluted whole placental samples (n=36) with robust partial correlation based on the top 50 hyper- and hypomethylated sites per cell type. To test deconvolution performance, we evaluated RMSE in predicting principal component one of DNAm variation in 204 external placental samples. We analyzed DNAm profiles (n=368,435 sites) from 12 cell types: cytotrophoblasts (n=18), endothelial cells (n=19), Hofbauer cells (n=26), stromal cells (n=21), syncytiotrophoblasts (n=4), six lymphocyte types (n=36), and nucleated red blood cells (n=11). Median cell composition was consistent with placental biology: 60.4% syncytiotrophoblast, 17.1% stromal, 8.8% endothelial, 4.5% cytotrophoblast, 3.9% Hofbauer, 1.7% nucleated red blood cells, and 1.2% neutrophils. Our expanded reference outperformed an existing reference in predicting DNAm variation (15.4% variance explained, IQR=21.61) with cell composition estimates (RMSE:10.51 vs. 11.43, p-value<0.001). This cell type reference can robustly estimate cell composition from whole placental DNAm data to detect important cell types, reveal biological mechanisms, and improve casual inference.
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Affiliation(s)
- Kyle A. Campbell
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Justin A. Colacino
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - John Dou
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana C. Dolinoy
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sung Kyun Park
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rita Loch-Caruso
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vasantha Padmanabhan
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Obstetrics and Gynecology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kelly M. Bakulski
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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Graves AJ, Danoff JS, Kim M, Brindley SR, Skyberg AM, Giamberardino SN, Lynch ME, Straka BC, Lillard TS, Gregory SG, Connelly JJ, Morris JP. Accelerated epigenetic age is associated with whole-brain functional connectivity and impaired cognitive performance in older adults. Sci Rep 2024; 14:9646. [PMID: 38671048 PMCID: PMC11053089 DOI: 10.1038/s41598-024-60311-3] [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: 01/05/2024] [Accepted: 04/21/2024] [Indexed: 04/28/2024] Open
Abstract
While chronological age is a strong predictor for health-related risk factors, it is an incomplete metric that fails to fully characterize the unique aging process of individuals with different genetic makeup, neurodevelopment, and environmental experiences. Recent advances in epigenomic array technologies have made it possible to generate DNA methylation-based biomarkers of biological aging, which may be useful in predicting a myriad of cognitive abilities and functional brain network organization across older individuals. It is currently unclear which cognitive domains are negatively correlated with epigenetic age above and beyond chronological age, and it is unknown if functional brain organization is an important mechanism for explaining these associations. In this study, individuals with accelerated epigenetic age (i.e. AgeAccelGrim) performed worse on tasks that spanned a wide variety of cognitive faculties including both fluid and crystallized intelligence (N = 103, average age = 68.98 years, 73 females, 30 males). Additionally, fMRI connectome-based predictive models suggested a mediating mechanism of functional connectivity on epigenetic age acceleration-cognition associations primarily in medial temporal lobe and limbic structures. This research highlights the important role of epigenetic aging processes on the development and maintenance of healthy cognitive capacities and function of the aging brain.
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Affiliation(s)
| | | | - Minah Kim
- University of Virginia, Charlottesville, USA
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25
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Li JL, Jain N, Tamayo LI, Tong L, Jasmine F, Kibriya MG, Demanelis K, Oliva M, Chen LS, Pierce BL. The association of cigarette smoking with DNA methylation and gene expression in human tissue samples. Am J Hum Genet 2024; 111:636-653. [PMID: 38490207 PMCID: PMC11023923 DOI: 10.1016/j.ajhg.2024.02.012] [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: 08/14/2023] [Revised: 02/17/2024] [Accepted: 02/21/2024] [Indexed: 03/17/2024] Open
Abstract
Cigarette smoking adversely affects many aspects of human health, and epigenetic responses to smoking may reflect mechanisms that mediate or defend against these effects. Prior studies of smoking and DNA methylation (DNAm), typically measured in leukocytes, have identified numerous smoking-associated regions (e.g., AHRR). To identify smoking-associated DNAm features in typically inaccessible tissues, we generated array-based DNAm data for 916 tissue samples from the GTEx (Genotype-Tissue Expression) project representing 9 tissue types (lung, colon, ovary, prostate, blood, breast, testis, kidney, and muscle). We identified 6,350 smoking-associated CpGs in lung tissue (n = 212) and 2,735 in colon tissue (n = 210), most not reported previously. For all 7 other tissue types (sample sizes 38-153), no clear associations were observed (false discovery rate 0.05), but some tissues showed enrichment for smoking-associated CpGs reported previously. For 1,646 loci (in lung) and 22 (in colon), smoking was associated with both DNAm and local gene expression. For loci detected in both lung and colon (e.g., AHRR, CYP1B1, CYP1A1), top CpGs often differed between tissues, but similar clusters of hyper- or hypomethylated CpGs were observed, with hypomethylation at regulatory elements corresponding to increased expression. For lung tissue, 17 hallmark gene sets were enriched for smoking-associated CpGs, including xenobiotic- and cancer-related gene sets. At least four smoking-associated regions in lung were impacted by lung methylation quantitative trait loci (QTLs) that co-localize with genome-wide association study (GWAS) signals for lung function (FEV1/FVC), suggesting epigenetic alterations can mediate the effects of smoking on lung health. Our multi-tissue approach has identified smoking-associated regions in disease-relevant tissues, including effects that are shared across tissue types.
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Affiliation(s)
- James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL 60637, USA
| | - Niyati Jain
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Committee on Genetics, Genomics, Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Lizeth I Tamayo
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Lin Tong
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Farzana Jasmine
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Kathryn Demanelis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA; UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Meritxell Oliva
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Comprehensive Cancer Center, University of Chicago, Chicago, IL 60637, USA.
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26
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Labaut L, Lage-Castellanos A, Rodrigo MJ, Herrero-Roldán S, Mitchell C, Fisher J, León I. Mother adversity and co-residence time impact mother-child similarity in genome-wide and gene-specific methylation profiles. Clin Epigenetics 2024; 16:44. [PMID: 38509601 PMCID: PMC10953278 DOI: 10.1186/s13148-024-01655-5] [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: 12/15/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND The effects of adverse life events on physical and psychological health, with DNA methylation (DNAm) as a critical underlying mechanism, have been extensively studied. However, the epigenetic resemblance between mother and child in the context of neglectful caregiving, and whether it may be shaped by the emotional impact of maternal stressful events and the duration of co-residence (indexed by child age), remains unknown. The present study examined mother-child similarity in methylation profiles, considering the potential effect of mother adversity, mother empathy, neglect-control group, child age (an index of years of mother-child co-residence), and mother age. Using Illumina Epic arrays, we quantified DNAm in 115 mother-child saliva samples. We obtained a methylation similarity index by computing correlation coefficients between methylation profiles within dyads, for the entire epigenome, and five specific genes related to stress and empathy: NR3C1, FKPB5, OXTR, SCL6A4, and BDNF. RESULTS The methylation profiles of the mother-child familial pairs significantly correlated as compared to mother-child random pairs for the entire epigenome and NR3C1, FKBP5, OXTR and BDNF genes. Next, multiple linear regression models observed associations of mother adversity, child age, and neglect-control group on mother-child methylation similarity, only significant in mother-child familial pairs, after correcting for multiple comparisons. Higher mother adversity was associated with lower mother-child methylation similarity for the epigenome-wide analysis, for the BDNF gene, and in the neglect-control group for the OXTR gene. In turn, being an older child (longer co-residence) was associated with higher mother-child methylation similarity. CONCLUSIONS Mother adversity and co-residence time are modulating factors in the intergenerational methylation process that offer a window into development-dependent adaptations that can be affected by both hereditary and environmental factors, significantly observed only in biological dyads. A twofold implication for child well-being emerges, one is positive in that children of mothers exposed to life adversity or neglect did not necessarily inherit their methylation patterns. The other is concerning due to the influence of time spent living together, which affects similarity with the mother and potentially increases the risk of inheriting an epigenetic profile associated with future dysfunctional parenting patterns. This underscores the importance of the 'the earlier, the better' recommendation by the Child Protection System, which is not always followed.
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Affiliation(s)
- Lucía Labaut
- Instituto Universitario de Neurociencia, Campus de Guajara, Universidad de La Laguna, 38201, La Laguna, Tenerife, Spain
| | - Agustín Lage-Castellanos
- Department of NeuroInformatics, Cuban Center for Neuroscience, Havana, Cuba
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - María José Rodrigo
- Instituto Universitario de Neurociencia, Campus de Guajara, Universidad de La Laguna, 38201, La Laguna, Tenerife, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Silvia Herrero-Roldán
- Instituto Universitario de Neurociencia, Campus de Guajara, Universidad de La Laguna, 38201, La Laguna, Tenerife, Spain
- Facultad de Ciencias Sociales Aplicadas y de la Comunicación, UNIE Universidad, Madrid, Spain
| | - Colter Mitchell
- Institute for Social Research, University of Michigan, Ann Abor, MI, USA
| | - Jonah Fisher
- Institute for Social Research, University of Michigan, Ann Abor, MI, USA
| | - Inmaculada León
- Instituto Universitario de Neurociencia, Campus de Guajara, Universidad de La Laguna, 38201, La Laguna, Tenerife, Spain.
