Copenhagen provided the scenic backdrop for this year’s World Congress of Psychiatric Genetics. About 883 participants from 52 countries attended the 22nd meeting held by the International Society of Psychiatric Genetics (ISPG). The theme for this year was pathways to therapy and prevention. There was a clear increase in the number of epigenetic studies being presented at this meeting over the last few years. Two sessions were dedicated to epigenetic topics and in addition, several epigenetic and epigenomic topics were discussed during other sessions, including a plenary session.
Glucocorticoids and childhood maltreatment on system wide epigenetic effects
Nadine Provençal, Max Planck institute of Psychiatry
Excessive glucocorticoids (GC) release after early life stress exposure is thought to result in a long-lasting disruption of the stress hormone system and ultimately to an increase risk for psychiatric disorders later in life. Stress and GCs are known to regulate hippocampal neurogenesis and to induce long-lasting changes in DNA methylation in specific loci such as the glucocorticoid receptor (NR3C1) and FK506 binding protein 5 (FKBP5) in DNA from the hippocampus but also in peripheral blood cells. Dr. Provençal and colleagues aimed to extend these results to multiple loci using whole genomic comprehensive analysis of the epigenetic effects of GC activation during hippocampal neurogenesis as well as investigating DNA (extracted from blood) from adults who suffered child abuse.
The team specifically wanted to identify stable epigenetic modifications induced by GC activation during neurogenesis and were interested to see which of these modifications were also detectable in DNA extracted form peripheral blood cells of adults that were exposed to severe child abuse; with a particular focus on glucocorticoid response elements. They used Illumina arrays to analyse gene expression and CpG methylation levels of immortalised human hippocampal progenitor cells (HPC) treated with dexamethasone (Dex) or vehicle at different stages during neurogenesis and also adults exposed or not to severe child abuse (n=415).
The preliminary results revealed an effect of Dex treatment on the DNA methylation levels of more than 5000 CpG sites (P value < 0.05 and FDR < 0.05) during hippocampal differentiation where a significant portion of these alterations where maintained after differentiation, including CpGs in the FKBP5 locus. Some of these differentially methylated CpG sites in the HPCs following Dex treatment, were also differentially methylated in blood cells of adults exposed to child abuse. These preliminary analyses provide evidence of clustered and genome-wide epigenetic effects of GC activation during hippocampal neurogenesis where the timing of the exposure seems to be critical to induce long-lasting changes.
Parental effects on the epigenome
Michael Meaney, McGill University
Professor Meaney presented a very comprehensive overview during his plenary session, illustrating how epigenetic signals serve as the interface between the dynamic environment and the fixed genome. He presented data on maternal rat models illustrating how maternal care (the amount of licking and grooming performed by the dam) can alter the epigenetic and gene expression profiles in the offspring, which subsequently affects various phenotypic outcomes, including stress responses, neural development, learning and memory, metabolism and reproduction in female pups. These phenotypic traits were reversed by cross fostering the pups, illustrating that maternal care was driving the phenotypic traits.
Due to the importance of the HPA axis in the stress response, they investigated the levels of glucocorticoid receptors (GRs) in the pups and found that pups that received better maternal care (high LG) had higher expression levels of GR in the hippocampus, which was attributed to lower levels of CpG methylation of the exon 17 promoter of the GR. This subsequently affects the binding of NGFI-A to the promoter region. They also showed that NGFI-A expression and occupancy of the exon 17 promoter is driven by increased levels of serotonin, induced by increased maternal licking and grooming. Administration of HDAC inhibitors reversed these effects.
Dr. Meaney also emphasized the fact that DNA methylation comes in many forms, including hydroxymethylcytosine (5hmC) and that, following bisulfite treatment, one cannot discriminate between 5mC and 5hmC. High levels of 5hmC have been observed in the brain, which makes it an important epigenetic feature to investigate in psychiatric genetics. By comparing whole genome bisulfite sequencing and TET assisted bisulfite sequencing data, one is able to discriminate between 5mC and 5hmC. Such analyses have revealed that the levels of 5hmC are more variable and widespread in areas of transcriptional regulation.
Prof. Meaney also provided evidence for comparable processes that occur in humans. In a study of suicide victims, they found increased levels of GRs exon 1-F in brain samples of controls vs. suicide victims. Following subgrouping of the samples, CpG methylation analysis indicated lower levels of CpG methylation of the GR exon 1-F region in control subjects and suicide victims that didn’t suffer from child abuse compared to suicide victims that experienced child abuse. Other studies have replicated these findings in DNA from peripheral samples (Tyrka et al., 2012; Radtke et al., 2011). Although there are some correlation between DNA methylation profiles in the brain and blood, it should be noted that DNA methylomes have a high level of tissue specificity. The overlap in methylation levels across specific genomic regions, such as retrotransposons and CpG islands, might inflate estimates of concordance.
Epigenetic studies have not only shown differences in DNA methylation profiles between patients and controls and in response to environmental stressors, it also has clinical relevance for predicting treatment effects on HPA function. Yehuda et al., (2013, 2014) observed lower levels of GR promoter methylation in combat veterans with PTSD compared with combat-exposed veterans who did not develop PTSD. Lower methylation levels of the promoter region were associated with increased sensitivity to cortisol suppression in response to administration of low-dose dexamethasone (previously shown to be associated with PTSD).
