1
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays. Epigenetics 2024; 19:2333660. [PMID: 38564759 PMCID: PMC10989698 DOI: 10.1080/15592294.2024.2333660] [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: 10/06/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC v1.0 arrays. We conducted a comprehensive assessment of the EPIC v1.0 array probe reliability using 69 blood DNA samples, each measured twice, generated by the Alzheimer's Disease Neuroimaging Initiative study. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliability information for probes on the EPIC v1.0 array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Juan I Young
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael A Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - X Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Brian Kunkle
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eden R Martin
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
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2
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Schaffner SL, Casazza W, Artaud F, Konwar C, Merrill SM, Domenighetti C, Schulze-Hentrich JM, Lesage S, Brice A, Corvol JC, Mostafavi S, Dennis JK, Elbaz A, Kobor MS. Genetic variation and pesticide exposure influence blood DNA methylation signatures in females with early-stage Parkinson's disease. NPJ Parkinsons Dis 2024; 10:98. [PMID: 38714693 PMCID: PMC11076573 DOI: 10.1038/s41531-024-00704-3] [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: 08/07/2023] [Accepted: 04/05/2024] [Indexed: 05/10/2024] Open
Abstract
Although sex, genetics, and exposures can individually influence risk for sporadic Parkinson's disease (PD), the joint contributions of these factors to the epigenetic etiology of PD have not been comprehensively assessed. Here, we profiled sex-stratified genome-wide blood DNAm patterns, SNP genotype, and pesticide exposure in agricultural workers (71 early-stage PD cases, 147 controls) and explored replication in three independent samples of varying demographics (n = 218, 222, and 872). Using a region-based approach, we found more associations of blood DNAm with PD in females (69 regions) than in males (2 regions, Δβadj| ≥0.03, padj ≤ 0.05). For 48 regions in females, models including genotype or genotype and pesticide exposure substantially improved in explaining interindividual variation in DNAm (padj ≤ 0.05), and accounting for these variables decreased the estimated effect of PD on DNAm. The results suggested that genotype, and to a lesser degree, genotype-exposure interactions contributed to variation in PD-associated DNAm. Our findings should be further explored in larger study populations and in experimental systems, preferably with precise measures of exposure.
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Affiliation(s)
- S L Schaffner
- Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - W Casazza
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - F Artaud
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, 94805, Villejuif, France
| | - C Konwar
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
| | - S M Merrill
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
| | - C Domenighetti
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, 94805, Villejuif, France
| | - J M Schulze-Hentrich
- Department of Genetics/Epigenetics, Faculty NT, Saarland University, 66041, Saarbrücken, Germany
| | - S Lesage
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Paris, France
| | - A Brice
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Paris, France
| | - J C Corvol
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Paris, France
- Sorbonne University, Assistance Publique Hôpitaux de Paris, Paris Brain Insitute - ICM, Inserm, CNRS, Department of Neurology and CIC Neurosciences, Pitié-Salpêtrière Hospital, Paris, France
| | - S Mostafavi
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
- Paul Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - J K Dennis
- Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - A Elbaz
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, 94805, Villejuif, France
| | - M S Kobor
- Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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3
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Taylor JY, Jones-Patten A, Prescott L, Potts-Thompson S, Joyce C, Tayo B, Saban K. The race-based stress reduction intervention (RiSE) study on African American women in NYC and Chicago: Design and methods for complex genomic analysis. PLoS One 2024; 19:e0295293. [PMID: 38598554 PMCID: PMC11006145 DOI: 10.1371/journal.pone.0295293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/19/2023] [Indexed: 04/12/2024] Open
Abstract
RiSE study aims to evaluate a race-based stress-reduction intervention as an effective strategy to improve coping and decrease stress-related symptoms, inflammatory burden, and modify DNA methylation of stress response-related genes in older AA women. This article will describe genomic analytic methods to be utilized in this longitudinal, randomized clinical trial of older adult AA women in Chicago and NYC that examines the effect of the RiSE intervention on DNAm pre- and post-intervention, and its overall influence on inflammatory burden. Salivary DNAm will be measured at baseline and 6 months following the intervention, using the Oragene-DNA kit. Measures of perceived stress, depressive symptoms, fatigue, sleep, inflammatory burden, and coping strategies will be assessed at 4 time points including at baseline, 4 weeks, 8 weeks, and 6 months. Genomic data analysis will include the use of pre-processed and quality-controlled methylation data expressed as beta (β) values. Association analyses will be performed to detect differentially methylated sites on the targeted candidate genes between the intervention and non-intervention groups using the Δβ (changes in methylation) with adjustment for age, health behaviors, early life adversity, hybridization batch, and top principal components of the probes as covariates. To account for multiple testing, we will use FDR adjustment with a corrected p-value of <0.05 regarded as statistically significant. To assess the relationship between inflammatory burden and Δβ among the study samples, we will repeat association analyses with the inclusion of individual inflammation protein measures. ANCOVA will be used because it is more statistically powerful to detect differences.
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Affiliation(s)
- Jacquelyn Y. Taylor
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Alexandria Jones-Patten
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Laura Prescott
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Stephanie Potts-Thompson
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Cara Joyce
- Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Bamidele Tayo
- Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Karen Saban
- Marcella Niehoff School of Nursing, Center for Translational Research and Education, Loyola University Chicago, Maywood, Illinois, United States of America
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Knihtilä HM, Kachroo P, Shadid I, Raissadati A, Peng C, McElrath TF, Litonjua AA, Demeo DL, Loscalzo J, Weiss ST, Mirzakhani H. Cord blood DNA methylation signatures associated with preeclampsia are enriched for cardiovascular pathways: insights from the VDAART trial. EBioMedicine 2023; 98:104890. [PMID: 37995466 PMCID: PMC10709000 DOI: 10.1016/j.ebiom.2023.104890] [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: 06/22/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Preeclampsia has been associated with maternal epigenetic changes, in particular DNA methylation changes in the placenta. It has been suggested that preeclampsia could also cause DNA methylation changes in the neonate. We examined DNA methylation in relation to gene expression in the cord blood of offspring born to mothers with preeclampsia. METHODS This study included 128 mother-child pairs who participated in the Vitamin D Antenatal Asthma Reduction Trial (VDAART), where assessment of preeclampsia served as secondary outcome. We performed an epigenome-wide association study of preeclampsia and cord blood DNA methylation (Illumina 450 K chip). We then examined gene expression of the same subjects for validation and replicated the gene signatures in independent DNA methylation datasets. Lastly, we applied functional enrichment and network analyses to identify biological pathways that could potentially be involved in preeclampsia. FINDINGS In the cord blood samples (n = 128), 263 CpGs were differentially methylated (FDR <0.10) in preeclampsia (n = 16), of which 217 were annotated. Top pathways in the functional enrichment analysis included apelin signaling pathway and other endothelial and cardiovascular pathways. Of the 217 genes, 13 showed differential expression (p's < 0.001) in preeclampsia and 11 had been previously related to preeclampsia (p's < 0.0001). These genes were linked to apelin, cGMP and Notch signaling pathways, all having a role in angiogenic process and cardiovascular function. INTERPRETATION Preeclampsia is related to differential cord blood DNA methylation signatures of cardiovascular pathways, including the apelin signaling pathway. The association of these cord blood DNA methylation signatures with offspring's long-term morbidities due to preeclampsia should be further investigated. FUNDING VDAART is funded by National Heart, Lung, and Blood Institute grants of R01HL091528 and UH3OD023268. HMK is supported by Jane and Aatos Erkko Foundation, Paulo Foundation, and the Pediatric Research Foundation. HM is supported by K01 award from NHLBI (1K01HL146977-01A1). PK is supported by K99HL159234 from NIH/NHLBI.
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Affiliation(s)
- Hanna M Knihtilä
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Iskander Shadid
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alireza Raissadati
- Department of Pediatric Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Cheng Peng
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Thomas F McElrath
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Augusto A Litonjua
- Division of Pediatric Pulmonary Medicine, Golisano Children's Hospital, University of Rochester Medical Center, Rochester, NY, USA
| | - Dawn L Demeo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hooman Mirzakhani
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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5
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Andersen MS, Leikfoss IS, Brorson IS, Cappelletti C, Bettencourt C, Toft M, Pihlstrøm L. Epigenome-wide association study of peripheral immune cell populations in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:149. [PMID: 37903812 PMCID: PMC10616224 DOI: 10.1038/s41531-023-00594-x] [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: 06/13/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Understanding the contribution of immune mechanisms to Parkinson's disease pathogenesis is an important challenge, potentially of major therapeutic implications. To further elucidate the involvement of peripheral immune cells, we studied epigenome-wide DNA methylation in isolated populations of CD14+ monocytes, CD19+ B cells, CD4+ T cells, and CD8+ T cells from Parkinson's disease patients and healthy control participants. We included 25 patients with a maximum five years of disease duration and 25 controls, and isolated four immune cell populations from each fresh blood sample. Epigenome-wide DNA methylation profiles were generated from 186 samples using the Illumina MethylationEpic array and association with disease status was tested using linear regression models. We identified six differentially methylated CpGs in CD14+ monocytes and one in CD8 + T cells. Four differentially methylated regions were identified in monocytes, including a region upstream of RAB32, a gene that has been linked to LRRK2. Methylation upstream of RAB32 correlated negatively with mRNA expression, and RAB32 expression was upregulated in Parkinson's disease both in our samples and in summary statistics from a previous study. Our epigenome-wide association study of early Parkinson's disease provides evidence for methylation changes across different peripheral immune cell types, highlighting monocytes and the RAB32 locus. The findings were predominantly cell-type-specific, demonstrating the value of isolating purified cell populations for genomic studies.
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Affiliation(s)
- Maren Stolp Andersen
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | | | - Conceicao Bettencourt
- Department of Neurodegenerative Disease and Queen Square Brain Bank for Neurological Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway.
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6
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays. RESEARCH SQUARE 2023:rs.3.rs-3068938. [PMID: 37461726 PMCID: PMC10350239 DOI: 10.21203/rs.3.rs-3068938/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC arrays. We conducted a comprehensive assessment of the EPIC array probe reliability using 138 duplicated blood DNAm samples generated by the Alzheimer's Disease Neuroimaging Initiative study. We introduced a novel statistical measure, the modified intraclass correlation, to better account for the disagreement in duplicate measurements. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliable information for probes on the EPIC array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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7
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Tsalenchuk M, Gentleman SM, Marzi SJ. Linking environmental risk factors with epigenetic mechanisms in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:123. [PMID: 37626097 PMCID: PMC10457362 DOI: 10.1038/s41531-023-00568-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Sporadic Parkinson's disease (PD) is a progressive neurodegenerative disease, with a complex risk structure thought to be influenced by interactions between genetic variants and environmental exposures, although the full aetiology is unknown. Environmental factors, including pesticides, have been reported to increase the risk of developing the disease. Growing evidence suggests epigenetic changes are key mechanisms by which these environmental factors act upon gene regulation, in disease-relevant cell types. We present a systematic review critically appraising and summarising the current body of evidence of the relationship between epigenetic mechanisms and environmental risk factors in PD to inform future research in this area. Epigenetic studies of relevant environmental risk factors in animal and cell models have yielded promising results, however, research in humans is just emerging. While published studies in humans are currently relatively limited, the importance of the field for the elucidation of molecular mechanisms of pathogenesis opens clear and promising avenues for the future of PD research. Carefully designed epidemiological studies carried out in PD patients hold great potential to uncover disease-relevant gene regulatory mechanisms. Therefore, to advance this burgeoning field, we recommend broadening the scope of investigations to include more environmental exposures, increasing sample sizes, focusing on disease-relevant cell types, and recruiting more diverse cohorts.