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de La Laguna, Spain.
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27
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Malta TM, Sabedot TS, Morosini NS, Datta I, Garofano L, Vallentgoed W, Varn FS, Aldape K, D'Angelo F, Bakas S, Barnholtz-Sloan JS, Gan HK, Hasanain M, Hau AC, Johnson KC, Cazacu S, deCarvalho AC, Khasraw M, Kocakavuk E, Kouwenhoven MC, Migliozzi S, Niclou SP, Niers JM, Ormond DR, Paek SH, Reifenberger G, Sillevis Smitt PA, Smits M, Stead LF, van den Bent MJ, Van Meir EG, Walenkamp A, Weiss T, Weller M, Westerman BA, Ylstra B, Wesseling P, Lasorella A, French PJ, Poisson LM, Verhaak RG, Iavarone A, Noushmehr H. The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen. Cancer Res 2024; 84:741-756. [PMID: 38117484 PMCID: PMC10911804 DOI: 10.1158/0008-5472.can-23-2093] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/15/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
Tumor adaptation or selection is thought to underlie therapy resistance in glioma. To investigate longitudinal epigenetic evolution of gliomas in response to therapeutic pressure, we performed an epigenomic analysis of 132 matched initial and recurrent tumors from patients with IDH-wildtype (IDHwt) and IDH-mutant (IDHmut) glioma. IDHwt gliomas showed a stable epigenome over time with relatively low levels of global methylation. The epigenome of IDHmut gliomas showed initial high levels of genome-wide DNA methylation that was progressively reduced to levels similar to those of IDHwt tumors. Integration of epigenomics, gene expression, and functional genomics identified HOXD13 as a master regulator of IDHmut astrocytoma evolution. Furthermore, relapse of IDHmut tumors was accompanied by histologic progression that was associated with survival, as validated in an independent cohort. Finally, the initial cell composition of the tumor microenvironment varied between IDHwt and IDHmut tumors and changed differentially following treatment, suggesting increased neoangiogenesis and T-cell infiltration upon treatment of IDHmut gliomas. This study provides one of the largest cohorts of paired longitudinal glioma samples with epigenomic, transcriptomic, and genomic profiling and suggests that treatment of IDHmut glioma is associated with epigenomic evolution toward an IDHwt-like phenotype. SIGNIFICANCE Standard treatments are related to loss of DNA methylation in IDHmut glioma, resulting in epigenetic activation of genes associated with tumor progression and alterations in the microenvironment that resemble treatment-naïve IDHwt glioma.
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Affiliation(s)
- Tathiane M. Malta
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thais S. Sabedot
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | | | - Indrani Datta
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | - Luciano Garofano
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Wies Vallentgoed
- Neurology Department, The Brain Tumour Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Frederick S. Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | | | - Fulvio D'Angelo
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Spyridon Bakas
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Hui K. Gan
- Olivia Newton-John Cancer Research Institute, Austin Health, Heidelberg, Melbourne, Australia
| | - Mohammad Hasanain
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | | | - Kevin C. Johnson
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
| | - Simona Cazacu
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | - Ana C. deCarvalho
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | | | - Emre Kocakavuk
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center (WTZ), National Center for Tumor Diseases (NCT) West, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Mathilde C.M. Kouwenhoven
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Simona Migliozzi
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | | | - Johanna M. Niers
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - D. Ryan Ormond
- University of Colorado School of Medicine, Department of Neurosurgery, Aurora, Colorado
| | - Sun Ha Paek
- Department of Neurosurgery, Cancer Research Institute, Hypoxia Ischemia Disease Institute, Seoul National University, Seoul, Republic of Korea (South)
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Dusseldorf, Germany
| | - Peter A. Sillevis Smitt
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- The Brain Tumour Centre, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Marion Smits
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Lucy F. Stead
- Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Martin J. van den Bent
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- The Brain Tumour Centre, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Erwin G. Van Meir
- Department of Neurosurgery and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Tobias Weiss
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Bart A. Westerman
- Department of Neurology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Pieter Wesseling
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands
- Laboratory for Childhood Cancer Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Anna Lasorella
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida
| | - Pim J. French
- Neurology Department, The Brain Tumour Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Laila M. Poisson
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
| | - Roel G.W. Verhaak
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
- Department of Neurosurgery, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Antonio Iavarone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Houtan Noushmehr
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, Michigan
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28
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Willems YE, deSteiguer A, Tanksley PT, Vinnik L, Fraemke D, Okbay A, Richter D, Wagner GG, Hertwig R, Koellinger P, Tucker-Drob EM, Harden KP, Raffington L. Self-control is associated with health-relevant disparities in buccal DNA-methylation measures of biological aging in older adults. Clin Epigenetics 2024; 16:22. [PMID: 38331797 PMCID: PMC10854186 DOI: 10.1186/s13148-024-01637-7] [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: 09/08/2023] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
Self-control is a personality dimension that is associated with better physical health and a longer lifespan. Here, we examined (1) whether self-control is associated with buccal and saliva DNA-methylation (DNAm) measures of biological aging quantified in children, adolescents, and adults, and (2) whether biological aging measured in buccal DNAm is associated with self-reported health. Following preregistered analyses, we computed two DNAm measures of advanced biological age (principal-component PhenoAge and GrimAge Acceleration) and a DNAm measure of pace of aging (DunedinPACE) in buccal samples from the German Socioeconomic Panel Study (SOEP-G[ene], n = 1058, age range 0-72, Mage = 42.65) and saliva samples from the Texas Twin Project (TTP, n = 1327, age range 8-20, Mage = 13.50). We found that lower self-control was associated with advanced biological age in older adults (PhenoAge Acceleration β = - .34, [- .51, - .17], p < .001; GrimAge Acceleration β = - .34, [- .49, - .19], p < .001), but not young adults, adolescents or children. These associations remained statistically robust even after correcting for possible confounders such as socioeconomic contexts, BMI, or genetic correlates of low self-control. Moreover, a faster pace of aging and advanced biological age measured in buccal DNAm were associated with self-reported disease (PhenoAge Acceleration: β = .13 [.06, .19], p < .001; GrimAge Acceleration: β = .19 [.12, .26], p < .001; DunedinPACE: β = .09 [.02, .17], p = .01). However, effect sizes were weaker than observations in blood, suggesting that customization of DNAm aging measures to buccal and saliva tissues may be necessary. Our findings are consistent with the hypothesis that self-control is associated with health via pathways that accelerate biological aging in older adults.
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Affiliation(s)
- Y E Willems
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany
| | - A deSteiguer
- Population Research Center, The University of Texas, Austin, USA
| | - P T Tanksley
- Population Research Center, The University of Texas, Austin, USA
| | - L Vinnik
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany
| | - D Fraemke
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany
| | - A Okbay
- School of Business and Economics, Economics Fellow, Tinbergen Institute, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - D Richter
- SHARE Berlin Institute GmbH, Berlin, Germany
- Department of Education and Psychology, Freie Universität Berlin, Berlin, Germany
| | - G G Wagner
- Max Planck Institute for Human Development, Berlin, Germany
- German Socio Economic Panel Study (SOEP), Berlin, Germany
| | - R Hertwig
- Max Planck Institute for Human Development, Berlin, Germany
| | - P Koellinger
- School of Business and Economics, Economics Fellow, Tinbergen Institute, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - E M Tucker-Drob
- Population Research Center, The University of Texas, Austin, USA
| | - K P Harden
- Population Research Center, The University of Texas, Austin, USA
| | - Laurel Raffington
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany.
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29
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Pike SC, Havrda M, Gilli F, Zhang Z, Salas LA. Immunological shifts during early-stage Parkinson's disease identified with DNA methylation data on longitudinally collected blood samples. NPJ Parkinsons Dis 2024; 10:21. [PMID: 38212355 PMCID: PMC10784484 DOI: 10.1038/s41531-023-00626-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease in the United States. Decades before motor symptoms manifest, non-motor symptoms such as hyposmia and rapid eye movement (REM) sleep behavior disorder are highly predictive of PD. Previous immune profiling studies have identified alterations to the proportions of immune cells in the blood of clinically defined PD patients. However, it remains unclear if these phenotypes manifest before the clinical diagnosis of PD. We utilized longitudinal DNA methylation (DNAm) microarray data from the Parkinson's Progression Marker's Initiative (PPMI) to perform immune profiling in clinically defined PD and prodromal PD patients (Prod). We identified previously reported changes in neutrophil, monocyte, and T cell numbers in PD patients. Additionally, we noted previously unrecognized decreases in the naive B cell compartment in the defined PD and Prod patient group. Over time, we observed the proportion of innate immune cells in PD blood increased, but the proportion of adaptive immune cells decreased. We identified decreases in T and B cell subsets associated with REM sleep disturbances and early cognitive decline. Lastly, we identified increases in B memory cells associated with both genetic (LRRK2 genotype) and infectious (cytomegalovirus seropositivity) risk factors of PD. Our analysis shows that the peripheral immune system is dynamic as the disease progresses. The study provides a platform to understand how and when peripheral immune alterations occur in PD and whether intervention at particular stages may be therapeutically advantageous.
