scholarly journals Epigenome-wide Association Study of Alcohol Use Disorder in Five Brain Regions

2021 ◽  
Author(s):  
Lea Zillich ◽  
Josef Frank ◽  
Fabian Streit ◽  
Marion M Friske ◽  
Jerome C Foo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Alcohol Use ◽  
Brain Region ◽  
Alcohol Use Disorder ◽  
Brain Regions ◽  
Anterior Cingulate ◽  
Human Brain Tissue ◽  
Postmortem Human Brain ◽  
Association Analyses ◽  
Cpg Sites

Alcohol Use Disorder (AUD) is closely linked to the brain regions forming the neurocircuitry of addiction. Postmortem human brain tissue enables the direct study of the molecular pathomechanisms of AUD. This study aims to identify these mechanisms by examining differential DNA-methylation between cases with severe AUD (n=53) and controls (n=58) using a brain region-specific approach. Samples of the anterior cingulate cortex (ACC), Brodmann Area 9 (BA9), caudate nucleus (CN), ventral striatum (VS), and putamen (PUT) were investigated. DNA-methylation levels were determined using the Illumina HumanMethylationEPIC Beadchip. Epigenome-wide association analyses were carried out to identify differentially methylated CpG-sites and regions between cases and controls in each brain region. Weighted Correlation Network Analysis (WGCNA), gene-set and GWAS-enrichment analyses were performed. Two differentially methylated CpG-sites were associated with AUD in the CN, and 18 in VS (q < .05). No epigenome-wide significant CpG-sites were found in BA9, ACC, or PUT. Differentially methylated regions associated with AUD case-/control status (q < .05) were found in the CN (n=6), VS (n=18) and ACC (n=1). These findings were mapped to several genes including IREB2, SLC30A8, and DDAH2. In the VS, the WGCNA-module showing the strongest association with AUD was enriched for immune-related pathways. This study is the first to analyze methylation differences between AUD cases and controls in multiple brain regions and consists of the largest sample to date. Several novel CpG-sites and regions implicated in AUD were identified, providing a first basis to explore epigenetic correlates of AUD

scholarly journals Epigenome-wide association study of alcohol use disorder in five brain regions

2021 ◽  
Author(s):  
Lea Zillich ◽  
Josef Frank ◽  
Fabian Streit ◽  
Marion M. Friske ◽  
Jerome C. Foo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Alcohol Use ◽  
Brain Region ◽  
Alcohol Use Disorder ◽  
Brain Regions ◽  
Anterior Cingulate ◽  
Human Brain Tissue ◽  
Postmortem Human Brain ◽  
Association Analyses ◽  
Cpg Sites

AbstractAlcohol use disorder (AUD) is closely linked to the brain regions forming the neurocircuitry of addiction. Postmortem human brain tissue enables the direct study of the molecular pathomechanisms of AUD. This study aims to identify these mechanisms by examining differential DNA-methylation between cases with severe AUD (n = 53) and controls (n = 58) using a brain-region-specific approach, in which sample sizes ranged between 46 and 94. Samples of the anterior cingulate cortex (ACC), Brodmann Area 9 (BA9), caudate nucleus (CN), ventral striatum (VS), and putamen (PUT) were investigated. DNA-methylation levels were determined using the Illumina HumanMethylationEPIC Beadchip. Epigenome-wide association analyses were carried out to identify differentially methylated CpG-sites and regions between cases and controls in each brain region. Weighted correlation network analysis (WGCNA), gene-set, and GWAS-enrichment analyses were performed. Two differentially methylated CpG-sites were associated with AUD in the CN, and 18 in VS (q < 0.05). No epigenome-wide significant CpG-sites were found in BA9, ACC, or PUT. Differentially methylated regions associated with AUD case-/control status (q < 0.05) were found in the CN (n = 6), VS (n = 18), and ACC (n = 1). In the VS, the WGCNA-module showing the strongest association with AUD was enriched for immune-related pathways. This study is the first to analyze methylation differences between AUD cases and controls in multiple brain regions and consists of the largest sample to date. Several novel CpG-sites and regions implicated in AUD were identified, providing a first basis to explore epigenetic correlates of AUD.

scholarly journals Human brain region-specific variably methylated regions (VMRs) are enriched for heritability of distinct neuropsychiatric traits

2021 ◽  
Author(s):  
Lindsay F. Rizzardi ◽  
Peter F. Hickey ◽  
Adrian Idrizi ◽  
Rakel Tryggvadóttir ◽  
Colin M. Callahan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Human Brain ◽  
Brain Region ◽  
Brain Regions ◽  
Differential Methylation ◽  
Anterior Cingulate ◽  
Single Pair ◽  
Regulatory Regions ◽  
Neuronal Nuclei ◽  
The Brain

