Methylomic profiling of cortex samples from completed suicide cases implicates a role for PSORS1C3 in major depression and suicide

Canonical and non-canonical roles of oligodendrocyte precursor cells in mental disorders

Psychiatric research has shifted from a neuroncentric view to understanding mental disorders as disturbances of heterogeneous brain networks. Oligodendrocyte precursor cells (OPCs)- actively involved in the modulation of neuronal functions - are altered in psychiatric patients, but the extent and related consequences are unclear. This review explores canonical and non-canonical OPC-related pathways in schizophrenia, bipolar disorder, post-traumatic stress disorder, and depression in humans, highlighting potential mechanisms shared across diagnostic entities.

Transcranial direct current stimulation in patients with depression: An electric field modeling meta-analysis

Transcranial Direct Current Stimulation (tDCS) has shown potential in modulating cortical activity and treating depression. Despite its promise, variability in electrode montage configurations and electric field strength across studies has resulted in inconsistent outcomes. Traditional meta-analytic methods assessing the effect of tDCS in depression typically do not compare tDCS montage and the anatomical distribution of electric field, which is a major source of inter-experimental variability. We hypothesize that considering these parameters and anatomical variability in a meta-analysis might unravel brain regions associated with tDCS response in patients with depression. We correlate the clinical outcome (Effect size) with electric field intensities across 8 diverse head models, analyzing data from 29 studies involving 1766 patients between 2000 and 2023. Our analysis found a significant effect of tDCS on depression, with a Hedge's g = 0.66 (95 % CI: 0.565 to 0.767). Although studies aimed to target the L-DLPFC, particularly Brodmann area (BA) 46, based on the Frontal Brain Asymmetry theory, our findings show that all the montages do not selectively target the L-DLPFC as intended. Instead, our findings indicated that the electric field impact was dispersing broadly across the frontal lobes and exhibiting significant heterogeneity. We found a correlation between electric field strength and clinical outcomes in BA 10, BA 11, and the anterior part of BA 46 despite tDCS montages heterogeneity and individual variability, suggesting that targeting frontopolar prefrontal and orbitofrontal cortices could be ideal for tDCS in treating depression. Our work underscores brain regions associated with tDCS response and highlights the need for simulation-guided, personalized trials that consider individual anatomical differences.

Genome-wide methylome-based molecular pathologies associated with depression and suicide

Major depressive disorder (MDD) is a debilitating disorder. Suicide attempts are 5-times higher in MDD patients than in the general population. Interestingly, not all MDD patients develop suicidal thoughts or complete suicide. Thus, it is important to study the risk factors that can distinguish suicidality among MDD patients. The present study examined if DNA methylation changes can distinguish suicidal behavior among depressed subjects. Genome-wide DNA methylation was examined in the dorsolateral prefrontal cortex of depressed suicide (MDD+S; n = 15), depressed non-suicide (MDD-S; n = 17), and nonpsychiatric control (C; n = 16) subjects using 850 K Infinium Methylation EPIC BeadChip. The significantly differentially methylated genes were used to determine the functional enrichment of genes for ontological clustering and pathway analysis. Based on the number of CpG content and their relative distribution from specific landmark regions of genes, 32,958 methylation sites were identified across 12,574 genes in C vs. MDD+/-S subjects, 30,852 methylation sites across 12,019 genes in C vs. MDD-S, 41,648 methylation sites across 13,941 genes in C vs. MDD+S, and 49,848 methylation sites across 15,015 genes in MDD-S vs. MDD+S groups. A comparison of methylation sites showed 33,129 unique methylation sites and 5451 genes in the MDD-S group compared to the MDD+S group. Functional analysis suggested oxytocin, GABA, VGFA, TNFA, and mTOR pathways associated with suicide in the MDD group. Altogether, our data show a distinct pattern of DNA methylation, the genomic distribution of differentially methylated sites, gene enrichment, and pathways in MDD suicide compared to non-suicide MDD subjects.