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Affiliation(s)
- Steven C Pike
- Integrative Neuroscience at Dartmouth, Guarini School of Graduate and Advanced Studies at Dartmouth College, Hanover, NH, USA.
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA.
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA.
| | - Matthew Havrda
- Integrative Neuroscience at Dartmouth, Guarini School of Graduate and Advanced Studies at Dartmouth College, Hanover, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Francesca Gilli
- Integrative Neuroscience at Dartmouth, Guarini School of Graduate and Advanced Studies at Dartmouth College, Hanover, NH, USA
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Lucas A Salas
- Integrative Neuroscience at Dartmouth, Guarini School of Graduate and Advanced Studies at Dartmouth College, Hanover, NH, USA.
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA.
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30
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Aronoff JE, McDade TW, Adair LS, Lee NR, Carba DB, MacIsaac JL, Dever K, Atashzay P, Kobor MS, Kuzawa CW. Socioeconomic status is negatively associated with immunosenescence but positively associated with inflammation among middle-aged women in Cebu, Philippines. Brain Behav Immun 2024; 115:101-108. [PMID: 37820972 PMCID: PMC10841485 DOI: 10.1016/j.bbi.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/30/2023] [Accepted: 10/07/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Socioeconomic status (SES) gradients in health are well-documented, and while biological pathways are incompletely understood, chronic inflammation and accelerated immune aging (immunosenescence) among lower SES individuals have been implicated. However, previous findings have come from samples in higher income countries, and it is unclear how generalizable they are to lower- and middle-income countries (LMIC) with different infectious exposures and where adiposity-an important contributor to chronic inflammation-might show different SES patterning. To address this gap, we explored associations between SES and inflammation and immunosenescence in a sample of women in Cebu, Philippines. METHODS Data came from the mothers of the Cebu Longitudinal Health and Nutrition Survey birth cohort (mean age: 47.7, range: 35-69 years). SES was measured as a combination of annual household income, education level, and assets. Chronic inflammation was measured using C-reactive protein (CRP) in plasma samples from 1,834 women. Immunosenescence was measured by the abundance of exhausted CD8T (CD8 + CD28-CD45RA-) and naïve CD8T and CD4T cells, estimated from DNA methylation in whole blood in a random subsample of 1,028. Possible mediators included waist circumference and a collection of proxy measures of pathogen exposure. RESULTS SES was negatively associated with the measures of immunosenescence, with slight evidence for mediation by a proxy measure for pathogen exposure from the household's drinking water source. In contrast, SES was positively associated with CRP, which was explained by the positive association with waist circumference. CONCLUSIONS Similar to higher income populations, in Cebu there is an SES-gradient in pathogen exposures and immunosenescence. However, lifestyle changes occurring more rapidly among higher SES individuals is contributing to a positive association between SES and adiposity and inflammation. Our results suggest more studies are needed to clarify the relationship between SES and inflammation and immunosenescence across LMIC.
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Affiliation(s)
- Jacob E Aronoff
- Department of Anthropology, Northwestern University, Evanston, IL, USA; Institute for Policy Research, Northwestern University, Evanston, IL, USA.
| | - Thomas W McDade
- Department of Anthropology, Northwestern University, Evanston, IL, USA; Institute for Policy Research, Northwestern University, Evanston, IL, USA
| | - Linda S Adair
- Department of Nutrition, Gillings School of Global Public Health, Carolina Population Center, CB #8120, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nanette R Lee
- Office of Population Studies Foundation, University of San Carlos, Cebu City, Philippines
| | - Delia B Carba
- Office of Population Studies Foundation, University of San Carlos, Cebu City, Philippines
| | - Julia L MacIsaac
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Edwin S.H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Kristy Dever
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Edwin S.H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Parmida Atashzay
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Edwin S.H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Michael S Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Edwin S.H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Christopher W Kuzawa
- Department of Anthropology, Northwestern University, Evanston, IL, USA; Institute for Policy Research, Northwestern University, Evanston, IL, USA
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Reiner A, Bakulski KM, Fisher JD, Dou JF, Schneper L, Mitchell C, Notterman DA, Zawistowski M, Ware EB. Sex-specific DNA methylation in saliva from the multi-ethnic Future of Families and Child Wellbeing Study. Epigenetics 2023; 18:2222244. [PMID: 37300819 PMCID: PMC10259311 DOI: 10.1080/15592294.2023.2222244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/11/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
The prevalence and severity of many diseases differs by sex, potentially due to sex-specific patterns in DNA methylation. Autosomal sex-specific differences in DNA methylation have been observed in cord blood and placental tissue but are not well studied in saliva or in diverse populations. We sought to characterize sex-specific DNA methylation on autosomal chromosomes in saliva samples from children in the Future of Families and Child Wellbeing Study, a multi-ethnic prospective birth cohort containing an oversampling of Black, Hispanic and low-income families. DNA methylation from saliva samples was analysed on 796 children (50.6% male) at both ages 9 and 15 with DNA methylation measured using the Illumina HumanMethylation 450k array. An epigenome-wide association analysis of the age 9 samples identified 8,430 sex-differentiated autosomal DNA methylation sites (P < 2.4 × 10-7), of which 76.2% had higher DNA methylation in female children. The strongest sex-difference was in the cg26921482 probe, in the AMDHD2 gene, with 30.6% higher DNA methylation in female compared to male children (P < 1 × 10-300). Treating the age 15 samples as an internal replication set, we observed highly consistent results between the ages 9 and 15 measurements, indicating stable and replicable sex-differentiation. Further, we directly compared our results to previously published DNA methylation sex differences in both cord blood and saliva and again found strong consistency. Our findings support widespread and robust sex-differential DNA methylation across age, human tissues, and populations. These findings help inform our understanding of potential biological processes contributing to sex differences in human physiology and disease.
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Affiliation(s)
- Allison Reiner
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Kelly M. Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonah D. Fisher
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Lisa Schneper
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Colter Mitchell
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Erin B. Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
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Quinn EB, Hsiao CJ, Maisha FM, Mulligan CJ. Prenatal maternal stress is associated with site-specific and age acceleration changes in maternal and newborn DNA methylation. Epigenetics 2023; 18:2222473. [PMID: 37300821 PMCID: PMC10259347 DOI: 10.1080/15592294.2023.2222473] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/10/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
Prenatal maternal stress has a negative impact on child health but the mechanisms through which maternal stress affects child health are unclear. Epigenetic variation, such as DNA methylation, is a likely mechanistic candidate as DNA methylation is sensitive to environmental insults and can regulate long-term changes in gene expression. We recruited 155 mother-newborn dyads in the Democratic Republic of Congo to investigate the effects of maternal stress on DNA methylation in mothers and newborns. We used four measures of maternal stress to capture a range of stressful experiences: general trauma, sexual trauma, war trauma, and chronic stress. We identified differentially methylated positions (DMPs) associated with general trauma, sexual trauma, and war trauma in both mothers and newborns. No DMPs were associated with chronic stress. Sexual trauma was positively associated with epigenetic age acceleration across several epigenetic clocks in mothers. General trauma and war trauma were positively associated with newborn epigenetic age acceleration using the extrinsic epigenetic age clock. We tested the top DMPs for enrichment of DNase I hypersensitive sites (DHS) and found no enrichment in mothers. In newborns, top DMPs associated with war trauma were enriched for DHS in embryonic and foetal cell types. Finally, one of the top DMPs associated with war trauma in newborns also predicted birthweight, completing the cycle from maternal stress to DNA methylation to newborn health outcome. Our results indicate that maternal stress is associated with site-specific changes in DNAm and epigenetic age acceleration in both mothers and newborns.