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Affiliation(s)
- Maria Tsalenchuk
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | | | - Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London, UK.
- Department of Brain Sciences, Imperial College London, London, UK.
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8
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Sung HY, Lee S, Han M, An WJ, Ryu H, Kang E, Park YS, Lee SE, Ahn C, Oh KH, Park SK, Ahn JH. Epigenome-wide association study of diabetic chronic kidney disease progression in the Korean population: the KNOW-CKD study. Sci Rep 2023; 13:8175. [PMID: 37210443 DOI: 10.1038/s41598-023-35485-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/18/2023] [Indexed: 05/22/2023] Open
Abstract
Since the etiology of diabetic chronic kidney disease (CKD) is multifactorial, studies on DNA methylation for kidney function deterioration have rarely been performed despite the need for an epigenetic approach. Therefore, this study aimed to identify epigenetic markers associated with CKD progression based on the decline in the estimated glomerular filtration rate in diabetic CKD in Korea. An epigenome-wide association study was performed using whole blood samples from 180 CKD recruited from the KNOW-CKD cohort. Pyrosequencing was also performed on 133 CKD participants as an external replication analysis. Functional analyses, including the analysis of disease-gene networks, reactome pathways, and protein-protein interaction networks, were conducted to identify the biological mechanisms of CpG sites. A phenome-wide association study was performed to determine the associations between CpG sites and other phenotypes. Two epigenetic markers, cg10297223 on AGTR1 and cg02990553 on KRT28 indicated a potential association with diabetic CKD progression. Based on the functional analyses, other phenotypes (blood pressure and cardiac arrhythmia for AGTR1) and biological pathways (keratinization and cornified envelope for KRT28) related to CKD were also identified. This study suggests a potential association between the cg10297223 and cg02990553 and the progression of diabetic CKD in Koreans. Nevertheless, further validation is needed through additional studies.
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Affiliation(s)
- Hye Youn Sung
- Department of Biochemistry, Ewha Womans University College of Medicine, 25 Magokdong‑ro 2‑gil, Gangseo‑gu, Seoul, 07804, South Korea
| | - Sangjun Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, 103, Daehak-ro, Jongro-gu, Seoul, 03080, South Korea
- Cancer Research Institute, Seoul National University, Seoul, South Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea
| | - Miyeun Han
- Department of Internal Medicine, National Medical Center, Seoul, South Korea
| | - Woo Ju An
- Department of Preventive Medicine, Seoul National University College of Medicine, 103, Daehak-ro, Jongro-gu, Seoul, 03080, South Korea
- Cancer Research Institute, Seoul National University, Seoul, South Korea
- Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyunjin Ryu
- Department of Internal Medicine, Seoul National University Hospital, 103, Daehak-ro, Jongro-gu, Seoul, 03080, Republic of Korea
| | - Eunjeong Kang
- Department of Internal Medicine, Ewha Womans University Seoul Hospital, Ewha Womans University College of Medicine, Seoul, South Korea
| | - Yong Seek Park
- Department of Microbiology, School of Medicine, Kyung Hee University, Seoul, South Korea
| | - Seung Eun Lee
- Department of Microbiology, School of Medicine, Kyung Hee University, Seoul, South Korea
| | - Curie Ahn
- Department of Internal Medicine, National Medical Center, Seoul, South Korea
- Department of Internal Medicine, Seoul National University Hospital, 103, Daehak-ro, Jongro-gu, Seoul, 03080, Republic of Korea
| | - Kook-Hwan Oh
- Department of Internal Medicine, Seoul National University Hospital, 103, Daehak-ro, Jongro-gu, Seoul, 03080, Republic of Korea.
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, 103, Daehak-ro, Jongro-gu, Seoul, 03080, South Korea.
- Cancer Research Institute, Seoul National University, Seoul, South Korea.
- Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, South Korea.
| | - Jung-Hyuck Ahn
- Department of Biochemistry, Ewha Womans University College of Medicine, 25 Magokdong‑ro 2‑gil, Gangseo‑gu, Seoul, 07804, South Korea.
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9
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Olstad EW, Nordeng HME, Sandve GK, Lyle R, Gervin K. Effects of prenatal exposure to (es)citalopram and maternal depression during pregnancy on DNA methylation and child neurodevelopment. Transl Psychiatry 2023; 13:149. [PMID: 37147306 PMCID: PMC10163054 DOI: 10.1038/s41398-023-02441-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
Studies assessing associations between prenatal exposure to antidepressants, maternal depression, and offspring DNA methylation (DNAm) have been inconsistent. Here, we investigated whether prenatal exposure to citalopram or escitalopram ((es)citalopram) and maternal depression is associated with differences in DNAm. Then, we examined if there is an interaction effect of (es)citalopram exposure and DNAm on offspring neurodevelopmental outcomes. Finally, we investigated whether DNAm at birth correlates with neurodevelopmental trajectories in childhood. We analyzed DNAm in cord blood from the Norwegian Mother, Father and Child Cohort Study (MoBa) biobank. MoBa contains questionnaire data on maternal (es)citalopram use and depression during pregnancy and information about child neurodevelopmental outcomes assessed by internationally recognized psychometric tests. In addition, we retrieved ADHD diagnoses from the Norwegian Patient Registry and information on pregnancies from the Medical Birth Registry of Norway. In total, 958 newborn cord blood samples were divided into three groups: (1) prenatal (es)citalopram exposed (n = 306), (2) prenatal maternal depression exposed (n = 308), and (3) propensity score-selected controls (n = 344). Among children exposed to (es)citalopram, there were more ADHD diagnoses and symptoms and delayed communication and psychomotor development. We did not identify differential DNAm associated with (es)citalopram or depression, nor any interaction effects on neurodevelopmental outcomes throughout childhood. Trajectory modeling identified subgroups of children following similar developmental patterns. Some of these subgroups were enriched for children exposed to maternal depression, and some subgroups were associated with differences in DNAm at birth. Interestingly, several of the differentially methylated genes are involved in neuronal processes and development. These results suggest DNAm as a potential predictive molecular marker of later abnormal neurodevelopmental outcomes, but we cannot conclude whether DNAm links prenatal (es)citalopram exposure or maternal depression with child neurodevelopmental outcomes.
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Affiliation(s)
- Emilie Willoch Olstad
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
- UiO:RealArt Convergence Environment, University of Oslo, Oslo, Norway.
| | - Hedvig Marie Egeland Nordeng
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- UiO:RealArt Convergence Environment, University of Oslo, Oslo, Norway
- Department of Child Health and Development, Norwegian Institute of Public Health, Oslo, Norway
| | - Geir Kjetil Sandve
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- UiO:RealArt Convergence Environment, University of Oslo, Oslo, Norway
- Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Robert Lyle
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Kristina Gervin
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- UiO:RealArt Convergence Environment, University of Oslo, Oslo, Norway
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
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10
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Yazar V, Ruf WP, Knehr A, Günther K, Ammerpohl O, Danzer KM, Ludolph AC. DNA Methylation Analysis in Monozygotic Twins Discordant for ALS in Blood Cells. Epigenet Insights 2023; 16:25168657231172159. [PMID: 37152709 PMCID: PMC10161312 DOI: 10.1177/25168657231172159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/09/2023] [Indexed: 05/09/2023] Open
Abstract
ALS is a fatal motor neuron disease that displays a broad variety of phenotypes ranging from early fatal courses to slowly progressing and rather benign courses. Such divergence can also be seen in genetic ALS cases with varying phenotypes bearing specific mutations, suggesting epigenetic mechanisms like DNA methylation act as disease modifiers. However, the epigenotype dictated by, in addition to other mechanisms, DNA methylation is also strongly influenced by the individual's genotype. Hence, we performed a DNA methylation study using EPIC arrays on 7 monozygotic (MZ) twin pairs discordant for ALS in whole blood, which serves as an ideal model for eliminating the effects of the genetic-epigenetic interplay to a large extent. We found one CpG site showing intra-pair hypermethylation in the affected co-twins, which maps to the Glutamate Ionotropic Receptor Kainate Type Subunit 1 gene (GRIK1). Additionally, we found 4 DMPs which were subsequently confirmed using 2 different statistical approaches. Differentially methylated regions or blocks could not be detected within the scope of this work. In conclusion, we revealed that despite a low sample size, monozygotic twin studies discordant for the disease can bring new insights into epigenetic processes in ALS, pointing to new target loci for further investigations.
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Affiliation(s)
- Volkan Yazar
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), German Center for Neurodegenerative Diseases, Ulm, Germany
| | - Wolfgang P Ruf
- Department of Neurology, Ulm University, Ulm, Baden-Württemberg, Germany
| | - Antje Knehr
- Department of Neurology, Ulm University, Ulm, Baden-Württemberg, Germany
| | - Kornelia Günther
- Department of Neurology, Ulm University, Ulm, Baden-Württemberg, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Ulm, Germany
| | - Karin M Danzer
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), German Center for Neurodegenerative Diseases, Ulm, Germany
- Department of Neurology, Ulm University, Ulm, Baden-Württemberg, Germany
| | - Albert C Ludolph
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), German Center for Neurodegenerative Diseases, Ulm, Germany
- Department of Neurology, Ulm University, Ulm, Baden-Württemberg, Germany
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11
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Carlsen LN, Hansen CS, Kogelman LJA, Werge TM, Ullum H, Bybjerg-Grauholm J, Hansen TF, Jensen RH. DNA-methylation and immunological response in medication overuse headache. Cephalalgia 2023; 43:3331024221147482. [PMID: 36786322 DOI: 10.1177/03331024221147482] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
OBJECTIVE To investigate whether medication-overuse headache patients have differential DNA-methylation pattern. METHODS We collected blood samples from 120 medication-overuse headache-patients, 57 controls (29 episodic migraine patients and 28 healthy controls) in a hypothesis-generating cross-sectional case-control pilot study; 100 of the medication-overuse headache-patients were followed for six months and samples were collected at two and six months for the longitudinal methylation analyses. Blood cell proportions of leucocytes (neutrophils, NK-cells, monocytes, CD8+ and CD4+ T-cells, and B-cells) and the neutrophile-lymphocyte ratio were estimated using methylation data as a measure for immunological analysis and a cell type-specific epigenome wide association study was conducted between medication-overuse headache-patients and controls, and longitudinally for reduction in headache days/month among medication-overuse headache-patients. RESULTS We found a higher neutrophile-lymphocyte ratio in medication-overuse headache-patients compared to controls, indicating a higher immunological response in medication-overuse headache-patients (false discovery rate (adjusted p-value)<0.001). Reduction in headache days/month (9.8; 95% CI 8.1-11.5) was associated with lower neutrophile-lymphocyte ratio (false discovery rate adjusted p-value = 0.041).Three genes (CORIN, CCKBR and CLDN9) were hypermethylated in specific cell types in medication-overuse headache-patients compared to controls. No methylation differences were associated with reduction in headache days in medication-overuse headache-patients after six months. CONCLUSION This pilot study was consistent with higher immunological response in medication-overuse headache-patients which decreased with a reduction in headache days in longitudinal analysis. medication-overuse headache-patients exhibited differential methylation in innate immune cells but did not exhibit longitudinal differences with alterations in headache days. Our study creates hypotheses for further biomarker searches.ClinicalTrials.gov Identifier: NCT02993289.