ABSTRACTBACKGROUNDDNA methylation dynamics in the brain are associated with normal development and neuropsychiatric disease and differ across functionally distinct brain regions. Previous studies of genome-wide methylation differences among human brain regions focused on limited numbers of individuals and one to two brain regions.RESULTSUsing GTEx samples, we have generated a resource of DNA methylation in purified neuronal nuclei from 8 brain regions as well as lung and thyroid tissues from 12-23 donors. We identified differentially methylated regions between brain regions (DMRs) among neuronal nuclei in both CpG (181,146) and non-CpG (264,868) contexts, few of which were unique to a single pair-wise comparison. This significantly expands the knowledge of differential methylation across the brain by 10-fold. In addition, we present the first differential methylation analysis among neuronal nuclei from basal ganglia tissues and identified 2,295 unique CpG DMRs, many associated with ion transport. Consistent with prior studies, CpG DMRs were enriched in regulatory regions while non-CpG DMRs were enriched in intergenic regions. We also identified 81,130 regions of variably CpG methylated regions (VMRs), i.e. variable methylation among individuals in the same brain region, which were enriched in regulatory regions and in CpG DMRs. Many VMRs were unique to a specific brain region, with only 202 common across all brain regions, as well as lung and thyroid. VMRs identified in the amygdala, anterior cingulate cortex, and hippocampus were enriched for heritability of schizophrenia.CONCLUSIONSThese data suggest that epigenetic variation in these particular human brain regions could be associated with the risk for this neuropsychiatric disorder.

scholarly journals Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lindsay F. Rizzardi ◽  
◽  
Peter F. Hickey ◽  
Adrian Idrizi ◽  
Rakel Tryggvadóttir ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Human Brain ◽  
Brain Region ◽  
Pairwise Comparison ◽  
Brain Regions ◽  
Differential Methylation ◽  
Anterior Cingulate ◽  
Differentially Methylated Regions ◽  
Neuronal Nuclei ◽  
The Brain

Abstract Background DNA methylation dynamics in the brain are associated with normal development and neuropsychiatric disease and differ across functionally distinct brain regions. Previous studies of genome-wide methylation differences among human brain regions focus on limited numbers of individuals and one to two brain regions. Results Using GTEx samples, we generate a resource of DNA methylation in purified neuronal nuclei from 8 brain regions as well as lung and thyroid tissues from 12 to 23 donors. We identify differentially methylated regions between brain regions among neuronal nuclei in both CpG (181,146) and non-CpG (264,868) contexts, few of which were unique to a single pairwise comparison. This significantly expands the knowledge of differential methylation across the brain by 10-fold. In addition, we present the first differential methylation analysis among neuronal nuclei from basal ganglia tissues and identify unique CpG differentially methylated regions, many associated with ion transport. We also identify 81,130 regions of variably CpG methylated regions, i.e., variable methylation among individuals in the same brain region, which are enriched in regulatory regions and in CpG differentially methylated regions. Many variably methylated regions are unique to a specific brain region, with only 202 common across all brain regions, as well as lung and thyroid. Variably methylated regions identified in the amygdala, anterior cingulate cortex, and hippocampus are enriched for heritability of schizophrenia. Conclusions These data suggest that epigenetic variation in these particular human brain regions could be associated with the risk for this neuropsychiatric disorder.

scholarly journals Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric disease heritability

2017 ◽  
Author(s):  
Lindsay F. Rizzardi ◽  
Peter F. Hickey ◽  
Varenka Rodriguez DiBlasi ◽  
Rakel Tryggvadóttir ◽  
Colin M. Callahan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Prefrontal Cortex ◽  
Nucleus Accumbens ◽  
Brain Region ◽  
Brain Regions ◽  
Chromatin Accessibility ◽  
Differential Methylation ◽  
Synaptic Activity ◽  
Anterior Cingulate

AbstractEpigenetic modifications confer stable transcriptional patterns in the brain, and both normal and abnormal brain function involve specialized brain regions, yet little is known about brain region-specific epigenetic differences. Here, we compared prefrontal cortex, anterior cingulate gyrus, hippocampus and nucleus accumbens from 6 individuals, performing whole genome bisulfite sequencing for DNA methylation. In addition, we have performed ATAC-seq for chromatin accessibility, and RNA-seq for gene expression in the nucleus accumbens and prefrontal cortex from 6 additional individuals. We found substantial neuron- and brain region-specific differences in both DNA methylation and chromatin accessibility which were largely non-overlapping, and were greatest between nucleus accumbens and the other regions. In contrast, glial methylation and chromatin were relatively homogeneous across brain regions, although neuron/glia ratios varied greatly, demonstrating the necessity for cellular fractionation. Gene expression was also largely the same across glia from different brain regions and substantially different for neurons. Expression was correlated with methylation and accessibility across promoters and known enhancers. Several classes of transcription factor binding sites were enriched at regions of differential methylation and accessibility, including many that respond to synaptic activity. Finally, both regions of differential methylation and those of differential accessibility showed a surprising >10-fold enrichment of explained heritability associated with addictive behavior, as well as schizophrenia- and neuroticism-associated regions, suggesting that common psychiatric illness is mediated through brain region-specific epigenetic marks.