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Affiliation(s)
- Edward B. Quinn
- Department of Anthropology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Chu J. Hsiao
- Department of Anthropology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- College of Medicine, University of Florida, Gainesville, FL, USA
| | - Felicien M. Maisha
- Department of Anthropology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Democratic Republic of Congo, HEAL Africa Hospital, Goma, USA
- Democratic Republic of Congo, Maisha Institute, Goma, USA
| | - Connie J. Mulligan
- Department of Anthropology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
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Weckmann M, Reddy KD. Epigenome-wide association studies: the exposures of yesterday form the methylations of tomorrow. Eur Respir J 2023; 62:2301552. [PMID: 38128955 DOI: 10.1183/13993003.01552-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023]
Affiliation(s)
- Markus Weckmann
- Division of Epigenetics in Chronic Lung Disease, Priority Area Chronic Lung Diseases, Leibniz Lung Center, Research Center Borstel, Borstel, Germany
- Airway Research Centre North (ARCN), German Centre for Lung Research (DZL), Germany
- Department of Pediatric Pneumology and Allergology, University Children's Hospital Lübeck, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Karosham Diren Reddy
- Division of Epigenetics in Chronic Lung Disease, Priority Area Chronic Lung Diseases, Leibniz Lung Center, Research Center Borstel, Borstel, Germany
- Airway Research Centre North (ARCN), German Centre for Lung Research (DZL), Germany
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Barcelona V, Abuaish S, Lee S, Harkins S, Butler A, Tycko B, Baccarelli AA, Walsh K, Monk CE. Stress and DNA Methylation of Blood Leukocytes among Pregnant Latina Women. EPIGENOMES 2023; 7:27. [PMID: 37987302 PMCID: PMC10660842 DOI: 10.3390/epigenomes7040027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
Latinas experience physical and psychological stressors in pregnancy leading to increased morbidity and higher risk for adverse birth outcomes. Epigenetic changes, including DNA methylation (DNAm), have been proposed as markers to create more refined risk stratification, yet few of these studies have examined these changes in Latinas. We conducted a secondary analysis of stored blood leukocytes of Latina women (n = 58) enrolled in a larger National Institutes of Health funded R01 project (2011-2016). We examined DNAm on eight candidate stress genes to compare physically and psychologically stressed participants to healthy (low stress) participants. We found unique CpGs that were differentially methylated in stressed women early- and mid-pregnancy compared to the healthy group, though none remained significant after FDR correction. Both physical and psychological stress were associated with hypomethylation at two consecutive CpG sites on NR3C1 in early pregnancy and one CpG site on NR3C1 in mid-pregnancy before adjustment. Stress was also associated with hypomethylation at two CpG sites on FKBP5 in early and mid-pregnancy but were no longer significant after FDR adjustment. Though we did not find statistically significant differences in DNAm during pregnancy between stressed and healthy women in this sample, signals were consistent with previous findings. Future work in larger samples should further examine the associations between stress and DNAm in pregnancy as this mechanism may explain underlying perinatal health inequities.
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Affiliation(s)
| | - Sameera Abuaish
- Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Seonjoo Lee
- Mental Health Data Science, New York State Psychiatric Institute, New York, NY 10032, USA;
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, NY 10032, USA
- Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA;
| | - Sarah Harkins
- Columbia University School of Nursing, New York, NY 10032, USA;
| | - Ashlie Butler
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA;
| | - Benjamin Tycko
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA;
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA;
| | - Kate Walsh
- Department of Psychology, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Catherine E. Monk
- Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA;
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA;
- New York State Psychiatric Institute, New York, NY 10032, USA
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Perez-Garcia J, Pino-Yanes M, Plender EG, Everman JL, Eng C, Jackson ND, Moore CM, Beckman KB, Medina V, Sharma S, Winnica DE, Holguin F, Rodríguez-Santana J, Villar J, Ziv E, Seibold MA, Burchard EG. Epigenomic response to albuterol treatment in asthma-relevant airway epithelial cells. Clin Epigenetics 2023; 15:156. [PMID: 37784136 PMCID: PMC10546710 DOI: 10.1186/s13148-023-01571-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Albuterol is the first-line asthma medication used in diverse populations. Although DNA methylation (DNAm) is an epigenetic mechanism involved in asthma and bronchodilator drug response (BDR), no study has assessed whether albuterol could induce changes in the airway epithelial methylome. We aimed to characterize albuterol-induced DNAm changes in airway epithelial cells, and assess potential functional consequences and the influence of genetic variation and asthma-related clinical variables. RESULTS We followed a discovery and validation study design to characterize albuterol-induced DNAm changes in paired airway epithelial cultures stimulated in vitro with albuterol. In the discovery phase, an epigenome-wide association study using paired nasal epithelial cultures from Puerto Rican children (n = 97) identified 22 CpGs genome-wide associated with repeated-use albuterol treatment (p < 9 × 10-8). Albuterol predominantly induced a hypomethylation effect on CpGs captured by the EPIC array across the genome (probability of hypomethylation: 76%, p value = 3.3 × 10-5). DNAm changes on the CpGs cg23032799 (CREB3L1), cg00483640 (MYLK4-LINC01600), and cg05673431 (KSR1) were validated in nasal epithelia from 10 independent donors (false discovery rate [FDR] < 0.05). The effect on the CpG cg23032799 (CREB3L1) was cross-tissue validated in bronchial epithelial cells at nominal level (p = 0.030). DNAm changes in these three CpGs were shown to be influenced by three independent genetic variants (FDR < 0.05). In silico analyses showed these polymorphisms regulated gene expression of nearby genes in lungs and/or fibroblasts including KSR1 and LINC01600 (6.30 × 10-14 ≤ p ≤ 6.60 × 10-5). Additionally, hypomethylation at the CpGs cg10290200 (FLNC) and cg05673431 (KSR1) was associated with increased gene expression of the genes where they are located (FDR < 0.05). Furthermore, while the epigenetic effect of albuterol was independent of the asthma status, severity, and use of medication, BDR was nominally associated with the effect on the CpG cg23032799 (CREB3L1) (p = 0.004). Gene-set enrichment analyses revealed that epigenomic modifications of albuterol could participate in asthma-relevant processes (e.g., IL-2, TNF-α, and NF-κB signaling pathways). Finally, nine differentially methylated regions were associated with albuterol treatment, including CREB3L1, MYLK4, and KSR1 (adjusted p value < 0.05). CONCLUSIONS This study revealed evidence of epigenetic modifications induced by albuterol in the mucociliary airway epithelium. The epigenomic response induced by albuterol might have potential clinical implications by affecting biological pathways relevant to asthma.
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Grants
- R01 ES015794 NIEHS NIH HHS
- R01 HL120393 NHLBI NIH HHS
- R01ES015794, R21ES24844 NIEHS NIH HHS
- UM1 HG008901 NHGRI NIH HHS
- R01MD010443, R56MD013312 NIMHD NIH HHS
- R01 HL135156 NHLBI NIH HHS
- R01 HL128439 NHLBI NIH HHS
- R01 HL117004 NHLBI NIH HHS
- R21 ES024844 NIEHS NIH HHS
- R01 HL117626 NHLBI NIH HHS
- R56 MD013312 NIMHD NIH HHS
- R01 MD010443 NIMHD NIH HHS
- R01 HL155024 NHLBI NIH HHS
- R01HL155024-01, HHSN268201600032I, 3R01HL-117626-02S1, HHSN268201800002I, 3R01HL117004-02S3, 3R01HL-120393-02S1, R01HL117004, R01HL128439, R01HL135156, X01HL134589 NHLBI NIH HHS
- HHSN268201600032C NHLBI NIH HHS
- U24 HG008956 NHGRI NIH HHS
- Ministerio de Universidades
- Ministerio de Ciencia e Innovación
- Instituto de Salud Carlos III
- National Heart, Lung, and Blood Institute
- National Human Genome Research Institute
- National Institute of Environmental Health Sciences
- National Institute on Minority Health and Health Disparities
- The Centers for Common Disease Genomics of the Genome Sequencing Program
- Tobacco-Related Disease Research Program
- Sandler Family Foundation
- American Asthma Foundation
- Amos Medical Faculty Development Program from the Robert Wood Johnson Foundation
- Harry Wm. and Diana V. Hind Distinguished Professor in Pharmaceutical Sciences II
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Affiliation(s)
- Javier Perez-Garcia
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Canary Islands, Spain.
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Canary Islands, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), La Laguna, Spain.
| | - Elizabeth G Plender
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Jamie L Everman
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Camille M Moore
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Biomedical Research, National Jewish Health, Denver, CO, USA
- Department of Biostatistics and Informatics, University of Colorado, Denver, CO, USA
| | - Kenneth B Beckman
- University of Minnesota Genomics Center (UMNGC), Minneapolis, MN, USA
| | | | - Sunita Sharma
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Daniel Efrain Winnica
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Fernando Holguin
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Jesús Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Multidisciplinary Organ Dysfunction Evaluation Research Network (MODERN), Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria, Spain
- Li Ka Shing Knowledge Institute at the St. Michael's Hospital, Toronto, ON, Canada
| | - Elad Ziv
- Institute for Human Genetics, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco (UCSF), San Francisco, CA, USA
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Mastrotheodoros S, Boks MP, Rousseau C, Meeus W, Branje S. Negative parenting, epigenetic age, and psychological problems: prospective associations from adolescence to young adulthood. J Child Psychol Psychiatry 2023; 64:1446-1461. [PMID: 37203368 DOI: 10.1111/jcpp.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Epigenetic clocks are based on DNA methylation levels of several genomic loci and have been developed as indices of biological aging. Studies examining the effects of stressful environmental exposures have shown that stress is associated with differences between epigenetic age and chronological age (i.e., Epigenetic Age acceleration, EA). This pre-registered longitudinal study examined the long-term effects of negative parenting and psychological problems throughout adolescence (ages 13-17 years) on EA in late adolescence (age 17 years) and EA changes from late adolescence to young adulthood (age 25 years). Further, it examined how (change in) EA is related to changes in psychological problems from adolescence to young adulthood. METHODS We used data from a sample of 434 participants followed from age 13 to age 25, with saliva collected at ages 17 and 25. We estimated EA using four commonly used epigenetic clocks and analyzed the data using Structural Equation Modeling. RESULTS While negative parenting was not related to EA nor change in EA, (change in) EA was related to developmental indices such as externalizing problems and self-concept clarity. CONCLUSIONS Declining psychological well-being during young adulthood was preceded by EA.