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Affiliation(s)
| | | | | | - Thomas Mears Werge
- Novo Nordisk Foundation Center for Protein Research, Copenhagen University, Denmark
| | | | | | - Thomas Folkmann Hansen
- Danish Headache Center, Rigshospitalet, Denmark.,Novo Nordisk Foundation Center for Protein Research, Copenhagen University, Denmark
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12
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Allen PC, Smith S, Wilson RC, Wirth JR, Wilson NH, Baker Frost D, Flume J, Gilkeson GS, Cunningham MA, Langefeld CD, Absher DM, Ramos PS. Distinct genome-wide DNA methylation and gene expression signatures in classical monocytes from African American patients with systemic sclerosis. Clin Epigenetics 2023; 15:25. [PMID: 36803404 PMCID: PMC9938585 DOI: 10.1186/s13148-023-01445-5] [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] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 02/08/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Systemic sclerosis (SSc) is a multisystem autoimmune disorder that has an unclear etiology and disproportionately affects women and African Americans. Despite this, African Americans are dramatically underrepresented in SSc research. Additionally, monocytes show heightened activation in SSc and in African Americans relative to European Americans. In this study, we sought to investigate DNA methylation and gene expression patterns in classical monocytes in a health disparity population. METHODS Classical monocytes (CD14+ + CD16-) were FACS-isolated from 34 self-reported African American women. Samples from 12 SSc patients and 12 healthy controls were hybridized on MethylationEPIC BeadChip array, while RNA-seq was performed on 16 SSc patients and 18 healthy controls. Analyses were computed to identify differentially methylated CpGs (DMCs), differentially expressed genes (DEGs), and CpGs associated with changes in gene expression (eQTM analysis). RESULTS We observed modest DNA methylation and gene expression differences between cases and controls. The genes harboring the top DMCs, the top DEGs, as well as the top eQTM loci were enriched for metabolic processes. Genes involved in immune processes and pathways showed a weak upregulation in the transcriptomic analysis. While many genes were newly identified, several other have been previously reported as differentially methylated or expressed in different blood cells from patients with SSc, supporting for their potential dysregulation in SSc. CONCLUSIONS While contrasting with results found in other blood cell types in largely European-descent groups, the results of this study support that variation in DNA methylation and gene expression exists among different cell types and individuals of different genetic, clinical, social, and environmental backgrounds. This finding supports the importance of including diverse, well-characterized patients to understand the different roles of DNA methylation and gene expression variability in the dysregulation of classical monocytes in diverse populations, which might help explaining the health disparities.
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Affiliation(s)
- Peter C Allen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sarah Smith
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Robert C Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Jena R Wirth
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Nathan H Wilson
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - DeAnna Baker Frost
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Jonathan Flume
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Gary S Gilkeson
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Melissa A Cunningham
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Paula S Ramos
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA.
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13
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Merrill SM, Gladish N, Fu MP, Moore SR, Konwar C, Giesbrecht GF, MacIssac JL, Kobor MS, Letourneau NL. Associations of peripheral blood DNA methylation and estimated monocyte proportion differences during infancy with toddler attachment style. Attach Hum Dev 2023; 25:132-161. [PMID: 34196256 DOI: 10.1080/14616734.2021.1938872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Attachment is a motivational system promoting felt security to a caregiver resulting in a persistent internal working model of interpersonal behavior. Attachment styles are developed in early social environments and predict future health and development outcomes with potential biological signatures, such as epigenetic modifications like DNA methylation (DNAm). Thus, we hypothesized infant DNAm would associate with toddler attachment styles. An epigenome-wide association study (EWAS) of blood DNAm from 3-month-old infants was regressed onto children's attachment style from the Strange Situation Procedure at 22-months at multiple DNAm Cytosine-phosphate-Guanine (CpG) sites. The 26 identified CpGs associated with proinflammatory immune phenotypes and cognitive development. In post-hoc analyses, only maternal cognitive-growth fostering, encouraging intellectual exploration, contributed. For disorganized children, DNAm-derived cell-type proportions estimated higher monocytes -cells in immune responses hypothesized to increase with early adversity. Collectively, these findings suggested the potential biological embedding of both adverse and advantageous social environments as early as 3-months-old.
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Affiliation(s)
- Sarah M Merrill
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Nicole Gladish
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Maggie P Fu
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Sarah R Moore
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Chaini Konwar
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Gerald F Giesbrecht
- Department of Pediatrics, University of Calgary, Calgary, Canada.,Owerko Centre at the Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Julia L MacIssac
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Michael S Kobor
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada.,Program in Child and Brain Development, CIFAR, Toronto, Canada
| | - Nicole L Letourneau
- Department of Pediatrics, University of Calgary, Calgary, Canada.,Owerko Centre at the Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada.,Department of Psychiatry, University of Calgary, Calgary, Canada.,Faculty of Nursing, University of Calgary, Calgary, Canada
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14
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Shao X, Vishweswaraiah S, Čuperlović-Culf M, Yilmaz A, Greenwood CMT, Surendra A, McGuinness B, Passmore P, Kehoe PG, Maddens ME, Bennett SAL, Green BD, Radhakrishna U, Graham SF. Dementia with Lewy bodies post-mortem brains reveal differentially methylated CpG sites with biomarker potential. Commun Biol 2022; 5:1279. [PMID: 36418427 PMCID: PMC9684551 DOI: 10.1038/s42003-022-03965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/08/2022] [Indexed: 11/25/2022] Open
Abstract
Dementia with Lewy bodies (DLB) is a common form of dementia with known genetic and environmental interactions. However, the underlying epigenetic mechanisms which reflect these gene-environment interactions are poorly studied. Herein, we measure genome-wide DNA methylation profiles of post-mortem brain tissue (Broadmann area 7) from 15 pathologically confirmed DLB brains and compare them with 16 cognitively normal controls using Illumina MethylationEPIC arrays. We identify 17 significantly differentially methylated CpGs (DMCs) and 17 differentially methylated regions (DMRs) between the groups. The DMCs are mainly located at the CpG islands, promoter and first exon regions. Genes associated with the DMCs are linked to "Parkinson's disease" and "metabolic pathway", as well as the diseases of "severe intellectual disability" and "mood disorders". Overall, our study highlights previously unreported DMCs offering insights into DLB pathogenesis with the possibility that some of these could be used as biomarkers of DLB in the future.
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Affiliation(s)
- Xiaojian Shao
- National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada.
| | | | - Miroslava Čuperlović-Culf
- National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, sand Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Ali Yilmaz
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
- Beaumont Research Institute, Royal Oak, MI, 48073, USA
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Canada
| | - Anuradha Surendra
- National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada
| | - Bernadette McGuinness
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Peter Passmore
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Patrick G Kehoe
- Dementia Research Group, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael E Maddens
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
- Beaumont Research Institute, Royal Oak, MI, 48073, USA
| | - Steffany A L Bennett
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, sand Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Brian D Green
- Institute for Global Food Security, School of Biological Sciences, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Northern Ireland, UK
| | - Uppala Radhakrishna
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
- Beaumont Research Institute, Royal Oak, MI, 48073, USA
| | - Stewart F Graham
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA.
- Beaumont Research Institute, Royal Oak, MI, 48073, USA.
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15
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Designing Studies for Epigenetic Biomarker Development in Autoimmune Rheumatic Diseases. RHEUMATOLOGY AND IMMUNOLOGY RESEARCH 2022; 3:103-110. [PMID: 36788968 PMCID: PMC9895872 DOI: 10.2478/rir-2022-0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/13/2022] [Indexed: 02/16/2023]
Abstract
In just a few years, the number of epigenetic studies in autoimmune rheumatic and inflammatory diseases has greatly increased. This is in part due to the need of identifying additional determinants to genetics to explain the pathogenesis and development of these disorders. In this regard, epigenetics provides potential mechanisms that determine gene function, are linked to environmental factors, and could explain a wide range of phenotypic variability among patients with these diseases. Despite the high interest and number of studies describing epigenetic alterations under these conditions and exploring their relationship to various clinical aspects, few of the proposed biomarkers have yet reached clinical practice. The potential of epigenetic markers is high, as these alterations link measurable features with a number of biological traits. In the present article, we present published studies in the field, discuss some frequent limitations in the existing research, and propose a number of considerations that should be taken into account by those starting new projects in the field, with an aim to generate biomarkers that could make it into the clinics.
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16
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Miao R, Dang Q, Cai J, Huang HH, Xie SL, Liang Y. Sparse principal component analysis based on genome network for correcting cell type heterogeneity in epigenome-wide association studies. Med Biol Eng Comput 2022; 60:2601-2618. [DOI: 10.1007/s11517-022-02599-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 04/30/2022] [Indexed: 10/17/2022]
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17
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Cullell N, Soriano-Tárraga C, Gallego-Fábrega C, Cárcel-Márquez J, Torres-Águila NP, Muiño E, Lledós M, Llucià-Carol L, Esteller M, Castro de Moura M, Montaner J, Fernández-Sanlés A, Elosua R, Delgado P, Martí-Fábregas J, Krupinski J, Roquer J, Jiménez-Conde J, Fernández-Cadenas I. DNA Methylation and Ischemic Stroke Risk: An Epigenome-Wide Association Study. Thromb Haemost 2022; 122:1767-1778. [PMID: 35717949 DOI: 10.1055/s-0042-1749328] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
BACKGROUND Ischemic stroke (IS) risk heritability is partly explained by genetics. Other heritable factors, such as epigenetics, could explain an unknown proportion of the IS risk. The objective of this study is to evaluate DNA methylation association with IS using epigenome-wide association studies (EWAS). METHODS We performed a two-stage EWAS comprising 1,156 subjects. Differentially methylated positions (DMPs) and differentially methylated regions (DMRs) were assessed using the Infinium 450K and EPIC BeadChip in the discovery cohort (252 IS and 43 controls). Significant DMPs were replicated in an independent cohort (618 IS and 243 controls). Stroke subtype associations were also evaluated. Differentially methylated cell-type (DMCT) was analyzed in the replicated CpG sites using EpiDISH. We additionally performed pathway enrichment analysis and causality analysis with Mendelian randomization for the replicated CpG sites. RESULTS A total of 957 CpG sites were epigenome-wide-significant (p ≤ 10-7) in the discovery cohort, being CpG sites in the top signals (logFC = 0.058, p = 2.35 × 10-22; logFC = 0.035, p = 3.22 × 10-22, respectively). ZFHX3 and MAP3K1 were among the most significant DMRs. In addition, 697 CpG sites were replicated considering Bonferroni-corrected p-values (p < 5.22 × 10-5). All the replicated DMPs were associated with risk of cardioembolic, atherothrombotic, and undetermined stroke. The DMCT analysis demonstrated that the significant associations were driven by natural killer cells. The pathway enrichment analysis showed overrepresentation of genes belonging to certain pathways including oxidative stress. ZFHX3 and MAP3K1 methylation was causally associated with specific stroke-subtype risk. CONCLUSION Specific DNA methylation pattern is causally associated with IS risk. These results could be useful for specifically predicting stroke occurrence and could potentially be evaluated as therapeutic targets.