The investigation of gene-environment studies with the methalome as the outcome was also discussed. Studies have shown that methylation at multiple CpG sites across the BDNF gene (a gene associated with plasticity), is associated with the Val66Met (rs6265) polymorphism, where the AA genotype had lower methylation levels compared to the AG and GG genotypes. Furthermore, results indicated that antenatal maternal anxiety was a significant source of variation in DNA methylation across the genome among Met/Met carriers. The importance of longitudinal study design for gene-environment studies in the context of epigenetics was emphasized.
Prof Meaney concluded that the function of the genome is regulated by epigenetic signals, which in turn are subject to environmental regulation. These epigenetic signals are reflective of the quality of the early environment and have the ability to regulate genomic function in the brain. Finally, these environmental influences on the epigenome appear to be highly moderated by genotype.
Methylome-wide investigation of SNP-CpGs in schizophrenia
Karolina Aberg, Virginia Commonwealth University
Dr. Aberg presented data on one of the first genome-wide SNP-CpGs analyses, which aimed to identify sites associated with schizophrenia that are consistent between blood and brain. About 1.4 million CpGs are created or destroyed by common SNPs (SNP-CpGs). Investigations into SNP-CpGs provide an elegant complement to DNA sequence analysis studies as these sites encompass variation in both DNA sequence and methylation status. By performing methyl-binding domain 2 enrichment followed by sequencing (MBD-seq) in DNA from blood samples of schizophrenia cases and controls in conjunction with GWAS genotyping and 1000-genomes imputation, they investigated the methylation status of SNP-CpGs (with a minor allele frequency [MAF] > 5%). In addition, they replicated the results in post-mortem brain tissue from individuals diagnosed with schizophrenia, bipolar disorder and controls. They also replicated findings from the methylome-wide SNP-CpG analysis in blood and brain samples from independent schizophrenia cohorts, by using targeted bisulfite pyrosequencing.
They found that 68.3% and 67.7% of SNP-CpGs were methylated in blood and brain samples respectively and that the majority of methylated sites overlapped (94%). One of the methylome-wide significant sites that were associated with schizophrenia (that was detected in blood samples) was also associated with the presence of psychotic features (when detected in brain samples). This site is located in the interleukin 1 receptor accessory protein (IL1RAP), a gene important for, e.g., immune response. They were also able to replicate this finding with pyrosequencing in the independent schizophrenia cohort. These types of analyses may provide additional insight into the results from GWAS and can improve our understanding of disease etiology.
Using epigenomics to predict psychological treatment response
One of the last sessions of the conference was dedicated to data pertaining to genomic and epigenomic data of psychological treatment response in anxiety and depressive disorders and included some of the well-known researchers in the field of epigenetics. Psychological interventions are a popular choice in the treatment of both anxiety disorders and depression. However, not all individuals respond to psychological interventions. Therapy genomics investigates genetic, genomic and epigenetic factors as both predictors and mechanisms of treatment response.
Prof Meaney (McGill University) presented data, on behalf of Professor Yehuda, of a study investigating the role of cytosine methylation and gene expression in response to psychotherapy for Post-Traumatic Stress Disorder (PTSD). They investigated the role of methylation levels prior to treatment, as a predictor of treatment outcome, and increase/decrease in methylation levels as a potential mechanism of change, focusing on the promoter regions of the GR gene and FKBP5 gene. Methylation levels of these two promoter regions could be used to discriminate between responders and non-responders prior to treatment. Methylation levels of the GR promoter were associated with PTSD symptom severity at post-treatment. This session nicely echoed the theme of this year’s meeting, namely pathways to therapy and prevention and highlighted the fact that, in order to understand the molecular mechanisms involved in response to treatment, we need to look beyond the genotype. Changes in gene expression and DNA methylation during psychological interventions may provide useful indicators of potential underlying mechanisms; predict treatment outcome and perhaps aid in the development of new treatment strategies.
**EpiGenie offers a big “Thank You!” to Stefanie Malan-Muller who is a Postdoctoral Fellow in the Dept. of Psychiatry at Stellenbosch University in Tygerberg, South Africa for providing this great conference coverage**
- Radtke KM, Ruf M, Gunter HM, Dohrmann K, Schauer M, Meyer A, et al. Transgenerational impact of intimate partner violence on methylation in the promoter of the glucocorticoid receptor. Translational Psychiatry 2011;1:1–6.
- Tyrka AR, Wier L, Price LH, Ross N, Anderson GM, Wilkinson CW, et al. Childhood parental loss and adult hypothalamic–pituitary–adrenal function. Biological Psychiatry. 2008;63:1147–1154.
- Yehuda R, Daskalakis NP, Desamaud F, et al. Epigenetic biomarkers as predictors and correlates of symptom improvement following psychotherapy in combat veterans with PTDS. Front Psychiatry 2013;4:18.
- Yehuda R, Flory JD, Bierer LM, Henn-Haase C, Lehrner A, Desarnaud F, Makotkine I, Daskalakis NP, Marmar CR, Meaney MJ. Lower Methylation of Glucocorticoid Receptor Gene Promoter 1F in Peripheral Blood of Veterans with Posttraumatic Stress Disorder. Biol Psychiatry 2014; In Press