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Affiliation(s)
- Stefanos Mastrotheodoros
- Department of Youth and Family, Utrecht University, Utrecht, The Netherlands
- Department of Psychology, University of Crete, Rethymno, Greece
| | - Marco P Boks
- Department of Psychiatry, Brain Center University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Céline Rousseau
- Department of Psychiatry, Brain Center University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Wim Meeus
- Department of Youth and Family, Utrecht University, Utrecht, The Netherlands
| | - Susan Branje
- Department of Youth and Family, Utrecht University, Utrecht, The Netherlands
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37
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Coleman C, Wang M, Wang E, Micallef C, Shao Z, Vicari JM, Li Y, Yu K, Cai D, Peng J, Haroutunian V, Fullard JF, Bendl J, Zhang B, Roussos P. Multi-omic atlas of the parahippocampal gyrus in Alzheimer's disease. Sci Data 2023; 10:602. [PMID: 37684260 PMCID: PMC10491684 DOI: 10.1038/s41597-023-02507-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia worldwide, with a projection of 151 million cases by 2050. Previous genetic studies have identified three main genes associated with early-onset familial Alzheimer's disease, however this subtype accounts for less than 5% of total cases. Next-generation sequencing has been well established and holds great promise to assist in the development of novel therapeutics as well as biomarkers to prevent or slow the progression of this devastating disease. Here we present a public resource of functional genomic data from the parahippocampal gyrus of 201 postmortem control, mild cognitively impaired (MCI) and AD individuals from the Mount Sinai brain bank, of which whole-genome sequencing (WGS), and bulk RNA sequencing (RNA-seq) were previously published. The genomic data include bulk proteomics and DNA methylation, as well as cell-type-specific RNA-seq and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) data. We have performed extensive preprocessing and quality control, allowing the research community to access and utilize this public resource available on the Synapse platform at https://doi.org/10.7303/syn51180043.2 .
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Affiliation(s)
- Claire Coleman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Courtney Micallef
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhiping Shao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - James M Vicari
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yuxin Li
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kaiwen Yu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Dongming Cai
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
- Alzheimer Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John F Fullard
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jaroslav Bendl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA.
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Fernández-Boyano I, Inkster AM, Yuan V, Robinson WP. eoPred: predicting the placental phenotype of early-onset preeclampsia using public DNA methylation data. Front Genet 2023; 14:1248088. [PMID: 37736302 PMCID: PMC10509376 DOI: 10.3389/fgene.2023.1248088] [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: 06/26/2023] [Accepted: 08/08/2023] [Indexed: 09/23/2023] Open
Abstract
Background: A growing body of literature has reported molecular and histological changes in the human placenta in association with preeclampsia (PE). Placental DNA methylation (DNAme) and transcriptomic patterns have revealed molecular subgroups of PE that are associated with placental histopathology and clinical phenotypes of the disease. However, the clinical and molecular heterogeneity of PE both across and within subtypes complicates the study of this disease. PE is most strongly associated with placental pathology and adverse fetal and maternal outcomes when it develops early in pregnancy. We focused on placentae from pregnancies affected by preeclampsia that were delivered before 34 weeks of gestation to develop eoPred, a predictor of the DNAme signature associated with the placental phenotype of early-onset preeclampsia (EOPE). Results: Public data from 83 placental samples (HM450K), consisting of 42 EOPE and 41 normotensive preterm birth (nPTB) cases, was used to develop eoPred-a supervised model that relies on a highly discriminative 45 CpG DNAme signature of EOPE in the placenta. The performance of eoPred was assessed using cross-validation (AUC = 0.95) and tested in an independent validation cohort (n = 49, AUC = 0.725). A subset of fetal growth restriction (FGR) and late-PE cases showed a similar DNAme profile at the 45 predictive CpGs, consistent with the overlap in placental pathology between these conditions. The relationship between the EOPE probability generated by eoPred and various phenotypic variables was also assessed, revealing that it is associated with gestational age, and it is not driven by cell composition differences. Conclusion: eoPred relies on a 45-CpG DNAme signature to predict a homogeneous placental phenotype of EOPE in a discrete or continuous manner. Using this classifier should 1) aid in the study of placental insufficiency and improve the consistency of future placental DNAme studies of PE, 2) facilitate identifying the placental phenotype of EOPE in public data sets and 3) importantly, standardize the placental diagnosis of EOPE to allow better cross-cohort comparisons. Lastly, classification of cases with eoPred will be useful for investigating the relationship between placental pathology and genetic or environmental variables.
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Affiliation(s)
- I. Fernández-Boyano
- BC Children’s Hospital Research Institute (BCCHR), Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - A. M. Inkster
- BC Children’s Hospital Research Institute (BCCHR), Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - V. Yuan
- BC Children’s Hospital Research Institute (BCCHR), Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - W. P. Robinson
- BC Children’s Hospital Research Institute (BCCHR), Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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Willems YE, deSteiguer A, Tanksley PT, Vinnik L, Främke D, Okbay A, Richter D, Wagner GG, Hertwig R, Koellinger P, Tucker-Drob EM, Harden KP, Raffington L. Self-control is associated with health-relevant disparities in buccal DNA-methylation measures of biological aging in older adults. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.30.23294816. [PMID: 37693450 PMCID: PMC10491374 DOI: 10.1101/2023.08.30.23294816] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Self-control is a personality dimension that is associated with better physical health and a longer lifespan. Here we examined (1) whether self-control is associated with buccal and saliva DNA-methylation (DNAm) measures of biological aging quantified in children, adolescents, and adults, and (2) whether biological aging measured in buccal DNAm is associated with self-reported health. Following preregistered analyses, we computed two DNAm measures of advanced biological age (PhenoAge and GrimAge Acceleration) and a DNAm measure of pace of aging (DunedinPACE) in buccal samples from the German Socioeconomic Panel Study (SOEP-G[ene], n = 1058, age range 0-72, Mage = 42.65) and saliva samples from the Texas Twin Project (TTP, n = 1327, age range 8-20, Mage = 13.50). We found that lower self-control was associated with advanced biological age in older adults (β =-.34), but not young adults, adolescents or children. This association was not accounted for by statistical correction for socioeconomic contexts, BMI, or genetic correlates of low self-control. Moreover, a faster pace of aging and advanced biological age measured in buccal DNAm were associated with worse self-reported health (β =.13 to β = .19). But, effect sizes were weaker than observations in blood, thus customization of DNAm aging measures to buccal and saliva tissues may be necessary. Our findings are consistent with the hypothesis that self-control is associated with health via pathways that accelerate biological aging in older adults.
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Affiliation(s)
- Y E Willems
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Berlin
| | - A deSteiguer
- Population Research Center, The University of Texas, Austin
| | - P T Tanksley
- Population Research Center, The University of Texas, Austin
| | - L Vinnik
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Berlin
| | - D Främke
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Berlin
| | - A Okbay
- School of Business and Economics, Economics Fellow, Tinbergen Institute, Amsterdam
- Amsterdam Neuroscience, Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam
| | - D Richter
- Department of Education and Psychology, Freie Universität Berlin
- SHARE Berlin, Berlin
| | - G G Wagner
- Max Planck Institute for Human Development, Berlin
- German Socio Economic Panel Study (SOEP), Berlin
| | - R Hertwig
- Max Planck Institute for Human Development, Berlin
| | - P Koellinger
- School of Business and Economics, Economics Fellow, Tinbergen Institute, Amsterdam
- Amsterdam Neuroscience, Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam
| | | | - K P Harden
- Population Research Center, The University of Texas, Austin
| | - L Raffington
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Berlin
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Wang C, Amini H, Xu Z, Peralta AA, Yazdi MD, Qiu X, Wei Y, Just A, Heiss J, Hou L, Zheng Y, Coull BA, Kosheleva A, Baccarelli AA, Schwartz JD. Long-term exposure to ambient fine particulate components and leukocyte epigenome-wide DNA Methylation in older men: the Normative Aging Study. Environ Health 2023; 22:54. [PMID: 37550674 PMCID: PMC10405403 DOI: 10.1186/s12940-023-01007-5] [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: 02/08/2023] [Accepted: 07/26/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Epigenome-wide association studies of ambient fine particulate matter (PM2.5) have been reported. However, few have examined PM2.5 components (PMCs) and sources or included repeated measures. The lack of high-resolution exposure measurements is the key limitation. We hypothesized that significant changes in DNA methylation might vary by PMCs and the sources. METHODS We predicted the annual average of 14 PMCs using novel high-resolution exposure models across the contiguous U.S., between 2000-2018. The resolution was 50 m × 50 m in the Greater Boston Area. We also identified PM2.5 sources using positive matrix factorization. We repeatedly collected blood samples and measured leukocyte DNAm with the Illumina HumanMethylation450K BeadChip in the Normative Aging Study. We then used median regression with subject-specific intercepts to estimate the associations between long-term (one-year) exposure to PMCs / PM2.5 sources and DNA methylation at individual cytosine-phosphate-guanine CpG sites. Significant probes were identified by the number of independent degrees of freedom approach, using the number of principal components explaining > 95% of the variation of the DNA methylation data. We also performed regional and pathway analyses to identify significant regions and pathways. RESULTS We included 669 men with 1,178 visits between 2000-2013. The subjects had a mean age of 75 years. The identified probes, regions, and pathways varied by PMCs and their sources. For example, iron was associated with 6 probes and 6 regions, whereas nitrate was associated with 15 probes and 3 regions. The identified pathways from biomass burning, coal burning, and heavy fuel oil combustion sources were associated with cancer, inflammation, and cardiovascular diseases, whereas there were no pathways associated with all traffic. CONCLUSIONS Our findings showed that the effects of PM2.5 on DNAm varied by its PMCs and sources.