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Affiliation(s)
- Natalia Cullell
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain.,Department of Neurology, Hospital Universitari MútuaTerrassa/Fundacio Docència i Recerca MútuaTerrassa, Barcelona, Spain.,Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Carolina Soriano-Tárraga
- Neurovascular Research Group, Department of Neurology, Hospital del Mar, IMIM, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain.,Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, Missouri, United States
| | | | - Jara Cárcel-Márquez
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain
| | - Nuria P Torres-Águila
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain.,Evolutionary Developmental Genomics Research Group, The Scottish Oceans Institute, University of St Andrews, St Andrews, United Kingdom
| | - Elena Muiño
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain
| | - Miquel Lledós
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain
| | - Laia Llucià-Carol
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain.,Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.,Centro de Investigación Biomédica en Red Cancer, Barcelona, Spain
| | | | - Joan Montaner
- Department of Neurology, Hospital Universitario Virgen Macarena, Institute of Biomedicine of Seville/Hospital Universitario Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Alba Fernández-Sanlés
- Cardiovascular Epidemiology and Genetics Research Group, IMIM, Barcelona, Spain.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics Research Group, IMIM, Barcelona, Spain.,CIBER Cardiovascular Diseases, Instituto Carlos III, Barcelona, Spain.,School of Medicine, University of Vic-Central University of Catalonia, Barcelona, Spain
| | - Pilar Delgado
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research, Barcelona, Spain
| | - Joan Martí-Fábregas
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Jerzy Krupinski
- Department of Neurology, Hospital Universitari MútuaTerrassa/Fundacio Docència i Recerca MútuaTerrassa, Barcelona, Spain.,Centre for Bioscience, School of HealthCare Science, Manchester Metropolitan University, Manchester, England
| | - Jaume Roquer
- Neurovascular Research Group, Department of Neurology, Hospital del Mar, IMIM, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Jordi Jiménez-Conde
- Neurovascular Research Group, Department of Neurology, Hospital del Mar, IMIM, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Israel Fernández-Cadenas
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain.,Department of Neurology, Hospital Universitari MútuaTerrassa/Fundacio Docència i Recerca MútuaTerrassa, Barcelona, Spain
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18
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Vara EL, Langefeld CD, Wolf BJ, Howard TD, Hawkins GA, Quet Q, Moultrie LH, Quinnette King L, Molano ID, Bray SL, Ueberroth LA, Lim SS, Williams EM, Kamen DL, Ramos PS. Social Factors, Epigenomics and Lupus in African American Women (SELA) Study: protocol for an observational mechanistic study examining the interplay of multiple individual and social factors on lupus outcomes in a health disparity population. Lupus Sci Med 2022; 9:9/1/e000698. [PMID: 35768168 PMCID: PMC9244713 DOI: 10.1136/lupus-2022-000698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/14/2022] [Indexed: 11/08/2022]
Abstract
Introduction Despite the disproportional impact of SLE on historically marginalised communities, the individual and sociocultural factors underlying these health disparities remain elusive. We report the design and methods for a study aimed at identifying epigenetic biomarkers associated with racism and resiliency that affect gene function and thereby influence SLE in a health disparity population. Methods and analysis The Social Factors, Epigenomics and Lupus in African American Women (SELA) Study is a cross-sectional, case–control study. A total of 600 self-reported African American women will be invited to participate. All participants will respond to questionnaires that capture detailed sociodemographic and medical history, validated measures of racial discrimination, social support, as well as disease activity and damage for cases. Participants who wish will receive their genetic ancestry estimates and be involved in research. Blood samples are required to provide peripheral blood mononuclear cell counts, DNA and RNA. The primary goals of SELA are to identify variation in DNA methylation (DNAm) associated with self-reported exposure to racial discrimination and social support, to evaluate whether social DNAm sites affect gene expression, to identify the synergistic effects of social factors on DNAm changes on SLE and to develop a social factors-DNAm predictive model for disease outcomes. This study is conducted in cooperation with the Sea Island Families Project Citizen Advisory Committee. Discussion and dissemination SELA will respond to the pressing need to clarify the interplay and regulatory mechanism by which various positive and negative social exposures influence SLE. Results will be published and shared with patients and the community. Knowledge of the biological impact of social exposures on SLE, as informed by the results of this study, can be leveraged by advocacy efforts to develop psychosocial interventions that prevent or mitigate risk exposures, and services or interventions that promote positive exposures. Implementation of such interventions is paramount to the closure of the health disparities gap.
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Affiliation(s)
- Emily L Vara
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.,Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Bethany J Wolf
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Timothy D Howard
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.,Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Gregory A Hawkins
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.,Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Queen Quet
- Gullah/Geechee Nation, St Helena Island, South Carolina, USA
| | - Lee H Moultrie
- Lee H Moultrie & Associates, North Charleston, South Carolina, USA
| | - L Quinnette King
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Ivan D Molano
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Stephanie L Bray
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Lori Ann Ueberroth
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - S Sam Lim
- Department of Medicine, Emory University, Atlanta, Georgia, USA.,Department of Epidemiology, Emory University, Atlanta, Georgia, USA
| | - Edith M Williams
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA.,Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Diane L Kamen
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Paula S Ramos
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA .,Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
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19
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Bhat B, Jones GT. Data Analysis of DNA Methylation Epigenome-Wide Association Studies (EWAS): A Guide to the Principles of Best Practice. Methods Mol Biol 2022; 2458:23-45. [PMID: 35103960 DOI: 10.1007/978-1-0716-2140-0_2] [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] [Indexed: 06/14/2023]
Abstract
Array-based EWAS have become an increasingly popular technique to identify population epigenetic effects, particularly in humans. With the arrival of nonhuman species arrays, such as the mouse, this is likely to become an even more widely used technology. This chapter provides the less experienced researcher a guide to the analysis of data from the most widely used platform, the Illumina Infinium Methylation assay. This includes an overview of quality filtering, data normalization, analysis options, and techniques to improve the interpretation of results.
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Affiliation(s)
- Basharat Bhat
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Gregory T Jones
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
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20
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Xia Q, Thompson JA, Koestler DC. pwrBRIDGE: a user-friendly web application for power and sample size estimation in batch-confounded microarray studies with dependent samples. Stat Appl Genet Mol Biol 2022; 21:sagmb-2022-0003. [PMID: 36215429 PMCID: PMC9550194 DOI: 10.1515/sagmb-2022-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 09/16/2022] [Indexed: 01/24/2023]
Abstract
Batch effect Reduction of mIcroarray data with Dependent samples usinG Empirical Bayes (BRIDGE) is a recently developed statistical method to address the issue of batch effect correction in batch-confounded microarray studies with dependent samples. The key component of the BRIDGE methodology is the use of samples run as technical replicates in two or more batches, "bridging samples", to inform batch effect correction/attenuation. While previously published results indicate a relationship between the number of bridging samples, M, and the statistical power of downstream statistical testing on the batch-corrected data, there is of yet no formal statistical framework or user-friendly software, for estimating M to achieve a specific statistical power for hypothesis tests conducted on the batch-corrected data. To fill this gap, we developed pwrBRIDGE, a simulation-based approach to estimate the bridging sample size, M, in batch-confounded longitudinal microarray studies. To illustrate the use of pwrBRIDGE, we consider a hypothetical, longitudinal batch-confounded study whose goal is to identify Alzheimer's disease (AD) progression-associated genes from amnestic mild cognitive impairment (aMCI) to AD in human blood after a 5-year follow-up. pwrBRIDGE helps researchers design and plan batch-confounded microarray studies with dependent samples to avoid over- or under-powered studies.
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Affiliation(s)
- Qing Xia
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, USA
| | - Jeffrey A. Thompson
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, USA
| | - Devin C. Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, USA
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21
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Smyth LJ, Cruise SM, Tang J, Young I, McGuinness B, Kee F, McKnight AJ. An investigation into DNA methylation patterns associated with risk preference in older individuals. Epigenetics 2021; 17:1159-1172. [PMID: 34696705 PMCID: PMC9542846 DOI: 10.1080/15592294.2021.1992910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Risk preference is a complex trait governed by psycho-social, environmental and genetic determinants. We aimed to examine how an individual’s risk preference associates with their epigenetic profile. Risk preferences were ascertained by asking participants of the Northern Ireland COhort for the Longitudinal study of Ageing to make a series of choices between hypothetical income scenarios. From these, four risk preference categories were derived, ranging from risk-averse to risk-seeking. Illumina’s Infinium High-Density Methylation Assay was used to evaluate the status of 862,927 CpGs. Risk preference and DNA methylation data were obtained for 1,656 individuals. The distribution of single-site DNA methylation levels between risk-averse and risk-seeking individuals was assessed whilst adjusting for age, sex and peripheral white cell counts. In this discovery cohort, 55 CpGs were identified with significantly different levels of methylation (p≤x10−5) between risk-averse and risk-seeking individuals when adjusting for the maximum number of covariates. No CpGs were significantly differentially methylated in any of the risk preference groups at an epigenome-wide association level (p<9x10−8) following covariate adjustment. Protein-coding genes NWD1 and LRP1 were among the genes in which the top-ranked dmCpGs were located for all analyses conducted. Mutations in these genes have previously been linked to neurological conditions. Epigenetic modifications have not previously been linked to risk-aversion using a population cohort, but may represent important biomarkers of accumulated, complex determinants of this trait. Several striking results from this study support further analysis of DNA methylation as an important link between measurable biomarkers and health behaviours.
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Affiliation(s)
- Laura J Smyth
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Sharon M Cruise
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Jianjun Tang
- School of Agricultural Economics and Rural Development, Renmin University of China, Beijing, China
| | - Ian Young
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Bernadette McGuinness
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Frank Kee
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Amy Jayne McKnight
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
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22
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Bainomugisa CK, Sutherland HG, Parker R, Mcrae AF, Haupt LM, Griffiths LR, Heath A, Nelson EC, Wright MJ, Hickie IB, Martin NG, Nyholt DR, Mehta D. Using Monozygotic Twins to Dissect Common Genes in Posttraumatic Stress Disorder and Migraine. Front Neurosci 2021; 15:678350. [PMID: 34239411 PMCID: PMC8258453 DOI: 10.3389/fnins.2021.678350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/31/2021] [Indexed: 01/03/2023] Open
Abstract
Epigenetic mechanisms have been associated with genes involved in Posttraumatic stress disorder (PTSD). PTSD often co-occurs with other health conditions such as depression, cardiovascular disorder and respiratory illnesses. PTSD and migraine have previously been reported to be symptomatically positively correlated with each other, but little is known about the genes involved. The aim of this study was to understand the comorbidity between PTSD and migraine using a monozygotic twin disease discordant study design in six pairs of monozygotic twins discordant for PTSD and 15 pairs of monozygotic twins discordant for migraine. DNA from peripheral blood was run on Illumina EPIC arrays and analyzed. Multiple testing correction was performed using the Bonferroni method and 10% false discovery rate (FDR). We validated 11 candidate genes previously associated with PTSD including DOCK2, DICER1, and ADCYAP1. In the epigenome-wide scan, seven novel CpGs were significantly associated with PTSD within/near IL37, WNT3, ADNP2, HTT, SLFN11, and NQO2, with all CpGs except the IL37 CpG hypermethylated in PTSD. These results were significantly enriched for genes whose DNA methylation was previously associated with migraine (p-value = 0.036). At 10% FDR, 132 CpGs in 99 genes associated with PTSD were also associated with migraine in the migraine twin samples. Genes associated with PTSD were overrepresented in vascular smooth muscle, axon guidance and oxytocin signaling pathways, while genes associated with both PTSD and migraine were enriched for AMPK signaling and longevity regulating pathways. In conclusion, these results suggest that common genes and pathways are likely involved in PTSD and migraine, explaining at least in part the co-morbidity between the two disorders.