scholarly journals Birthweight DNA methylation signatures in infant saliva

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Chiara Moccia ◽  
Maja Popovic ◽  
Elena Isaevska ◽  
Valentina Fiano ◽  
Morena Trevisan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cord Blood ◽  
Gestational Age ◽  
Low Birthweight ◽  
Continuous Variable ◽  
Linear Regression Models ◽  
Association Analyses ◽  
Cpg Sites ◽  
Adverse Health Outcomes ◽  
The Look

Abstract Background Low birthweight has been repeatedly associated with long-term adverse health outcomes and many non-communicable diseases. Our aim was to look-up cord blood birthweight-associated CpG sites identified by the PACE Consortium in infant saliva, and to explore saliva-specific DNA methylation signatures of birthweight. Methods DNA methylation was assessed using Infinium HumanMethylation450K array in 135 saliva samples collected from children of the NINFEA birth cohort at an average age of 10.8 (range 7–17) months. The association analyses between birthweight and DNA methylation variations were carried out using robust linear regression models both in the exploratory EWAS analyses and in the look-up of the PACE findings in infant saliva. Results None of the cord blood birthweight-associated CpGs identified by the PACE Consortium was associated with birthweight when analysed in infant saliva. In saliva EWAS analyses, considering a false discovery rate p-values < 0.05, birthweight as continuous variable was associated with DNA methylation in 44 CpG sites; being born small for gestational age (SGA, lower 10th percentile of birthweight for gestational age according to WHO reference charts) was associated with DNA methylation in 44 CpGs, with only one overlapping CpG between the two analyses. Despite no overlap with PACE results at the CpG level, two of the top saliva birthweight CpGs mapped at genes associated with birthweight with the same direction of the effect also in the PACE Consortium (MACROD1 and RPTOR). Conclusion Our study provides an indication of the birthweight and SGA epigenetic salivary signatures in children around 10 months of age. DNA methylation signatures in cord blood may not be comparable with saliva DNA methylation signatures at about 10 months of age, suggesting that the birthweight epigenetic marks are likely time and tissue specific.

Changes in DNA methylation persist over time in males with severe alcohol use disorder—A longitudinal follow‐up study

2021 ◽  
Author(s):  
Soundarya Soundararajan ◽  
Arpana Agrawal ◽  
Meera Purushottam ◽  
Shravanthi Daphne Anand ◽  
Bhagyalakshmi Shankarappa ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Alcohol Use ◽  
Alcohol Use Disorder ◽  
Follow Up Study ◽  
Over Time

scholarly journals Alcohol use disorder causes global changes in splicing in the human brain

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Derek Van Booven ◽  
Mengying Li ◽  
J. Sunil Rao ◽  
Ilya O. Blokhin ◽  
R. Dayne Mayfield ◽  
...  
Keyword(s):  
Alcohol Use ◽  
Human Brain ◽  
Alcohol Use Disorder ◽  
Brain Regions ◽  
Gene Set Enrichment Analysis ◽  
Splicing Factor ◽  
Central Nucleus ◽  
Global Changes ◽  
Aberrant Expression ◽  
Altered Expression

AbstractAlcohol use disorder (AUD) is a widespread disease leading to the deterioration of cognitive and other functions. Mechanisms by which alcohol affects the brain are not fully elucidated. Splicing constitutes a nuclear process of RNA maturation, which results in the formation of the transcriptome. We tested the hypothesis as to whether AUD impairs splicing in the superior frontal cortex (SFC), nucleus accumbens (NA), basolateral amygdala (BLA), and central nucleus of the amygdala (CNA). To evaluate splicing, bam files from STAR alignments were indexed with samtools for use by rMATS software. Computational analysis of affected pathways was performed using Gene Ontology Consortium, Gene Set Enrichment Analysis, and LncRNA Ontology databases. Surprisingly, AUD was associated with limited changes in the transcriptome: expression of 23 genes was altered in SFC, 14 in NA, 102 in BLA, and 57 in CNA. However, strikingly, mis-splicing in AUD was profound: 1421 mis-splicing events were detected in SFC, 394 in NA, 1317 in BLA, and 469 in CNA. To determine the mechanism of mis-splicing, we analyzed the elements of the spliceosome: small nuclear RNAs (snRNAs) and splicing factors. While snRNAs were not affected by alcohol, expression of splicing factor heat shock protein family A (Hsp70) member 6 (HSPA6) was drastically increased in SFC, BLA, and CNA. Also, AUD was accompanied by aberrant expression of long noncoding RNAs (lncRNAs) related to splicing. In summary, alcohol is associated with genome-wide changes in splicing in multiple human brain regions, likely due to dysregulation of splicing factor(s) and/or altered expression of splicing-related lncRNAs.