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Affiliation(s)
- Cuicui Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Heresh Amini
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Public Health, Faculty of Health and Medical Sciences, Section of Environmental Health, University of Copenhagen, Copenhagen, Denmark
| | - Zongli Xu
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
| | - Adjani A Peralta
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Mahdieh Danesh Yazdi
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Program in Public Health, Department of Family, Population, and Preventive Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY, USA
| | - Xinye Qiu
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yaguang Wei
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Allan Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jonathan Heiss
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Brent A Coull
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Anna Kosheleva
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, 10032, USA
| | - Joel D Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
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Shi X, Qu M, Jiang Y, Zhu Z, Dai C, Jiang M, Ding L, Yan Y, Wang C, Zhang X, Cheng S, Hao X. Association of immune cell composition with the risk factors and incidence of acute coronary syndrome. Clin Epigenetics 2023; 15:115. [PMID: 37461090 PMCID: PMC10353119 DOI: 10.1186/s13148-023-01527-4] [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: 12/16/2022] [Accepted: 06/28/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Although immune cells are involved in acute coronary syndrome (ACS), few studies have explored the association of incident ACS with the relative immune cell proportions. We aimed to investigate the association of immune cell proportions with the incidence and risk factors of ACS in the Dongfeng-Tongji cohort. METHODS We conducted the analyses with 38,295 subjects from the first follow-up of the Dongfeng-Tongji cohort, including DNA methylation profiles for 1570 individuals. The proportions of immune cell types were observed from routine blood tests or estimated from DNA methylation profiles. For both observed and estimated immune cell proportions, we tested their associations with risk factors of ACS by multivariable linear regression models. In addition, the association of each immune cell proportion with incident ACS was assessed by the Cox regression model and conditional logistic regression model, respectively, adjusting for the risk factors of ACS. FINDINGS The proportions of lymphocytes, monocytes, and neutrophils showed strong associations with sex, followed by diabetes. Moreover, sex and current smoking were the two factors with strongest association with the proportions of lymphocyte subtypes. The hazard ratio (HR) and 95% confidence interval (CI) of incident ACS per standard deviation (SD) increase in proportions of lymphocytes and neutrophils were 0.91 (0.85-0.96) and 1.10 (1.03-1.16), respectively. Furthermore, the OR (95% CI) of incident ACS per SD increase in proportions of NK cells, CD4+ T cells, and B cells were 0.88 (0.78-0.99), 1.15 (1.03-1.30), and 1.13 (1.00-1.26), respectively. INTERPRETATION The proportions of immune cells were associated with several risk factors of ACS, including sex, diabetes, and current smoking. In addition, proportion of neutrophils had a risk effect, while proportion of lymphocytes had a protective effect on the incidence of ACS. The protective effect of lymphocytes was probably driven by NK cells.
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Affiliation(s)
- Xian Shi
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Minghan Qu
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Jiang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ziwei Zhu
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chengguqiu Dai
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Minghui Jiang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Ding
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Yan
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chaolong Wang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shanshan Cheng
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Xingjie Hao
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Peng G, Sosnowski DW, Murphy SK, Johnson SB, Skaar D, Schleif WS, Hernandez RG, Monforte H, Zhao H, Hoyo C. An epigenetic clock for gestational age based on human umbilical vein endothelial cells from a diverse population of newborns. RESEARCH SQUARE 2023:rs.3.rs-3112428. [PMID: 37461438 PMCID: PMC10350106 DOI: 10.21203/rs.3.rs-3112428/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Background Epigenetic clocks are emerging as a useful tool in many areas of research. Many epigenetic clocks have been developed for adults; however, there are fewer clocks focused on newborns and most are trained using blood from European ancestry populations. In this study, we built an epigenetic clock based on primary human umbilical vein endothelial cells from a racially and ethnically diverse population. Results Using human umbilical vein endothelial cell [HUVEC]-derived DNA, we calculated epigenetic gestational age using 83 CpG sites selected through elastic net regression. In this study with newborns from different racial/ethnic identities, epigenetic gestational age and clinical gestational age were more highly correlated (r = 0.85), than epigenetic clocks built from adult and other pediatric populations. The correlation was also higher than clocks based on blood samples from newborns with European ancestry. We also found that birth weight was positively associated with epigenetic gestational age acceleration (EGAA), while NICU admission was associated with lower EGAA. Newborns self-identified as Hispanic or non-Hispanic Black had lower EGAA than self-identified as non-Hispanic White. Conclusions Epigenetic gestational age can be used to estimate clinical gestational age and may help index neonatal development. Caution should be exercised when using epigenetic clocks built from adults with children, especially newborns. We highlight the importance of cell type-specific epigenetic clocks and general pan tissue epigenetic clocks derived from a large racially and ethnically diverse population.
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Affiliation(s)
- Gang Peng
- Indiana University School of Medicine
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Allen JP, Danoff JS, Costello MA, Loeb EL, Davis AA, Hunt GL, Gregory SG, Giamberardino SN, Connelly JJ. Adolescent peer struggles predict accelerated epigenetic aging in midlife. Dev Psychopathol 2023; 35:912-925. [PMID: 35379374 PMCID: PMC9532470 DOI: 10.1017/s0954579422000153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This study examined struggles to establish autonomy and relatedness with peers in adolescence and early adulthood as predictors of advanced epigenetic aging assessed at age 30. Participants (N = 154; 67 male and 87 female) were observed repeatedly, along with close friends and romantic partners, from ages 13 through 29. Observed difficulty establishing close friendships characterized by mutual autonomy and relatedness from ages 13 to 18, an interview-assessed attachment state of mind lacking autonomy and valuing of attachment at 24, and self-reported difficulties in social integration across adolescence and adulthood were all linked to greater epigenetic age at 30, after accounting for chronological age, gender, race, and income. Analyses assessing the unique and combined effects of these factors, along with lifetime history of cigarette smoking, indicated that each of these factors, except for adult social integration, contributed uniquely to explaining epigenetic age acceleration. Results are interpreted as evidence that the adolescent preoccupation with peer relationships may be highly functional given the relevance of such relationships to long-term physical outcomes.
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Lee J, Kim J, Zinia SS, Park J, Won S, Kim WJ. Prenatal phthalate exposure and cord blood DNA methylation. Sci Rep 2023; 13:7046. [PMID: 37120575 PMCID: PMC10148847 DOI: 10.1038/s41598-023-33002-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/05/2023] [Indexed: 05/01/2023] Open
Abstract
Exposure to phthalates has been shown to impede the human endocrine system, resulting in deleterious effects on pregnant women and their children. Phthalates modify DNA methylation patterns in infant cord blood. We examined the association between prenatal phthalate exposure and DNA methylation patterns in cord blood in a Korean birth cohort. Phthalate levels were measured in 274 maternal urine samples obtained during late pregnancy and 102 neonatal urine samples obtained at birth, and DNA methylation levels were measured in cord blood samples. For each infant in the cohort, associations between CpG methylation and both maternal and neonate phthalate levels were analyzed using linear mixed models. The results were combined with those from a meta-analysis of the levels of phthalates in maternal and neonatal urine samples, which were also analyzed for MEOHP, MEHHP, MnBP, and DEHP. This meta-analysis revealed significant associations between the methylation levels of CpG sites near the CHN2 and CUL3 genes, which were also associated with MEOHP and MnBP in neonatal urine. When the data were stratified by the sex of the infant, MnBP concentration was found to be associated with one CpG site near the OR2A2 and MEGF11 genes in female infants. In contrast, the concentrations of the three maternal phthalates showed no significant association with CpG site methylation. Furthermore, the data identified distinct differentially methylated regions in maternal and neonatal urine samples following exposure to phthalates. The CpGs with methylation levels that were positively associated with phthalate levels (particularly MEOHP and MnBP) were found to be enriched genes and related pathways. These results indicate that prenatal phthalate exposure is significantly associated with DNA methylation at multiple CpG sites. These alterations in DNA methylation may serve as biomarkers of maternal exposure to phthalates in infants and are potential candidates for investigating the mechanisms by which phthalates impact maternal and neonatal health.
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Affiliation(s)
- Jooah Lee
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Jeeyoung Kim
- Department of Internal Medicine and Environmental Health Center, School of Medicine, Kangwon National University, Chuncheon, 24341, South Korea
| | - Sabrina Shafi Zinia
- Department of Internal Medicine and Environmental Health Center, School of Medicine, Kangwon National University, Chuncheon, 24341, South Korea
| | - Jaehyun Park
- Interdisciplinary Program of Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Sungho Won
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea.
- Interdisciplinary Program of Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, 08826, South Korea.
- Institute of Health and Environment, Seoul National University, Seoul, South Korea.
- RexSoft Corp, Seoul, South Korea.