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Affiliation(s)
- Charlotte K Bainomugisa
- Centre for Genomics and Personalised Health, School of Biomedical Science, Faculty of Health, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Heidi G Sutherland
- Centre for Genomics and Personalised Health, School of Biomedical Science, Faculty of Health, Queensland University of Technology, Kelvin Grove, QLD, Australia.,Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Kelvin Grove, QLD, Australia
| | - Richard Parker
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Herston, QLD, Australia
| | - Allan F Mcrae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Larisa M Haupt
- Centre for Genomics and Personalised Health, School of Biomedical Science, Faculty of Health, Queensland University of Technology, Kelvin Grove, QLD, Australia.,Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Kelvin Grove, QLD, Australia
| | - Lyn R Griffiths
- Centre for Genomics and Personalised Health, School of Biomedical Science, Faculty of Health, Queensland University of Technology, Kelvin Grove, QLD, Australia.,Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Kelvin Grove, QLD, Australia
| | - Andrew Heath
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Elliot C Nelson
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Margaret J Wright
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.,Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Ian B Hickie
- Brain and Mind Centre, The University of Sydney, Sydney, NSW, Australia
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Herston, QLD, Australia
| | - Dale R Nyholt
- Centre for Genomics and Personalised Health, School of Biomedical Science, Faculty of Health, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Divya Mehta
- Centre for Genomics and Personalised Health, School of Biomedical Science, Faculty of Health, Queensland University of Technology, Kelvin Grove, QLD, Australia
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23
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Åsenius F, Danson AF, Marzi SJ. DNA methylation in human sperm: a systematic review. Hum Reprod Update 2021; 26:841-873. [PMID: 32790874 DOI: 10.1093/humupd/dmaa025] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 05/25/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Studies in non-human mammals suggest that environmental factors can influence spermatozoal DNA methylation, and some research suggests that spermatozoal DNA methylation is also implicated in conditions such as subfertility and imprinting disorders in the offspring. Together with an increased availability of cost-effective methods of interrogating DNA methylation, this premise has led to an increasing number of studies investigating the DNA methylation landscape of human spermatozoa. However, how the human spermatozoal DNA methylome is influenced by environmental factors is still unclear, as is the role of human spermatozoal DNA methylation in subfertility and in influencing offspring health. OBJECTIVE AND RATIONALE The aim of this systematic review was to critically appraise the quality of the current body of literature on DNA methylation in human spermatozoa, summarize current knowledge and generate recommendations for future research. SEARCH METHODS A comprehensive literature search of the PubMed, Web of Science and Cochrane Library databases was conducted using the search terms 'semen' OR 'sperm' AND 'DNA methylation'. Publications from 1 January 2003 to 2 March 2020 that studied human sperm and were written in English were included. Studies that used sperm DNA methylation to develop methodologies or forensically identify semen were excluded, as were reviews, commentaries, meta-analyses or editorial texts. The Grading of Recommendations, Assessment, Development and Evaluations (GRADE) criteria were used to objectively evaluate quality of evidence in each included publication. OUTCOMES The search identified 446 records, of which 135 were included in the systematic review. These 135 studies were divided into three groups according to area of research; 56 studies investigated the influence of spermatozoal DNA methylation on male fertility and abnormal semen parameters, 20 studies investigated spermatozoal DNA methylation in pregnancy outcomes including offspring health and 59 studies assessed the influence of environmental factors on spermatozoal DNA methylation. Findings from studies that scored as 'high' and 'moderate' quality of evidence according to GRADE criteria were summarized. We found that male subfertility and abnormal semen parameters, in particular oligozoospermia, appear to be associated with abnormal spermatozoal DNA methylation of imprinted regions. However, no specific DNA methylation signature of either subfertility or abnormal semen parameters has been convincingly replicated in genome-scale, unbiased analyses. Furthermore, although findings require independent replication, current evidence suggests that the spermatozoal DNA methylome is influenced by cigarette smoking, advanced age and environmental pollutants. Importantly however, from a clinical point of view, there is no convincing evidence that changes in spermatozoal DNA methylation influence pregnancy outcomes or offspring health. WIDER IMPLICATIONS Although it appears that the human sperm DNA methylome can be influenced by certain environmental and physiological traits, no findings have been robustly replicated between studies. We have generated a set of recommendations that would enhance the reliability and robustness of findings of future analyses of the human sperm methylome. Such studies will likely require multicentre collaborations to reach appropriate sample sizes, and should incorporate phenotype data in more complex statistical models.
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Affiliation(s)
| | - Amy F Danson
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London W12 0NN, UK.,Department of Brain Sciences, Imperial College London, London, UK
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24
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Lu M, Xueying Q, Hexiang P, Wenjing G, Hägg S, Weihua C, Chunxiao L, Canqing Y, Jun L, Zengchang P, Liming C, Hua W, Xianping W, Yunzhang W, Liming L. Genome-wide associations between alcohol consumption and blood DNA methylation: evidence from twin study. Epigenomics 2021; 13:939-951. [PMID: 33993705 DOI: 10.2217/epi-2021-0039] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Alcohol intake alters DNA methylation profiles and methylation might mediate the association between alcohol and disease, but limited number of positive CpG sites repeatedly replicated. Materials & methods: In total, 57 monozygotic (MZ) twin pairs discordant for alcohol drinking from the Chinese National Twin Registry and 158 MZ and dizygotic twin pairs in the Swedish Adoption/Twin Study of Aging were evaluated. DNA methylation was detected using the Infinium HumanMethylation450 BeadChip. Results: Among candidate CpG sites, cg07326074 was significantly correlated with drinking after adjusting for covariates in MZ twins in both datasets but not in the entire sample or dizygotic twins. Conclusion: The hypermethylation of cg07326074, located in the tumor-promoting gene C16orf59, was associated with alcohol consumption.
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Affiliation(s)
- Meng Lu
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Qin Xueying
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China.,Department of Medical Epidemiology & Biostatistics, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Peng Hexiang
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Gao Wenjing
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Sara Hägg
- Department of Medical Epidemiology & Biostatistics, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Cao Weihua
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Li Chunxiao
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Yu Canqing
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Lv Jun
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Pang Zengchang
- Qingdao Center for Disease Control & Prevention, Qingdao 266033, PR China
| | - Cong Liming
- Zhejiang Center for Disease Control & Prevention, Hangzhou 310051, PR China
| | - Wang Hua
- Jiangsu Center for Disease Control & Prevention, Nanjing 210009, PR China
| | - Wu Xianping
- Sichuan Center for Disease Control & Prevention, Chengdu 610041, PR China
| | - Wang Yunzhang
- Department of Medical Epidemiology & Biostatistics, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Li Liming
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
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25
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Olstad EW, Nordeng HME, Gervin K. Prenatal medication exposure and epigenetic outcomes: a systematic literature review and recommendations for prenatal pharmacoepigenetic studies. Epigenetics 2021; 17:357-380. [PMID: 33926354 PMCID: PMC8993058 DOI: 10.1080/15592294.2021.1903376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
When used during pregnancy, analgesics and psychotropics pass the placenta to enter the foetal circulation and may induce epigenetic modifications. Where such modifications occur and whether they disrupt normal foetal developme nt, are currently unanswered questions. This field of prenatal pharmacoepigenetics has received increasing attention, with several studies reporting associations between in utero medication exposure and offspring epigenetic outcomes. Nevertheless, no recent systematic review of the literature is available. Therefore, the objectives of this review were to (i) provide an overview of the literature on the association of prenatal exposure to psychotropics a nd analgesics with epigenetic outcomes, and (ii) suggest recommendations for future studies within prenatal pharmacoepigenetics. We performed systematic literature searches in five databases. The eligible studies assessed human prenatal exposure to psychotropics or analgesics, with epigenetic analyses of offspring tissue as an outcome. We identified 18 eligible studies including 4,419 neonates exposed to either antidepressants, antiepileptic drugs, paracetamol, acetylsalicylic acid, or methadone. The epigenetic outcome in all studies was DNA methylation in cord blood, placental tissue or buccal cells. Although most studies found significant differences in DNA methylation upon medication exposure, almost no differences were persistent across studies for similar medications and sequencing methods. The reviewed studies were challenging to compare due to poor transparency in reporting, and heterogeneous methodology, design, genome coverage, and statistical modelling. We propose 10 recommendations for future prenatal pharmacoepigenetic studies considering both epidemiological and epigenetic perspectives. These recommendations may improve the quality, comparability, and clinical relevance of such studies. PROSPERO registration ID: CRD42020166675.
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Affiliation(s)
- Emilie Willoch Olstad
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Hedvig Marie Egeland Nordeng
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,Department of Child Health and Development, Norwegian Institute of Public Health, Oslo, Norway
| | - Kristina Gervin
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
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26
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Individuals Diagnosed with Binge-Eating Disorder Have DNA Hypomethylated Sites in Genes of the Metabolic System: A Pilot Study. Nutrients 2021; 13:nu13051413. [PMID: 33922358 PMCID: PMC8145109 DOI: 10.3390/nu13051413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/06/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023] Open
Abstract
Binge-eating disorder, recently accepted as a diagnostic category, is differentiated from bulimia nervosa in that the former shows the presence of binge-eating episodes and the absence of compensatory behavior. Epigenetics is a conjunct of mechanisms (like DNA methylation) that regulate gene expression, which are dependent on environmental changes. Analysis of DNA methylation in eating disorders shows that it is reduced. The present study aimed to analyze the genome-wide DNA methylation differences between individuals diagnosed with BED and BN. A total of 46 individuals were analyzed using the Infinium Methylation EPIC array. We found 11 differentially methylated sites between BED- and BN-diagnosed individuals, with genome-wide significance. Most of the associations were found in genes related to metabolic processes (ST3GAL4, PRKAG2, and FRK), which are hypomethylated genes in BED. Cg04781532, located in the body of the PRKAG2 gene (protein kinase AMP-activated non-catalytic subunit gamma 2), was hypomethylated in individuals with BED. Agonists of PRKAG2, which is the subunit of AMPK (AMP-activated protein kinase), are proposed to treat obesity, BED, and BN. The present study contributes important insights into the effect that BED could have on PRKAG2 activation.
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27
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Mayén-Lobo YG, Martínez-Magaña JJ, Pérez-Aldana BE, Ortega-Vázquez A, Genis-Mendoza AD, Dávila-Ortiz de Montellano DJ, Soto-Reyes E, Nicolini H, López-López M, Monroy-Jaramillo N. Integrative Genomic-Epigenomic Analysis of Clozapine-Treated Patients with Refractory Psychosis. Pharmaceuticals (Basel) 2021; 14:118. [PMID: 33557049 PMCID: PMC7913835 DOI: 10.3390/ph14020118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 02/07/2023] Open
Abstract
Clozapine (CLZ) is the only antipsychotic drug that has been proven to be effective in patients with refractory psychosis, but it has also been proposed as an effective mood stabilizer; however, the complex mechanisms of action of CLZ are not yet fully known. To find predictors of CLZ-associated phenotypes (i.e., the metabolic ratio, dosage, and response), we explore the genomic and epigenomic characteristics of 44 patients with refractory psychosis who receive CLZ treatment based on the integration of polygenic risk score (PRS) analyses in simultaneous methylome profiles. Surprisingly, the PRS for bipolar disorder (BD-PRS) was associated with the CLZ metabolic ratio (pseudo-R2 = 0.2080, adjusted p-value = 0.0189). To better explain our findings in a biological context, we assess the protein-protein interactions between gene products with high impact variants in the top enriched pathways and those exhibiting differentially methylated sites. The GABAergic synapse pathway was found to be enriched in BD-PRS and was associated with the CLZ metabolic ratio. Such interplay supports the use of CLZ as a mood stabilizer and not just as an antipsychotic. Future studies with larger sample sizes should be pursued to confirm the findings of this study.
