scholarly journals Epigenetic Signatures in Antidepressant Treatment Response: a Methylome-wide Association Study in the EMC Trial

2022 ◽  
Author(s):  
Jan Engelmann ◽  
Lea Zillich ◽  
Josef Frank ◽  
Stefanie Wagner ◽  
Metin Cetin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Treatment Response ◽  
Antidepressant Treatment ◽  
Association Studies ◽  
Genetic Material ◽  
Differential Methylation ◽  
Secondary Outcome ◽  
Genome Wide Association Studies ◽  
Antidepressant Response ◽  
Early Improvement

Abstract Although the currently available antidepressants are well established in the treatment of major depressive disorder (MDD), there is strong variability in the response of individual patients. Reliable predictors to guide treatment decisions before or in an early stage of treatment are needed. DNA-methylation has been proven a useful biomarker in different clinical conditions, but its importance for mechanisms of antidepressant response has not yet been determined. 80 MDD patients were selected out of >500 participants from the Early Medication Change (EMC) cohort with available genetic material based on their antidepressant response after four weeks and stratified into clear responders and age- and sex-matched non-responders (N=40, each). Early improvement after two weeks was analyzed as a secondary outcome. DNA-methylation was determined using the Illumina EPIC BeadChip. Epigenome-wide association studies were performed and differentially methylated regions (DMRs) identified using the comb-p algorithm. Enrichment was tested for hallmark gene-sets and in genome-wide association studies of depression and antidepressant response. No epigenome-wide significant differentially methylated positions were found for treatment response or early improvement. Twenty DMRs were associated with response; the strongest in an enhancer region in SORBS2, which has been related to cardiovascular diseases and type II diabetes. Another DMR was located in CYP2C18, a gene previously linked to antidepressant response. Results pointed towards differential methylation in genes associated with cardiac function, neuroticism, and depression. Linking differential methylation to antidepressant treatment response is an emerging topic and represents a step towards personalized medicine, potentially facilitating the prediction of patients’ response before treatment.

scholarly journals New insights on the pharmacogenomics of antidepressant response from the GENDEP and STAR*D studies: rare variant analysis and high-density imputation

2017 ◽  
Author(s):  
Chiara Fabbri ◽  
Katherine E. Tansey ◽  
Roy H. Perlis ◽  
Joanna Hauser ◽  
Neven Henigsberg ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Antidepressant Treatment ◽  
Association Studies ◽  
Research Network ◽  
Antidepressant Effect ◽  
Symptom Improvement ◽  
Genome Wide Association Studies ◽  
Antidepressant Response ◽  
Genome Wide ◽  
Pathway Level

AbstractGenome-wide association studies have generally failed to identify polymorphisms associated with antidepressant response. Possible reasons include limited coverage of genetic variants that this study tried to address by exome genotyping and dense imputation.A meta-analysis of Genome-Based Therapeutic Drugs for Depression (GENDEP) and Sequenced Treatment Alternatives to Relieve Depression (STAR*D) studies was performed at SNP, gene and pathway level. Coverage of genetic variants was increased compared to previous studies by adding exome genotypes to previously available genome-wide data and using the Haplotype Reference Consortium panel for imputation. Standard quality control was applied. Phenotypes were symptom improvement and remission after 12 weeks of antidepressant treatment. NEWMEDS consortium samples and Pharmacogenomic Research Network Antidepressant Medication Pharmacogenomic Study (PGRN-AMPS) served for replication.7,062,950 SNPs were analysed in GENDEP (n=738) and STAR*D (n=1409). rs116692768 (p=1.80e-08, ITGA9 (integrin alpha 9)) and rs76191705 (p=2.59e-08, NRXN3 (neurexin 3)) were significantly associated with symptom improvement during citalopram/escitalopram treatment. At gene level, no consistent effect was found. At pathway level, the Gene Ontology terms GO:0005694 (chromosome) and GO:0044427 (chromosomal part) were associated with improvement (corrected p=0.007 and 0.045, respectively). The association between rs116692768 and symptom improvement was replicated in PGRN-AMPS (p=0.047), while rs76191705 was not. The two SNPs did not replicate in NEWMEDS.ITGA9 codes for a membrane receptor for neurotrophins and NRXN3 is a transmembrane neuronal adhesion receptor involved in synaptic differentiation. Despite their meaningful biological rationale for being involved in antidepressant effect, no convincing replication was achieved. Further studies may help in clarifying their role.

scholarly journals Schizophrenia-associated differential DNA methylation in the superior temporal gyrus is distributed to many sites across the genome and annotated by the risk gene MAD1L1