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, School of Medicine, Kangwon National University, Chuncheon, 24341, South Korea.
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Raffington L, Schwaba T, Aikins M, Richter D, Wagner GG, Harden KP, Belsky DW, Tucker-Drob EM. Associations of socioeconomic disparities with buccal DNA-methylation measures of biological aging. Clin Epigenetics 2023; 15:70. [PMID: 37118759 PMCID: PMC10148429 DOI: 10.1186/s13148-023-01489-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/20/2023] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Individuals who are socioeconomically disadvantaged are at increased risk for aging-related diseases and perform less well on tests of cognitive function. The weathering hypothesis proposes that these disparities in physical and cognitive health arise from an acceleration of biological processes of aging. Theories of how life adversity is biologically embedded identify epigenetic alterations, including DNA methylation (DNAm), as a mechanistic interface between the environment and health. Consistent with the weathering hypothesis and theories of biological embedding, recently developed DNAm algorithms have revealed profiles reflective of more advanced aging and lower cognitive function among socioeconomically-at-risk groups. These DNAm algorithms were developed using blood-DNA, but social and behavioral science research commonly collect saliva or cheek-swab DNA. This discrepancy is a potential barrier to research to elucidate mechanisms through which socioeconomic disadvantage affects aging and cognition. We therefore tested if social gradients observed in blood DNAm measures could be reproduced using buccal-cell DNA obtained from cheek swabs. RESULTS We analyzed three DNAm measures of biological aging and one DNAm measure of cognitive performance, all of which showed socioeconomic gradients in previous studies: the PhenoAge and GrimAge DNAm clocks, DunedinPACE, and Epigenetic-g. We first computed blood-buccal cross-tissue correlations in n = 21 adults (GEO111165). Cross-tissue correlations were low-to-moderate (r = .25 to r = .48). We next conducted analyses of socioeconomic gradients using buccal DNAm data from SOEP-G (n = 1128, 57% female; age mean = 42 yrs, SD = 21.56, range 0-72). Associations of socioeconomic status with DNAm measures of aging were in the expected direction, but were smaller as compared to reports from blood DNAm datasets (r = - .08 to r = - .13). CONCLUSIONS Our findings are consistent with the hypothesis that socioeconomic disadvantage is associated with DNAm indicators of worse physical health. However, relatively low cross-tissue correlations and attenuated effect sizes for socioeconomic gradients in buccal DNAm compared with reports from analysis of blood DNAm suggest that in order to take full advantage of buccal DNA samples, DNAm algorithms customized to buccal DNAm are needed.
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Affiliation(s)
- L Raffington
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany.
| | - T Schwaba
- Department of Psychology, The University of Texas at Austin, Austin, TX, USA
| | - M Aikins
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany
| | - D Richter
- SHARE Berlin Institute, Berlin, Germany
- Educational Science and Psychology, Free University Berlin, Berlin, Germany
| | - G G Wagner
- Max Planck Institute for Human Development, Berlin, Germany
- Federal Institute for Population Research, Wiesbaden, Berlin, Germany
- German Socio-Economic Panel Study (SOEP), Berlin, Germany
| | - K P Harden
- Department of Psychology, The University of Texas at Austin, Austin, TX, USA
| | - D W Belsky
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
- Robert N Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY, USA
| | - E M Tucker-Drob
- Department of Psychology, The University of Texas at Austin, Austin, TX, USA
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Mohanraj L, Lapato DM, Toor A, Swift-Scanlan T. DNA Methylation Research in Autologous Hematopoietic Stem Cell Transplant Population. Biol Res Nurs 2023; 25:220-226. [PMID: 36242509 DOI: 10.1177/10998004221132251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Despite increased sophistication in DNA methylation (DNAm) measurement and methods, conducting studies in specific populations such as the hematopoietic stem cell transplant (HCT) population, presents unique challenges and study design considerations. In this article, we explain the motivation for investigating DNAm in the HCT population, highlighting important study design features and key findings in a longitudinal prospective pilot study of DNAm in 32 patients undergoing autologous HCT in Central Virginia, USA. We also discuss limitations and challenges to generating robust results. We observed that HCT does not prevent high-quality DNA from being extracted from whole blood for DNAm research and that longitudinal prospective studies that span pre- and 2-months post-HCT are feasible. Critically, we did not observe significant impacts of cancer diagnosis, time since transplant, age, or chromosomal sex on overall DNAm data dimensionality. These observations demonstrate that while extreme care is required to ensure generalizable, accurate, and interpretable results, researchers should not avoid HCT-DNAm research simply for fear that the transplant procedure or presence of a cancer diagnosis will prevent meaningful conclusions from being drawn. DNAm is an attractive biomarker that is understudied in patients undergoing HCT and needs to expand to improve precise prediction of HCT outcomes.
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Affiliation(s)
- Lathika Mohanraj
- Department of Adult Health and Nursing Systems, 16197VCU School of Nursing, Richmond, VA, USA
| | - Dana M Lapato
- Department of Human and Molecular Genetics, VCU School of Medicine, Richmond, VA, USA
| | - Amir Toor
- Department of Internal Medicine, VCU School of Medicine, Richmond, VA, USA
| | - Theresa Swift-Scanlan
- Endowed Professor and Director, Biobehavioral Research Lab, 16197VCU School of Nursing, Richmond, VA, USA
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Lokmer A, Alladi CG, Troudet R, Bacq-Daian D, Boland-Auge A, Latapie V, Deleuze JF, RajKumar RP, Shewade DG, Bélivier F, Marie-Claire C, Jamain S. Risperidone response in patients with schizophrenia drives DNA methylation changes in immune and neuronal systems. Epigenomics 2023; 15:21-38. [PMID: 36919681 DOI: 10.2217/epi-2023-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Background: The choice of efficient antipsychotic therapy for schizophrenia relies on a time-consuming trial-and-error approach, whereas the social and economic burdens of the disease call for faster alternatives. Material & methods: In a search for predictive biomarkers of antipsychotic response, blood methylomes of 28 patients were analyzed before and 4 weeks into risperidone therapy. Results: Several CpGs exhibiting response-specific temporal dynamics were identified in otherwise temporally stable methylomes and noticeable global response-related differences were observed between good and bad responders. These were associated with genes involved in immunity, neurotransmission and neuronal development. Polymorphisms in many of these genes were previously linked with schizophrenia etiology and antipsychotic response. Conclusion: Antipsychotic response seems to be shaped by both stable and medication-induced methylation differences.
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Affiliation(s)
- Ana Lokmer
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, F-94000, France.,Fondation FondaMental, Créteil, F-94000, France
| | - Charanraj Goud Alladi
- Université de Paris, INSERM UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie (OTeN), Paris, F-75006, France
| | - Réjane Troudet
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, F-94000, France.,Fondation FondaMental, Créteil, F-94000, France
| | - Delphine Bacq-Daian
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, F-91057, France
| | - Anne Boland-Auge
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, F-91057, France
| | - Violaine Latapie
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, F-94000, France.,Fondation FondaMental, Créteil, F-94000, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, F-91057, France
| | - Ravi Philip RajKumar
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, 605006, India
| | - Deepak Gopal Shewade
- Department of Psychiatry, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, 605006, India.,Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, F-91000, France
| | - Frank Bélivier
- Fondation FondaMental, Créteil, F-94000, France.,Université de Paris, INSERM UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie (OTeN), Paris, F-75006, France.,Hôpitaux Lariboisière-Fernand Widal, GHU APHP Nord, Département de Psychiatrie et de Médecine Addicto-logique, Paris, F-75010, France
| | - Cynthia Marie-Claire
- Université de Paris, INSERM UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie (OTeN), Paris, F-75006, France
| | - Stéphane Jamain
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, F-94000, France.,Fondation FondaMental, Créteil, F-94000, France
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48
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Siecinski SK, Giamberardino SN, Spanos M, Hauser AC, Gibson JR, Chandrasekhar T, Trelles MDP, Rockhill CM, Palumbo ML, Cundiff AW, Montgomery A, Siper P, Minjarez M, Nowinski LA, Marler S, Kwee LC, Shuffrey LC, Alderman C, Weissman J, Zappone B, Mullett JE, Crosson H, Hong N, Luo S, She L, Bhapkar M, Dean R, Scheer A, Johnson JL, King BH, McDougle CJ, Sanders KB, Kim SJ, Kolevzon A, Veenstra-VanderWeele J, Hauser ER, Sikich L, Gregory SG. Genetic and epigenetic signatures associated with plasma oxytocin levels in children and adolescents with autism spectrum disorder. Autism Res 2023; 16:502-523. [PMID: 36609850 PMCID: PMC10023458 DOI: 10.1002/aur.2884] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023]
Abstract
Oxytocin (OT), the brain's most abundant neuropeptide, plays an important role in social salience and motivation. Clinical trials of the efficacy of OT in autism spectrum disorder (ASD) have reported mixed results due in part to ASD's complex etiology. We investigated whether genetic and epigenetic variation contribute to variable endogenous OT levels that modulate sensitivity to OT therapy. To carry out this analysis, we integrated genome-wide profiles of DNA-methylation, transcriptional activity, and genetic variation with plasma OT levels in 290 participants with ASD enrolled in a randomized controlled trial of OT. Our analysis identified genetic variants with novel association with plasma OT, several of which reside in known ASD risk genes. We also show subtle but statistically significant association of plasma OT levels with peripheral transcriptional activity and DNA-methylation profiles across several annotated gene sets. These findings broaden our understanding of the effects of the peripheral oxytocin system and provide novel genetic candidates for future studies to decode the complex etiology of ASD and its interaction with OT signaling and OT-based interventions. LAY SUMMARY: Oxytocin (OT) is an abundant chemical produced by neurons that plays an important role in social interaction and motivation. We investigated whether genetic and epigenetic factors contribute to variable OT levels in the blood. To this, we integrated genetic, gene expression, and non-DNA regulated (epigenetic) signatures with blood OT levels in 290 participants with autism enrolled in an OT clinical trial. We identified genetic association with plasma OT, several of which reside in known autism risk genes. We also show statistically significant association of plasma OT levels with gene expression and epigenetic across several gene pathways. These findings broaden our understanding of the factors that influence OT levels in the blood for future studies to decode the complex presentation of autism and its interaction with OT and OT-based treatment.