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Affiliation(s)
- Yerye Gibrán Mayén-Lobo
- Department of Biological Systems, Metropolitan Autonomous University-Xochimilco, Mexico City 04960, Mexico; (Y.G.M.-L.); (B.E.P.-A.); (A.O.-V.); (M.L.-L.)
- Department of Genetics, National Institute of Neurology and Neurosurgery, “Manuel Velasco Suárez”, Mexico City 14269, Mexico;
| | - José Jaime Martínez-Magaña
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, Instituto Nacional de Medicina Genómica, SSA, Mexico City 14610, Mexico; (J.J.M.-M.); (A.D.G.-M.); (H.N.)
| | - Blanca Estela Pérez-Aldana
- Department of Biological Systems, Metropolitan Autonomous University-Xochimilco, Mexico City 04960, Mexico; (Y.G.M.-L.); (B.E.P.-A.); (A.O.-V.); (M.L.-L.)
| | - Alberto Ortega-Vázquez
- Department of Biological Systems, Metropolitan Autonomous University-Xochimilco, Mexico City 04960, Mexico; (Y.G.M.-L.); (B.E.P.-A.); (A.O.-V.); (M.L.-L.)
| | - Alma Delia Genis-Mendoza
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, Instituto Nacional de Medicina Genómica, SSA, Mexico City 14610, Mexico; (J.J.M.-M.); (A.D.G.-M.); (H.N.)
| | | | - Ernesto Soto-Reyes
- Natural Sciences Department, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City 05348, Mexico;
| | - Humberto Nicolini
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, Instituto Nacional de Medicina Genómica, SSA, Mexico City 14610, Mexico; (J.J.M.-M.); (A.D.G.-M.); (H.N.)
- Grupo de Estudios Médicos y Familiares Carracci, Mexico City 03740, Mexico
| | - Marisol López-López
- Department of Biological Systems, Metropolitan Autonomous University-Xochimilco, Mexico City 04960, Mexico; (Y.G.M.-L.); (B.E.P.-A.); (A.O.-V.); (M.L.-L.)
| | - Nancy Monroy-Jaramillo
- Department of Genetics, National Institute of Neurology and Neurosurgery, “Manuel Velasco Suárez”, Mexico City 14269, Mexico;
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28
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Carmel M, Michaelovsky E, Weinberger R, Frisch A, Mekori-Domachevsky E, Gothelf D, Weizman A. Differential methylation of imprinting genes and MHC locus in 22q11.2 deletion syndrome-related schizophrenia spectrum disorders. World J Biol Psychiatry 2021; 22:46-57. [PMID: 32212948 DOI: 10.1080/15622975.2020.1747113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVES 22q11.2 deletion syndrome (DS) is the strongest known genetic risk for schizophrenia. Methylome screening was conducted to elucidate possible involvement of epigenetic alterations in the emergence of schizophrenia spectrum disorders (SZ-SD) in 22q11.2DS. METHODS Sixteen adult men with/without SZ-SD were recruited from a 22q11.2DS cohort and underwent genome-wide DNA methylation profile analysis. Differentially methylated probes (DMPs) and regions (DMRs) were analysed using the ChAMP software. RESULTS The DMPs (p-value <10-6) and DMRs (p-valueArea <0.01) were enriched in two gene sets, 'imprinting genes' and 'chr6p21', a region overlapping the MHC locus. Most of the identified imprinting genes are involved in neurodevelopment and located in clusters under imprinting control region (ICR) regulation, including PEG10, SGCE (7q21.3), GNAS, GNAS-AS1 (20q13.32) and SNHG14, SNURF-SNRPN, SNORD115 (15q11.2). The differentially methylated genes from the MHC locus included immune HLA-genes and non-immune genes, RNF39, PPP1R18 and NOTCH4, implicated in neurodevelopment and synaptic plasticity. The most significant DMR is located in MHC locus and covered the transcription regulator ZFP57 that is required for control and maintenance of gene imprinting at multiple ICRs. CONCLUSIONS The differential methylation in imprinting genes and in chr6p21-22 indicate the neurodevelopmental nature of 22q11.2DS-related SZ and the major role of MHC locus in the risk to develop SZ.
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Affiliation(s)
- Miri Carmel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Elena Michaelovsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Ronnie Weinberger
- The Behavioral Neurogenetics Center and Child Psychiatry Division, Sheba Medical Center, Ramat Gan, Israel
| | - Amos Frisch
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Ehud Mekori-Domachevsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Behavioral Neurogenetics Center and Child Psychiatry Division, Sheba Medical Center, Ramat Gan, Israel
| | - Doron Gothelf
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Behavioral Neurogenetics Center and Child Psychiatry Division, Sheba Medical Center, Ramat Gan, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Abraham Weizman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Geha Mental Health Center, Petach Tikva, Israel
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29
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Nuotio ML, Pervjakova N, Joensuu A, Karhunen V, Hiekkalinna T, Milani L, Kettunen J, Järvelin MR, Jousilahti P, Metspalu A, Salomaa V, Kristiansson K, Perola M. An epigenome-wide association study of metabolic syndrome and its components. Sci Rep 2020; 10:20567. [PMID: 33239708 PMCID: PMC7688654 DOI: 10.1038/s41598-020-77506-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 11/09/2020] [Indexed: 12/14/2022] Open
Abstract
The role of metabolic syndrome (MetS) as a preceding metabolic state for type 2 diabetes and cardiovascular disease is widely recognised. To accumulate knowledge of the pathological mechanisms behind the condition at the methylation level, we conducted an epigenome-wide association study (EWAS) of MetS and its components, testing 1187 individuals of European ancestry for approximately 470 000 methylation sites throughout the genome. Methylation site cg19693031 in gene TXNIP —previously associated with type 2 diabetes, glucose and lipid metabolism, associated with fasting glucose level (P = 1.80 × 10−8). Cg06500161 in gene ABCG1 associated both with serum triglycerides (P = 5.36 × 10−9) and waist circumference (P = 5.21 × 10−9). The previously identified type 2 diabetes–associated locus cg08309687 in chromosome 21 associated with waist circumference for the first time (P = 2.24 × 10−7). Furthermore, a novel HDL association with cg17901584 in chromosome 1 was identified (P = 7.81 × 10−8). Our study supports previous genetic studies of MetS, finding that lipid metabolism plays a key role in pathology of the syndrome. We provide evidence regarding a close interplay with glucose metabolism. Finally, we suggest that in attempts to identify methylation loci linking separate MetS components, cg19693031 appears to represent a strong candidate.
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Affiliation(s)
- Marja-Liisa Nuotio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland. .,Genomics and Biobank Unit, Department of Public Health Solutions, National Institute for Health and Welfare, Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland. .,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Natalia Pervjakova
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anni Joensuu
- Genomics and Biobank Unit, Department of Public Health Solutions, National Institute for Health and Welfare, Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ville Karhunen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland.,Oulu University Hospital, Oulu, Finland.,Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Tero Hiekkalinna
- Genomics and Biobank Unit, Department of Public Health Solutions, National Institute for Health and Welfare, Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland
| | - Lili Milani
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Johannes Kettunen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland.,Population Health Science, Bristol Medical School, University of Bristol and Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland.,Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | | | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kati Kristiansson
- Genomics and Biobank Unit, Department of Public Health Solutions, National Institute for Health and Welfare, Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Markus Perola
- Genomics and Biobank Unit, Department of Public Health Solutions, National Institute for Health and Welfare, Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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30
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De Lillo A, Pathak GA, De Angelis F, Di Girolamo M, Luigetti M, Sabatelli M, Perfetto F, Frusconi S, Manfellotto D, Fuciarelli M, Polimanti R. Epigenetic profiling of Italian patients identified methylation sites associated with hereditary transthyretin amyloidosis. Clin Epigenetics 2020; 12:176. [PMID: 33203445 PMCID: PMC7672937 DOI: 10.1186/s13148-020-00967-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 11/03/2020] [Indexed: 11/10/2022] Open
Abstract
Hereditary transthyretin (TTR) amyloidosis (hATTR) is a rare life-threatening disorder caused by amyloidogenic coding mutations located in TTR gene. To understand the high phenotypic variability observed among carriers of TTR disease-causing mutations, we conducted an epigenome-wide association study (EWAS) assessing more than 700,000 methylation sites and testing epigenetic difference of TTR coding mutation carriers vs. non-carriers. We observed a significant methylation change at cg09097335 site located in Beta-secretase 2 (BACE2) gene (standardized regression coefficient = -0.60, p = 6.26 × 10-8). This gene is involved in a protein interaction network enriched for biological processes and molecular pathways related to amyloid-beta metabolism (Gene Ontology: 0050435, q = 0.007), amyloid fiber formation (Reactome HSA-977225, q = 0.008), and Alzheimer's disease (KEGG hsa05010, q = 2.2 × 10-4). Additionally, TTR and BACE2 share APP (amyloid-beta precursor protein) as a validated protein interactor. Within TTR gene region, we observed that Val30Met disrupts a methylation site, cg13139646, causing a drastic hypomethylation in carriers of this amyloidogenic mutation (standardized regression coefficient = -2.18, p = 3.34 × 10-11). Cg13139646 showed co-methylation with cg19203115 (Pearson's r2 = 0.32), which showed significant epigenetic differences between symptomatic and asymptomatic carriers of amyloidogenic mutations (standardized regression coefficient = -0.56, p = 8.6 × 10-4). In conclusion, we provide novel insights related to the molecular mechanisms involved in the complex heterogeneity of hATTR, highlighting the role of epigenetic regulation in this rare disorder.
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Affiliation(s)
| | - Gita A Pathak
- Department of Psychiatry, Yale University School of Medicine, VA CT Healthcare Center, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, USA
- VA CT Healthcare Center, West Haven, CT, USA
| | - Flavio De Angelis
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- Department of Psychiatry, Yale University School of Medicine, VA CT Healthcare Center, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, USA
- VA CT Healthcare Center, West Haven, CT, USA
| | - Marco Di Girolamo
- Clinical Pathophysiology Center, Fatebenefratelli Foundation -'San Giovanni Calibita' Fatebenefratelli Hospital, Rome, Italy
| | - Marco Luigetti
- Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Neurologia, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Mario Sabatelli
- Università Cattolica del Sacro Cuore, Rome, Italy
- Centro Clinico NEMO Adulti, Rome, Italy
| | - Federico Perfetto
- Regional Amyloid Centre, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Sabrina Frusconi
- Genetic Diagnostics Unit, Laboratory Department, Careggi University Hospital, Florence, Italy
| | - Dario Manfellotto
- Clinical Pathophysiology Center, Fatebenefratelli Foundation -'San Giovanni Calibita' Fatebenefratelli Hospital, Rome, Italy
| | - Maria Fuciarelli
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, VA CT Healthcare Center, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, USA.