2020 ◽  
Author(s):  
Brandon C McKinney ◽  
Christopher M Hensler ◽  
Yue Wei ◽  
David A Lewis ◽  
Jiebiao Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Environmental Factors ◽  
Genetic Variants ◽  
Association Studies ◽  
Superior Temporal Gyrus ◽  
Differential Methylation ◽  
Composition Analysis ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
The Individual

Background: Many genetic variants and multiple environmental factors increase risk for schizophrenia (SZ). SZ-associated genetic variants and environmental risk factors have been associated with altered DNA methylation (DNAm), the addition of a methyl group to a cytosine in DNA. DNAm changes, acting through effects on gene expression, represent one potential mechanism by which genetic and environmental factors confer risk for SZ and alter neurobiology. Methods: We investigated the hypothesis that DNAm in superior temporal gyrus (STG) is altered in SZ. We measured genome-wide DNAm in postmortem STG from 44 SZ subjects and 44 non-psychiatric comparison (NPC) subjects using Illumina Infinium MethylationEPIC BeadChip microarrays. We applied tensor composition analysis to extract cell type-specific DNAm signals. Results: We found that DNAm levels differed between SZ and NPC subjects at 242 sites, and 44 regions comprised of two or more sites, with a false discovery rate cutoff of q=0.1. We determined differential methylation at nine of the individual sites were driven by neuron-specific DNAm alterations. Glia-specific DNAm alterations drove the differences at two sites. Notably, we identied SZ-associated differential methylation within within mitotic arrest deficient 1-like 1 (MAD1L1), a gene strongly associated with SZ through genome-wide association studies. Conclusions: This study adds to a growing number of studies that implicate DNAm, and epigenetic pathways more generally, in SZ. Our findings suggest differential methylation may contribute to STG dysfunction in SZ. Future studies to identify the mechanisms by which altered DNAm, especially within MAD1L1, contributes to SZ neurobiology are warranted.

scholarly journals Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Daniel L. McCartney ◽  
Josine L. Min ◽  
Rebecca C. Richmond ◽  
Ake T. Lu ◽  
Maria K. Sobczyk ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Genome Wide Association ◽  
Biological Aging ◽  
Genome Wide Association Studies ◽  
Genetic Loci ◽  
Biomarkers Of Aging ◽  
Genome Wide ◽  
Shared Genetic

Abstract Background Biological aging estimators derived from DNA methylation data are heritable and correlate with morbidity and mortality. Consequently, identification of genetic and environmental contributors to the variation in these measures in populations has become a major goal in the field. Results Leveraging DNA methylation and SNP data from more than 40,000 individuals, we identify 137 genome-wide significant loci, of which 113 are novel, from genome-wide association study (GWAS) meta-analyses of four epigenetic clocks and epigenetic surrogate markers for granulocyte proportions and plasminogen activator inhibitor 1 levels, respectively. We find evidence for shared genetic loci associated with the Horvath clock and expression of transcripts encoding genes linked to lipid metabolism and immune function. Notably, these loci are independent of those reported to regulate DNA methylation levels at constituent clock CpGs. A polygenic score for GrimAge acceleration showed strong associations with adiposity-related traits, educational attainment, parental longevity, and C-reactive protein levels. Conclusion This study illuminates the genetic architecture underlying epigenetic aging and its shared genetic contributions with lifestyle factors and longevity.

scholarly journals Genetics and Epigenetics in Asthma

2021 ◽  
Vol 22 (5) ◽  
pp. 2412
Author(s):  
Polyxeni Ntontsi ◽  
Andreas Photiades ◽  
Eleftherios Zervas ◽  
Georgina Xanthou ◽  
Konstantinos Samitas
Keyword(s):  
Dna Methylation ◽  
Association Studies ◽  
Airway Remodeling ◽  
Methylation Pattern ◽  
Atopic Asthma ◽  
Genome Wide Association Studies ◽  
Childhood Onset ◽  
Gene Markers ◽  
Asthmatic Patients ◽  
Asthma Susceptibility