Extrastriatal Dopamine D2/3 Receptor Availability in Alcohol Use Disorder and Individuals at High Risk

2022 ◽  
pp. 1-10
Author(s):  
Gianna Spitta ◽  
Tobias Gleich ◽  
Kristin Zacharias ◽  
Oisin Butler ◽  
Ralph Buchert ◽  
...  
Keyword(s):  
High Risk ◽  
Alcohol Use ◽  
Alcohol Use Disorder ◽  
Protective Factor ◽  
Region Of Interest ◽  
Anterior Cingulate ◽  
Dopamine D2 ◽  
Positron Emission ◽  
Significant Difference ◽  
Meta Analyses

<b><i>Introduction:</i></b> Reduced striatal dopamine D2/3 receptor availability in alcohol use disorder (AUD) has been demonstrated in recent clinical studies and meta-analyses. However, only a limited number of studies investigated extrastriatal D2/3 availability in AUD or in at-risk populations. In line with a dimensional understanding of addiction, extrastriatal dopaminergic neuroadaptations have been suggested to be relevant from a pathobiological perspective. <b><i>Methods:</i></b> We investigated D2/3 receptor availability via <sup>18</sup>F-fallypride positron emission tomography applying a region of interest (ROI) approach. We selected ROIs for the prefrontal cortex (PFC) and the anterior cingulate cortex (ACC). Our sample included 19 healthy controls (low risk [LR]), 19 individuals at high risk (HR) to develop addiction, and 20 recently detoxified AUD patients. <b><i>Results:</i></b> We found significantly higher D2/3 receptor availability of HR compared to AUD in the left and right rostral ACC (rACC), as well as in the left ventrolateral PFC (vlPFC). We did not observe a significant difference between AUD and LR. After corrections for multiple comparisons none of the ROIs reached significance throughout the group comparison. The D2/3 receptor availability in the left rACC was inversely correlated with symptom severity assessed with the Alcohol Dependency Scale. <b><i>Discussion:</i></b> To our knowledge, the present work is the first study investigating extrastriatal D2/3 receptor availabilities in individuals at HR and patients with AUD. The observation that D2/3 receptor availabilities are highest in HR might suggest that their pathobiology differs from subjects with AUD. Future studies are necessary to clarify the intraindividual course of this biomarker over different disease stages and its possible role as a risk or protective factor.

scholarly journals An Initial Investigation of Disrupted Intracortical Myelin as a Novel Brain Marker of Alcohol Use Disorder

2020 ◽  
Author(s):  
Vanessa Morris ◽  
Luciano Minuzzi ◽  
Nicholas Bock ◽  
James MacKillop ◽  
Michael Amlung
Keyword(s):  
Sex Differences ◽  
Prefrontal Cortex ◽  
Alcohol Use ◽  
Gray Matter ◽  
Alcohol Use Disorder ◽  
A Priori ◽  
Anterior Cingulate ◽  
Posterior Cingulate ◽  
Cohen’S D ◽  
Cohen's D

Abstract: Although disruption of cortical gray matter and white matter tracts are well-established markers of alcohol use disorder (AUD), this is the first study to examine the specific role of intracortical myelin (ICM; i.e., highly myelinated gray matter in deeper cortical layers) in AUD. The current study used a 3T MRI sequence optimized for high intracortical contrast to examine patterns of ICM-related MRI signal in 30 individuals with AUD and 33 healthy social drinkers. Secondary aims included exploring continuous associations with alcohol problem severity and examining sex differences. Surface-based analytic techniques were used to quantify ICM-related MRI signal for a priori region of interest analyses (20 bilateral regions) and exploratory vertex-wise analyses (using Cohen’s d). Although the distribution of ICM-related signal was generally comparable between groups, the AUD group exhibited significantly (p&lt;.05) greater ICM-related MRI signal in precuneus, ventromedial prefrontal cortex, posterior cingulate, middle anterior cingulate, middle/posterior insula, dorsolateral prefrontal cortex, and posterior cingulate, among other regions (Cohen’s d = .50-.75, indicating medium magnitude effects). Significant positive correlations between ICM signal and AUD severity were found in several frontal, parietal, cingulate, and temporal regions (rs .25-.34). No sex differences in ICM were observed. These findings provide initial proof-of-concept for examining ICM in relation to AUD. Understanding the pathophysiological mechanisms of these associations (e.g., neuroinflammation) and the clinical relevance of ICM is warranted.

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