- VA CT Healthcare Center, West Haven, CT, USA.
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31
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Smyth LJ, Patterson CC, Swan EJ, Maxwell AP, McKnight AJ. DNA Methylation Associated With Diabetic Kidney Disease in Blood-Derived DNA. Front Cell Dev Biol 2020; 8:561907. [PMID: 33178681 PMCID: PMC7593403 DOI: 10.3389/fcell.2020.561907] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/15/2020] [Indexed: 12/23/2022] Open
Abstract
A subset of individuals with type 1 diabetes will develop diabetic kidney disease (DKD). DKD is heritable and large-scale genome-wide association studies have begun to identify genetic factors that influence DKD. Complementary to genetic factors, we know that a person’s epigenetic profile is also altered with DKD. This study reports analysis of DNA methylation, a major epigenetic feature, evaluating methylome-wide loci for association with DKD. Unique features (n = 485,577; 482,421 CpG probes) were evaluated in blood-derived DNA from carefully phenotyped White European individuals diagnosed with type 1 diabetes with (cases) or without (controls) DKD (n = 677 samples). Explicitly, 150 cases were compared to 100 controls using the 450K array, with subsequent analysis using data previously generated for a further 96 cases and 96 controls on the 27K array, and de novo methylation data generated for replication in 139 cases and 96 controls. Following stringent quality control, raw data were quantile normalized and beta values calculated to reflect the methylation status at each site. The difference in methylation status was evaluated between cases and controls; resultant P-values for array-based data were adjusted for multiple testing. Genes with significantly increased (hypermethylated) and/or decreased (hypomethylated) levels of DNA methylation were considered for biological relevance by functional enrichment analysis using KEGG pathways. Twenty-two loci demonstrated statistically significant fold changes associated with DKD and additional support for these associated loci was sought using independent samples derived from patients recruited with similar inclusion criteria. Markers associated with CCNL1 and ZNF187 genes are supported as differentially regulated loci (P < 10–8), with evidence also presented for AFF3, which has been identified from a meta-analysis and subsequent replication of genome-wide association studies. Further supporting evidence for differential gene expression in CCNL1 and ZNF187 is presented from kidney biopsy and blood-derived RNA in people with and without kidney disease from NephroSeq. Evidence confirming that methylation sites influence the development of DKD may aid risk prediction tools and stimulate research to identify epigenomic therapies which might be clinically useful for this disease.
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Affiliation(s)
- Laura J Smyth
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | | | - Elizabeth J Swan
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | - Alexander P Maxwell
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom.,Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom
| | - Amy Jayne McKnight
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
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32
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Dritsoula A, Kislikova M, Oomatia A, Webster AP, Beck S, Ponticos M, Lindsey B, Norman J, Wheeler DC, Oates T, Caplin B. "Epigenome-wide methylation profile of chronic kidney disease-derived arterial DNA uncovers novel pathways in disease-associated cardiovascular pathology.". Epigenetics 2020; 16:718-728. [PMID: 32930636 DOI: 10.1080/15592294.2020.1819666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chronic kidney disease (CKD) related cardiovascular disease (CVD) is characterized by vascular remodelling with well-established structural and functional changes in the vascular wall such as arterial stiffness, matrix deposition, and calcification. These phenotypic changes resemble pathology seen in ageing, and are likely to be mediated by sustained alterations in gene expression, which may be caused by epigenetic changes such as tissue-specific DNA methylation. We aimed to investigate tissue specific changes in DNA methylation that occur in CKD-related CVD. Genome-wide DNA methylation changes were examined in bisulphite converted genomic DNA isolated from the vascular media of CKD and healthy arteries. Methylation-specific PCR was used to validate the array data, and the association between DNA methylation and gene and protein expression was examined. The DNA methylation age was compared to the chronological age in both cases and controls. Three hundred and nineteen differentially methylated regions (DMR) were identified spread across the genome. Pathway analysis revealed that DMRs associated with genes were involved in embryonic and vascular development, and signalling pathways such as TGFβ and FGF. Expression of top differentially methylated gene HOXA5 showed a significant negative correlation with DNA methylation. Interestingly, DNA methylation age and chronological age were highly correlated, but there was no evidence of accelerated age-related DNA methylation in the arteries of CKD patients. In conclusion, we demonstrated that differential DNA methylation in the arterial tissue of CKD patients represents a potential mediator of arterial pathology and may be used to uncover novel pathways in the genesis of CKD-associated complications.
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Affiliation(s)
- Athina Dritsoula
- Department of Renal Medicine, Division of Medicine, UCL, London, UK
| | - Maria Kislikova
- Department of Renal Medicine, Division of Medicine, UCL, London, UK.,Department of Nephrology, University Hospital Marqués de Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Amin Oomatia
- Department of Renal Medicine, Division of Medicine, UCL, London, UK
| | - Amy P Webster
- Department of Cancer Biology, Cancer Institute, UCL, London, UK
| | - Stephan Beck
- Department of Cancer Biology, Cancer Institute, UCL, London, UK
| | - Markella Ponticos
- Centre for Rheumatology and Connective Tissue Diseases, Division of Medicine, UCL, London, UK
| | - Ben Lindsey
- Department of Renal Medicine, Division of Medicine, UCL, London, UK
| | - Jill Norman
- Department of Renal Medicine, Division of Medicine, UCL, London, UK
| | - David C Wheeler
- Department of Renal Medicine, Division of Medicine, UCL, London, UK
| | - Thomas Oates
- Department of Renal Medicine, Division of Medicine, UCL, London, UK.,Departments of Nephrology and General Medicine, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Ben Caplin
- Department of Renal Medicine, Division of Medicine, UCL, London, UK
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33
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Hughes DA, Bacigalupe R, Wang J, Rühlemann MC, Tito RY, Falony G, Joossens M, Vieira-Silva S, Henckaerts L, Rymenans L, Verspecht C, Ring S, Franke A, Wade KH, Timpson NJ, Raes J. Genome-wide associations of human gut microbiome variation and implications for causal inference analyses. Nat Microbiol 2020; 5:1079-1087. [PMID: 32572223 PMCID: PMC7610462 DOI: 10.1038/s41564-020-0743-8] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 05/18/2020] [Indexed: 12/15/2022]
Abstract
Recent population-based1-4 and clinical studies5 have identified a range of factors associated with human gut microbiome variation. Murine quantitative trait loci6, human twin studies7 and microbiome genome-wide association studies1,3,8-12 have provided evidence for genetic contributions to microbiome composition. Despite this, there is still poor overlap in genetic association across human studies. Using appropriate taxon-specific models, along with support from independent cohorts, we show an association between human host genotype and gut microbiome variation. We also suggest that interpretation of applied analyses using genetic associations is complicated by the probable overlap between genetic contributions and heritable components of host environment. Using faecal 16S ribosomal RNA gene sequences and host genotype data from the Flemish Gut Flora Project (n = 2,223) and two German cohorts (FoCus, n = 950; PopGen, n = 717), we identify genetic associations involving multiple microbial traits. Two of these associations achieved a study-level threshold of P = 1.57 × 10-10; an association between Ruminococcus and rs150018970 near RAPGEF1 on chromosome 9, and between Coprococcus and rs561177583 within LINC01787 on chromosome 1. Exploratory analyses were undertaken using 11 other genome-wide associations with strong evidence for association (P < 2.5 × 10-8) and a previously reported signal of association between rs4988235 (MCM6/LCT) and Bifidobacterium. Across these 14 single-nucleotide polymorphisms there was evidence of signal overlap with other genome-wide association studies, including those for age at menarche and cardiometabolic traits. Mendelian randomization analysis was able to estimate associations between microbial traits and disease (including Bifidobacterium and body composition); however, in the absence of clear microbiome-driven effects, caution is needed in interpretation. Overall, this work marks a growing catalogue of genetic associations that will provide insight into the contribution of host genotype to gut microbiome. Despite this, the uncertain origin of association signals will likely complicate future work looking to dissect function or use associations for causal inference analysis.
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Affiliation(s)
- David A Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Rodrigo Bacigalupe
- Department of Microbiology and Immunology, Rega Instituut, KU Leuven-University of Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Jun Wang
- Department of Microbiology and Immunology, Rega Instituut, KU Leuven-University of Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Malte C Rühlemann
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Raul Y Tito
- Department of Microbiology and Immunology, Rega Instituut, KU Leuven-University of Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Gwen Falony
- Department of Microbiology and Immunology, Rega Instituut, KU Leuven-University of Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Marie Joossens
- Department of Microbiology and Immunology, Rega Instituut, KU Leuven-University of Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, Rega Instituut, KU Leuven-University of Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Liesbet Henckaerts
- Department of Microbiology, Immunology and Transplantation, KU Leuven-University of Leuven, Leuven, Belgium
- Department of General Internal Medicine, KU Leuven-University Hospitals Leuven, Leuven, Belgium
| | - Leen Rymenans
- Department of Microbiology and Immunology, Rega Instituut, KU Leuven-University of Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Chloë Verspecht
- Department of Microbiology and Immunology, Rega Instituut, KU Leuven-University of Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Susan Ring
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol Bioresource Laboratories, University of Bristol, Bristol, UK
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Kaitlin H Wade
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Instituut, KU Leuven-University of Leuven, Leuven, Belgium.
- Center for Microbiology, VIB, Leuven, Belgium.
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34
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Shanthikumar S, Neeland MR, Maksimovic J, Ranganathan SC, Saffery R. DNA methylation biomarkers of future health outcomes in children. Mol Cell Pediatr 2020; 7:7. [PMID: 32642955 PMCID: PMC7343681 DOI: 10.1186/s40348-020-00099-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/25/2020] [Indexed: 11/10/2022] Open
Abstract
Biomarkers which predict future health outcomes are key to the goals of precision health. Such biomarkers do not have to be involved in the causal pathway of a disease, and their performance is best assessed using statistical tests of clinical performance and evaluation of net health impact. DNA methylation is the most commonly studied epigenetic process and represents a potential biomarker of future health outcomes. We review 25 studies in non-oncological paediatric conditions where DNA methylation biomarkers of future health outcomes are assessed. Whilst a number of positive findings have been described, the body of evidence is severely limited by issues with outcome measures, tissue-specific samples, accounting for sample cell type heterogeneity, lack of appropriate statistical testing, small effect sizes, limited validation, and no assessment of net health impact. Future studies should concentrate on careful study design to overcome these issues, and integration of DNA methylation data with other 'omic', clinical, and environmental data to generate the most clinically useful biomarkers of paediatric disease.