Asthma is one of the most common respiratory disease that affects both children and adults worldwide, with diverse phenotypes and underlying pathogenetic mechanisms poorly understood. As technology in genome sequencing progressed, scientific efforts were made to explain and predict asthma’s complexity and heterogeneity, and genome-wide association studies (GWAS) quickly became the preferred study method. Several gene markers and loci associated with asthma susceptibility, atopic and childhood-onset asthma were identified during the last few decades. Markers near the ORMDL3/GSDMB genes were associated with childhood-onset asthma, interleukin (IL)33 and IL1RL1 SNPs were associated with atopic asthma, and the Thymic Stromal Lymphopoietin (TSLP) gene was identified as protective against the risk to TH2-asthma. The latest efforts and advances in identifying and decoding asthma susceptibility are focused on epigenetics, heritable characteristics that affect gene expression without altering DNA sequence, with DNA methylation being the most described mechanism. Other less studied epigenetic mechanisms include histone modifications and alterations of miR expression. Recent findings suggest that the DNA methylation pattern is tissue and cell-specific. Several studies attempt to describe DNA methylation of different types of cells and tissues of asthmatic patients that regulate airway remodeling, phagocytosis, and other lung functions in asthma. In this review, we attempt to briefly present the latest advancements in the field of genetics and mainly epigenetics concerning asthma susceptibility.

scholarly journals Children’s Greenness Exposure and IQ-Associated DNA Methylation: A Prospective Cohort Study

2021 ◽  
Vol 18 (14) ◽  
pp. 7429
Author(s):  
Kyung-Shin Lee ◽  
Yoon-Jung Choi ◽  
Jin-Woo Cho ◽  
Sung-Ji Moon ◽  
Youn-Hee Lim ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cohort Study ◽  
Literature Review ◽  
Cognitive Ability ◽  
Prospective Cohort Study ◽  
Prospective Cohort ◽  
Association Studies ◽  
The Body ◽  
Genome Wide Association Studies ◽  
Regulatory Pathways

Epigenetics is known to be involved in regulatory pathways through which greenness exposure influences child development and health. We aimed to investigate the associations between residential surrounding greenness and DNA methylation changes in children, and further assessed the association between DNA methylation and children’s intelligence quotient (IQ) in a prospective cohort study. We identified cytosine-guanine dinucleotide sites (CpGs) associated with cognitive abilities from epigenome- and genome-wide association studies through a systematic literature review for candidate gene analysis. We estimated the residential surrounding greenness at age 2 using a geographic information system. DNA methylation was analyzed from whole blood using the HumanMethylationEPIC array in 59 children at age 2. We analyzed the association between greenness exposure and DNA methylation at age 2 at the selected CpGs using multivariable linear regression. We further investigated the relationship between DNA methylation and children’s IQ. We identified 8743 CpGs associated with cognitive ability based on the literature review. Among these CpGs, we found that 25 CpGs were significantly associated with greenness exposure at age 2, including cg26269038 (Bonferroni-corrected p ≤ 0.05) located in the body of SLC6A3, which encodes a dopamine transporter. DNA methylation at cg26269038 at age 2 was significantly associated with children’s performance IQ at age 6. Exposure to surrounding greenness was associated with cognitive ability-related DNA methylation changes, which was also associated with children’s IQ. Further studies are warranted to clarify the epigenetic pathways linking greenness exposure and neurocognitive function.

Abstract MP32: Epigenome-Wide DNA Methylation Profiling in a CVD Cohort: The ARIC Study

Circulation ◽  
2013 ◽  
Vol 127 (suppl_12) ◽  
Author(s):  
James S Pankow ◽  
Ellen W Demerath ◽  
Weihua Guan ◽  
Myriam Fornage ◽  
Thomas H Mosley ◽  
...  
Keyword(s):  
Dna Methylation ◽  
X Chromosome ◽  
Methylation Level ◽  
Association Studies ◽  
Univariate Analysis ◽  
European Ancestry ◽  
Genome Wide Association Studies ◽  
Stage Of Development ◽  
Average Methylation ◽  
Aric Study

DNA methylation is mitotically heritable modification in chromatin structure that impacts transcriptional control of genes and cellular function. Recent technological advances provide opportunities to systematically interrogate variation in DNA methylation across the genome in large epidemiologic studies. However, unlike inherited changes to the genetic sequence, variation in site-specific methylation varies by tissue, stage of development, disease state, and may be affected by gender, aging and exposure to environmental factors. As a result, there is likely a greater threat of confounding in epigenome-wide methylation studies compared to genome-wide association studies of SNPs. The Illumina Infinium HumanMethylation450 BeadChip was used to measure DNA methylation in peripheral blood obtained from African American participants from the Jackson, Mississippi and Forsyth County, North Carolina field centers of the Atherosclerosis Risk in Communities (ARIC) Study, a population-based cohort of middle-aged men and women. After excluding outlier samples and CpG sites using quality control filters, we analyzed 473,687 sites in 2873 subjects who were between 47-71 years of age at the time of DNA collection. We used linear regression with robust standard errors to examine cross-sectional associations of demographic factors with the beta value, an estimate of the average methylation level at each locus, and applied a Bonferroni correction to account for multiple testing. In univariate analysis, 91% of sites on the X chromosome and 10% of sites on the autosomes exhibited statistically significant gender differences in methylation level (p<1x10-7). Average methylation was higher in women than men for most of the significant sites (63% and 89% on the X chromosome and autosomes, respectively). Percent European ancestry estimated from ancestry informative markers was significantly associated with methylation level at 4% of sites. Age was also significantly associated with methylation at 4% of sites; average methylation was lower in older subjects compared to younger subjects for the majority (58%) of these sites. As we begin to implement epigenome-wide studies of DNA methylation and CVD outcomes, these results indicate that such studies will require careful consideration of adjustment techniques to avoid confounding by gender, age, and other covariates.