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Affiliation(s)
- Stephen K Siecinski
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Marina Spanos
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Annalise C Hauser
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jason R Gibson
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Tara Chandrasekhar
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - M D Pilar Trelles
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carol M Rockhill
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Michelle L Palumbo
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Paige Siper
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mendy Minjarez
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Lisa A Nowinski
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sarah Marler
- Department of Psychiatry, Vanderbilt University, Nashville, TN, USA
| | - Lydia C Kwee
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Cheryl Alderman
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jordana Weissman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brooke Zappone
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Jennifer E Mullett
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hope Crosson
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - Natalie Hong
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - Sheng Luo
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Lilin She
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Manjushri Bhapkar
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Russell Dean
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Abby Scheer
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Jacqueline L Johnson
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bryan H King
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Christopher J McDougle
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin B Sanders
- Department of Psychiatry, Vanderbilt University, Nashville, TN, USA
| | - Soo-Jeong Kim
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Alexander Kolevzon
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Elizabeth R Hauser
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Linmarie Sikich
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
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49
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Martin-Almeida M, Perez-Garcia J, Herrera-Luis E, Rosa-Baez C, Gorenjak M, Neerincx AH, Sardón-Prado O, Toncheva AA, Harner S, Wolff C, Brandstetter S, Valletta E, Abdel-Aziz MI, Hashimoto S, Berce V, Corcuera-Elosegui P, Korta-Murua J, Buntrock-Döpke H, Vijverberg SJH, Verster JC, Kerssemakers N, Hedman AM, Almqvist C, Villar J, Kraneveld AD, Potočnik U, Kabesch M, der Zee AHMV, Pino-Yanes M, Consortium OBOTS. Epigenome-Wide Association Studies of the Fractional Exhaled Nitric Oxide and Bronchodilator Drug Response in Moderate-to-Severe Pediatric Asthma. Biomedicines 2023; 11:biomedicines11030676. [PMID: 36979655 PMCID: PMC10044864 DOI: 10.3390/biomedicines11030676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/14/2023] [Accepted: 02/18/2023] [Indexed: 02/25/2023] Open
Abstract
Asthma is the most prevalent pediatric chronic disease. Bronchodilator drug response (BDR) and fractional exhaled nitric oxide (FeNO) are clinical biomarkers of asthma. Although DNA methylation (DNAm) contributes to asthma pathogenesis, the influence of DNAm on BDR and FeNO is scarcely investigated. This study aims to identify DNAm markers in whole blood associated either with BDR or FeNO in pediatric asthma. We analyzed 121 samples from children with moderate-to-severe asthma. The association of genome-wide DNAm with BDR and FeNO has been assessed using regression models, adjusting for age, sex, ancestry, and tissue heterogeneity. Cross-tissue validation was assessed in 50 nasal samples. Differentially methylated regions (DMRs) and enrichment in traits and biological pathways were assessed. A false discovery rate (FDR) < 0.1 and a genome-wide significance threshold of p < 9 × 10−8 were used to control for false-positive results. The CpG cg12835256 (PLA2G12A) was genome-wide associated with FeNO in blood samples (coefficient= −0.015, p = 2.53 × 10−9) and nominally associated in nasal samples (coefficient = −0.015, p = 0.045). Additionally, three CpGs were suggestively associated with BDR (FDR < 0.1). We identified 12 and four DMRs associated with FeNO and BDR (FDR < 0.05), respectively. An enrichment in allergic and inflammatory processes, smoking, and aging was observed. We reported novel associations of DNAm markers associated with BDR and FeNO enriched in asthma-related processes.
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Affiliation(s)
- Mario Martin-Almeida
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Spain
| | - Javier Perez-Garcia
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Spain
| | - Esther Herrera-Luis
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Spain
| | - Carlos Rosa-Baez
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Spain
| | - Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Anne H. Neerincx
- Department of Respiratory Medicine, Amsterdam University Medical Centres—Loc. AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Olaia Sardón-Prado
- Division of Pediatric Respiratory Medicine, Donostia University Hospital, 20014 San Sebastián, Spain
- Department of Pediatrics, University of the Basque Country (UPV/EHU), 48013 San Sebastián, Spain
| | - Antoaneta A. Toncheva
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Susanne Harner
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Christine Wolff
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Susanne Brandstetter
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Elisa Valletta
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Mahmoud I. Abdel-Aziz
- Department of Respiratory Medicine, Amsterdam University Medical Centres—Loc. AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Department of Clinical Pharmacy, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt
| | - Simone Hashimoto
- Department of Respiratory Medicine, Amsterdam University Medical Centres—Loc. AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Department of Pediatric Respiratory Medicine, Emma Children’s Hospital, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Vojko Berce
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
- Clinic of Pediatrics, University Medical Centre Maribor, 2000 Maribor, Slovenia
| | - Paula Corcuera-Elosegui
- Division of Pediatric Respiratory Medicine, Donostia University Hospital, 20014 San Sebastián, Spain
| | - Javier Korta-Murua
- Division of Pediatric Respiratory Medicine, Donostia University Hospital, 20014 San Sebastián, Spain
- Department of Pediatrics, University of the Basque Country (UPV/EHU), 48013 San Sebastián, Spain
| | - Heike Buntrock-Döpke
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Susanne J. H. Vijverberg
- Department of Respiratory Medicine, Amsterdam University Medical Centres—Loc. AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Joris C. Verster
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands
- Centre for Human Psychopharmacology, Swinburne University, Melbourne, VIC 3122, Australia
| | - Nikki Kerssemakers
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Anna M Hedman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, 171 77 Stockholm, Sweden
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, 171 77 Stockholm, Sweden
| | - Jesús Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Multidisciplinary Organ Dysfunction Evaluation Research Network, Research Unit, Hospital Universitario Dr. Negrín, 35010 Las Palmas de Gran Canaria, Spain
| | - Aletta D. Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
- Clinic of Pediatrics, University Medical Centre Maribor, 2000 Maribor, Slovenia
- Laboratory for Biochemistry, Molecular Biology, and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, 2000 Maribor, Slovenia
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Anke H. Maitland-van der Zee
- Department of Respiratory Medicine, Amsterdam University Medical Centres—Loc. AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Department of Pediatric Respiratory Medicine, Emma Children’s Hospital, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Spain
- Correspondence: ; Tel.: +34-9223-16502-6343
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50
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Oxytocin receptor DNA methylation is associated with exogenous oxytocin needs during parturition and postpartum hemorrhage. COMMUNICATIONS MEDICINE 2023; 3:11. [PMID: 36707542 PMCID: PMC9882749 DOI: 10.1038/s43856-023-00244-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 01/12/2023] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The oxytocin receptor gene (OXTR) is regulated, in part, by DNA methylation. This mechanism has implications for uterine contractility during labor and for prevention or treatment of postpartum hemorrhage, an important contributor to global maternal morbidity and mortality. METHODS We measured and compared the level of OXTR DNA methylation between matched blood and uterine myometrium to evaluate blood as an indicator of uterine methylation status using targeted pyrosequencing and sites from the Illumina EPIC Array. Next, we tested for OXTR DNA methylation differences in blood between individuals who experienced a postpartum hemorrhage arising from uterine atony and matched controls following vaginal birth. Bivariate statistical tests, generalized linear modeling and Poisson regression were used in the analyses. RESULTS Here we show a significant positive correlation between blood and uterine DNA methylation levels at several OXTR loci. Females with higher OXTR DNA methylation in blood had required significantly more exogenous oxytocin during parturition. With higher DNA methylation, those who had oxytocin administered during labor had significantly greater relative risk for postpartum hemorrhage (IRR 2.95, 95% CI 1.53-5.71). CONCLUSIONS We provide evidence that epigenetic variability in OXTR is associated with the amount of oxytocin administered during parturition and moderates subsequent postpartum hemorrhage. Methylation can be measured using a peripheral tissue, suggesting potential use in identifying individuals susceptible to postpartum hemorrhage. Future studies are needed to quantify myometrial gene expression in connection with OXTR methylation.
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