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Affiliation(s)
- Shivanthan Shanthikumar
- Respiratory and Sleep Medicine, Royal Children's Hospital, Flemington Road, Parkville, Melbourne, Victoria, 3052, Australia. .,Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Australia. .,Department of Paediatrics, The University of Melbourne, Melbourne, Australia.
| | - Melanie R Neeland
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia.,Epigenetics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Jovana Maksimovic
- Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia.,Computational Biology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Sarath C Ranganathan
- Respiratory and Sleep Medicine, Royal Children's Hospital, Flemington Road, Parkville, Melbourne, Victoria, 3052, Australia.,Respiratory Diseases, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Richard Saffery
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia.,Epigenetics, Murdoch Children's Research Institute, Melbourne, Australia
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35
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Stathopoulos S, Gaujoux R, Lindeque Z, Mahony C, Van Der Colff R, Van Der Westhuizen F, O'Ryan C. DNA Methylation Associated with Mitochondrial Dysfunction in a South African Autism Spectrum Disorder Cohort. Autism Res 2020; 13:1079-1093. [PMID: 32490597 PMCID: PMC7496548 DOI: 10.1002/aur.2310] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/24/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023]
Abstract
Autism spectrum disorder (ASD) is characterized by phenotypic heterogeneity and a complex genetic architecture which includes distinctive epigenetic patterns. We report differential DNA methylation patterns associated with ASD in South African children. An exploratory whole‐epigenome methylation screen using the Illumina 450 K MethylationArray identified differentially methylated CpG sites between ASD and controls that mapped to 898 genes (P ≤ 0.05) which were enriched for nine canonical pathways converging on mitochondrial metabolism and protein ubiquitination. Targeted Next Generation Bisulfite Sequencing of 27 genes confirmed differential methylation between ASD and control in our cohort. DNA pyrosequencing of two of these genes, the mitochondrial enzyme Propionyl‐CoA Carboxylase subunit Beta (PCCB) and Protocadherin Alpha 12 (PCDHA12), revealed a wide range of methylation levels (9–49% and 0–54%, respectively) in both ASD and controls. Three CpG loci were differentially methylated in PCCB (P ≤ 0.05), while PCDHA12, previously linked to ASD, had two significantly different CpG sites (P ≤ 0.001) between ASD and control. Differentially methylated CpGs were hypomethylated in ASD. Metabolomic analysis of urinary organic acids revealed that three metabolites, 3‐hydroxy‐3‐methylglutaric acid (P = 0.008), 3‐methyglutaconic acid (P = 0.018), and ethylmalonic acid (P = 0.043) were significantly elevated in individuals with ASD. These metabolites are directly linked to mitochondrial respiratory chain disorders, with a putative link to PCCB, consistent with impaired mitochondrial function. Our data support an association between DNA methylation and mitochondrial dysfunction in the etiology of ASD. Autism Res 2020, 13: 1079‐1093. © 2020 The Authors. Autism Research published by International Society for Autism Research published by Wiley Periodicals, Inc. Lay Summary Epigenetic changes are chemical modifications of DNA which can change gene function. DNA methylation, a type of epigenetic modification, is linked to autism. We examined DNA methylation in South African children with autism and identified mitochondrial genes associated with autism. Mitochondria are power‐suppliers in cells and mitochondrial genes are essential to metabolism and energy production, which are important for brain cells during development. Our findings suggest that some individuals with ASD also have mitochondrial dysfunction.
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Affiliation(s)
- Sofia Stathopoulos
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | | | - Zander Lindeque
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Caitlyn Mahony
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Rachelle Van Der Colff
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | | | - Colleen O'Ryan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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Housman G, Quillen EE, Stone AC. Intraspecific and interspecific investigations of skeletal DNA methylation and femur morphology in primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:34-49. [PMID: 32170728 DOI: 10.1002/ajpa.24041] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Epigenetic mechanisms influence the development and maintenance of complex phenotypes and may also contribute to the evolution of species-specific phenotypes. With respect to skeletal traits, little is known about the gene regulation underlying these hard tissues or how tissue-specific patterns are associated with bone morphology or vary among species. To begin exploring these topics, this study evaluates one epigenetic mechanism, DNA methylation, in skeletal tissues from five nonhuman primate species which display anatomical and locomotor differences representative of their phylogenetic groups. MATERIALS AND METHODS First, we test whether intraspecific variation in skeletal DNA methylation is associated with intraspecific variation in femur morphology. Second, we identify interspecific differences in DNA methylation and assess whether these lineage-specific patterns may have contributed to species-specific morphologies. Specifically, we use the Illumina Infinium MethylationEPIC BeadChip to identify DNA methylation patterns in femur trabecular bone from baboons (n = 28), macaques (n = 10), vervets (n = 10), chimpanzees (n = 4), and marmosets (n = 6). RESULTS Significant differentially methylated positions (DMPs) were associated with a subset of morphological variants, but these likely have small biological effects and may be confounded by other variables associated with morphological variation. Conversely, several species-specific DMPs were identified, and these are found in genes enriched for functions associated with complex skeletal traits. DISCUSSION Overall, these findings reveal that while intraspecific epigenetic variation is not readily associated with skeletal morphology differences, some interspecific epigenetic differences in skeletal tissues exist and may contribute to evolutionarily distinct phenotypes. This work forms a foundation for future explorations of gene regulation and skeletal trait evolution in primates.
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Affiliation(s)
- Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - Ellen E Quillen
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
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Silva R, Moran B, Russell NM, Fahey C, Vlajnic T, Manecksha RP, Finn SP, Brennan DJ, Gallagher WM, Perry AS. Evaluating liquid biopsies for methylomic profiling of prostate cancer. Epigenetics 2020; 15:715-727. [PMID: 32000564 PMCID: PMC7574384 DOI: 10.1080/15592294.2020.1712876] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background: Liquid biopsies offer significant potential for informing on cancer progression and therapeutic resistance via minimally invasive serial monitoring of genetic alterations. Although the cancer epigenome is a central driving force in most neoplasia, the accuracy of monitoring the tumor methylome using liquid biopsies remains relatively unknown. Objectives: to investigate how well two types of liquid biopsy (urine and blood) capture the prostate cancer methylome, and may thus serve as a non-invasive surrogate for studying the tumor epigenome. Methods: A cohort of four metastatic treatment naïve prostate cancer (PCa) patients was selected. Matched biopsy cores (tumor and histologically matched-normal), post-DRE, pre-biopsy urine, and peripheral blood plasma were available for each subject. DNA methylation was profiled utilizing the Infinium® MethylationEPIC BeadChip (Illumina) and analysed using the RnBeads software. Significantly (FDR adjusted P < 0.05) differentially methylated probes (DMPs) between tumor and MN were identified and examined in the liquids (done at a grouped and individual subject level). Results: DNA methylation analysis of urine and blood in men with metastatic PCa showed highly correlated patterns between the different liquid types (ρ = 0.93, P < 0.0001), with large contributions from non-tumor sources. DNA methylation profiles of liquids were more similar between subjects, than intra-individual liquid-tumor correlations. Overall, both urine and plasma are viable surrogates for tumor tissue biopsies, capturing up to 39.40% and 64.14% of tumor-specific methylation alterations, respectively. Conclusion: We conclude that both urine and blood plasma are easily accessible and sensitive biofluids for the study of PCa epigenomic alterations.
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Affiliation(s)
- Romina Silva
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin, Ireland.,School of Medicine, University College Dublin , Dublin, Ireland
| | - Bruce Moran
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin, Ireland.,Ireland East Hospital Group (IEHG), St. Vincent's University Hospital , Dublin, Ireland
| | - Niamh M Russell
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin, Ireland.,School of Biomolecular and Biomedical Science, University College Dublin , Dublin, Ireland
| | - Ciara Fahey
- Prostate Molecular Oncology, Trinity Translational Medicine Institute, Trinity College Dublin , Dublin, Ireland
| | - Tatjana Vlajnic
- Department of Histopathology, St James's Hospital , Dublin, Ireland.,Institute of Pathology, University Hospital Basel , Basel, Switzerland
| | - Rustom P Manecksha
- Department of Urology, St. James's Hospital and Trinity College Dublin , Dublin, Ireland
| | - Stephen P Finn
- Department of Histopathology, St James's Hospital , Dublin, Ireland
| | - Donal J Brennan
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin, Ireland.,School of Medicine, University College Dublin , Dublin, Ireland
| | - William M Gallagher
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin, Ireland.,School of Biomolecular and Biomedical Science, University College Dublin , Dublin, Ireland
| | - Antoinette S Perry
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin, Ireland.,Prostate Molecular Oncology, Trinity Translational Medicine Institute, Trinity College Dublin , Dublin, Ireland.,School of Biology and Environmental Science, University College Dublin , Dublin, Ireland
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Ringh MV, Hagemann-Jensen M, Needhamsen M, Kular L, Breeze CE, Sjöholm LK, Slavec L, Kullberg S, Wahlström J, Grunewald J, Brynedal B, Liu Y, Almgren M, Jagodic M, Öckinger J, Ekström TJ. Tobacco smoking induces changes in true DNA methylation, hydroxymethylation and gene expression in bronchoalveolar lavage cells. EBioMedicine 2019; 46:290-304. [PMID: 31303497 PMCID: PMC6710853 DOI: 10.1016/j.ebiom.2019.07.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 12/21/2022] Open
Abstract
Background While smoking is known to associate with development of multiple diseases, the underlying mechanisms are still poorly understood. Tobacco smoking can modify the chemical integrity of DNA leading to changes in transcriptional activity, partly through an altered epigenetic state. We aimed to investigate the impact of smoking on lung cells collected from bronchoalveolar lavage (BAL). Methods We profiled changes in DNA methylation (5mC) and its oxidised form hydroxymethylation (5hmC) using conventional bisulphite (BS) treatment and oxidative bisulphite treatment with Illumina Infinium MethylationEPIC BeadChip, and examined gene expression by RNA-seq in healthy smokers. Findings We identified 1667 total 5mC + 5hmC, 1756 5mC and 67 5hmC differentially methylated positions (DMPs) between smokers and non-smokers (FDR-adjusted P <.05, absolute Δβ >0.15). Both 5mC DMPs and to a lesser extent 5mC + 5hmC were predominantly hypomethylated. In contrast, almost all 5hmC DMPs were hypermethylated, supporting the hypothesis that smoking-associated oxidative stress can lead to DNA demethylation, via the established sequential oxidation of which 5hmC is the first step. While we confirmed differential methylation of previously reported smoking-associated 5mC + 5hmC CpGs using former generations of BeadChips in alveolar macrophages, the large majority of identified DMPs, 5mC + 5hmC (1639/1667), 5mC (1738/1756), and 5hmC (67/67), have not been previously reported. Most of these novel smoking-associating sites are specific to the EPIC BeadChip and, interestingly, many of them are associated to FANTOM5 enhancers. Transcriptional changes affecting 633 transcripts were consistent with DNA methylation profiles and converged to alteration of genes involved in migration, signalling and inflammatory response of immune cells. Interpretation Collectively, these findings suggest that tobacco smoke exposure epigenetically modifies BAL cells, possibly involving a continuous active demethylation and subsequent increased activity of inflammatory processes in the lungs. Fund The study was supported by the Swedish Research Council, the Swedish Heart-Lung Foundation, the Stockholm County Council (ALF), the King Gustav's and Queen Victoria's Freemasons' Foundation, Knut and Alice Wallenberg Foundation, Neuro Sweden, and the Swedish MS foundation.
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Affiliation(s)
- Mikael V Ringh
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden.
| | - Michael Hagemann-Jensen
- Department of Medicine, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
| | - Charles E Breeze
- Altius Institute for Biomedical Sciences, Seattle, USA; UCL Cancer Institute, University College London, London, United Kingdom
| | - Louise K Sjöholm
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
| | - Lara Slavec
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
| | - Susanna Kullberg
- Department of Medicine, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden; Department of Respiratory Medicine, Theme Inflammation and Infection, Karolinska University Hospital, Stockholm, Sweden
| | - Jan Wahlström
- Department of Medicine, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
| | - Johan Grunewald
- Department of Medicine, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
| | - Boel Brynedal
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yun Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Malin Almgren
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
| | - Johan Öckinger
- Department of Medicine, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
| | - Tomas J Ekström
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden.
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