scholarly journals Genome-wide identification of DNA methylation QTLs in whole blood highlights pathways for cardiovascular disease

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Tianxiao Huan ◽  
Roby Joehanes ◽  
Ci Song ◽  
Fen Peng ◽  
Yichen Guo ◽  
...  
Keyword(s):  
Cardiovascular Disease ◽  
Dna Methylation ◽  
Whole Blood ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Transcriptional Regulatory ◽  
Disease Associations ◽  
Independent Replication ◽  
Functional Mechanisms

Abstract Identifying methylation quantitative trait loci (meQTLs) and integrating them with disease-associated variants from genome-wide association studies (GWAS) may illuminate functional mechanisms underlying genetic variant-disease associations. Here, we perform GWAS of >415 thousand CpG methylation sites in whole blood from 4170 individuals and map 4.7 million cis- and 630 thousand trans-meQTL variants targeting >120 thousand CpGs. Independent replication is performed in 1347 participants from two studies. By linking cis-meQTL variants with GWAS results for cardiovascular disease (CVD) traits, we identify 92 putatively causal CpGs for CVD traits by Mendelian randomization analysis. Further integrating gene expression data reveals evidence of cis CpG-transcript pairs causally linked to CVD. In addition, we identify 22 trans-meQTL hotspots each targeting more than 30 CpGs and find that trans-meQTL hotspots appear to act in cis on expression of nearby transcriptional regulatory genes. Our findings provide a powerful meQTL resource and shed light on DNA methylation involvement in human diseases.

Exploration of baseline and early changes in neurocognitive characteristics as predictors of treatment response to bupropion, sertraline, and placebo in the EMBARC clinical trial

2020 ◽  
pp. 1-9
Author(s):  
Yuen-Siang Ang ◽  
Gerard E. Bruder ◽  
John G. Keilp ◽  
Ashleigh Rutherford ◽  
Daniel M. Alschuler ◽  
...  
Keyword(s):  
Cognitive Control ◽  
Treatment Response ◽  
Cognitive Processing ◽  
Reuptake Inhibitor ◽  
Verbal Fluency ◽  
Antidepressant Treatment ◽  
Clinical Care ◽  
Antidepressant Response ◽  
Clinical Value ◽  
Reward Responsiveness

Abstract Background Treatment for major depressive disorder (MDD) is imprecise and often involves trial-and-error to determine the most effective approach. To facilitate optimal treatment selection and inform timely adjustment, the current study investigated whether neurocognitive variables could predict an antidepressant response in a treatment-specific manner. Methods In the two-stage Establishing Moderators and Biosignatures of Antidepressant Response for Clinical Care (EMBARC) trial, outpatients with non-psychotic recurrent MDD were first randomized to an 8-week course of sertraline selective serotonin reuptake inhibitor or placebo. Behavioral measures of reward responsiveness, cognitive control, verbal fluency, psychomotor, and cognitive processing speeds were collected at baseline and week 1. Treatment responders then continued on another 8-week course of the same medication, whereas non-responders to sertraline or placebo were crossed-over under double-blinded conditions to bupropion noradrenaline/dopamine reuptake inhibitor or sertraline, respectively. Hamilton Rating for Depression scores were also assessed at baseline, weeks 8, and 16. Results Greater improvements in psychomotor and cognitive processing speeds within the first week, as well as better pretreatment performance in these domains, were specifically associated with higher likelihood of response to placebo. Moreover, better reward responsiveness, poorer cognitive control and greater verbal fluency were associated with greater likelihood of response to bupropion in patients who previously failed to respond to sertraline. Conclusion These exploratory results warrant further scrutiny, but demonstrate that quick and non-invasive behavioral tests may have substantial clinical value in predicting antidepressant treatment response.

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