Epigenetics and suicidal behavior in adolescents: a critical review

Suicide continues to be a significant public health issue globally, claiming over 700,000 lives annually. It is, therefore, important to assess the suicide risk properly and provide intervention in a timely fashion. While the heritability of suicidal behavior is around 50%, it does not explain the factors involved in causality. Recent evidence suggests that gene x environment interaction plays a vital role in suicidal behavior. In this paper, we critically evaluate the association between adolescent suicidal behavior and epigenetic modifications, including DNA methylation, histone modification, and non-coding RNAs, as well as epigenetic-based treatment options. It was noted that the prevalence of suicidal behavior in adolescents varied by age and sex and the presence of psychiatric disorders. Childhood adversity was closely associated with suicidal behavior. Studies show that alterations in epigenetic modifications may increase the risk of suicidal behavior independent of mental illnesses. Because epigenetic factors are reversible, environmental enrichment or the use of pharmacological agents that can target specific epigenetic modulation may be able to reduce suicidal behavior in this population.

Immune links in comorbid depression and psoriasis: A narrative mini-review and perspective

Evidence suggests a bidirectional association between psoriasis and depression, which is considered to reflect complex neuroimmunological and psychosocial interactions. Despite an early interest in the brain-skin axis and the role of stress in psoriasis immunopathogenesis, there is ongoing limited preclinical and clinical research into the inflammatory links between depression and psoriasis. Existing findings for serum inflammatory markers of depression in psoriasis are inconsistent and do not fully align with those in the general population, while brain imaging evidence is scarce and has not confirmed direct brain involvement in the systemic inflammation of psoriasis. The present paper reviews the available literature on the immune interplay of psoriasis with depression, highlights the significance of further work in the field and proposes avenues for future research.

Exploring the molecular mechanisms of comorbidity of myocardial infarction and anxiety disorders by combining multiple data sets with in vivo experimental validation

BACKGROUND

The incidence of comorbidity between myocardial infarction (MI) and anxiety disorders is increasing. However, the biological association between them has not been fully understood.

OBJECTIVE

This study aims to investigate the molecular mechanisms of comorbidity between MI and anxiety disorders and to predict their key genes and potential therapeutic drugs.

METHODS

We searched Gene Expression Omnibus databases and performed differential analyses using the limma package to identify the functional enrichment of differential genes. Next, we constructed regulatory networks to investigate the relationship between hub genes and autophagy, ferroptosis, and immunity. Furthermore, we predicted transcription factors by R package, constructed a miRNA network, performed the single-cell analysis of key gene expression, and predicted drug targeting of differential genes using the Connectivity Map database.

RESULTS

The datasets for MI and anxiety disorders were analyzed for up and down-regulated differential genes, resulting in 35 intersecting differential genes. The top 10 feature genes from each dataset were intersected using Random Forest, resulting in the identification of three intersecting genes: STK17B, AKIRIN2, and WDR77. Validation of the above key genes was carried out by in vitro experiments. We examined the gene expression of STK17B, WDR77 and AKIRIN2 in the hippocampus and myocardial infarction border zone respectively by qPCR and WB, and the results confirmed that the above are the key genes for myocardial infarction and anxiety. There is a significant correlation between the comorbidity mechanism of myocardial infarction and anxiety disorders with ferroptosis and immunity. The construction of the miRNA network revealed that miR-205 and let-7 had higher average connectivity among the three hub genes. The single-cell analysis revealed significant expression of key genes in Endothelial cells, Cardiomyocytes, Macrophages, and Fibroblasts datasets. Cd274 showed a higher correlation with key genes in myocardial infarction and anxiety disorders.

CONCLUSION

Validation by multiple datasets and in vitro experiments showed that STK17B, AKIRIN2, and WDR77 are the key genes in the comorbidity of myocardial infarction and anxiety disorders, and ferroptosis and immunity are the key links in the comorbidity mechanism of myocardial infarction and anxiety disorders.

Epigenetic insight into the suicidal biomarker of depression with suicide Ideation: A narrative review

Suicide ideation (SI) is the major cause of death in persons with depression, whereas effective and accurate biomarkers for suicidal behavior of persons with depression are still lack. Recently, manifold studies in vivo revealed that epigenetic alterations including DNA methylation, non-coding RNA regulation, RNA editing and histone modification, were associated with depressive severity and SI, and peripheral epigenetic molecules may be potential biomarkers for suicidal risk of persons with depression. Therefore, we firstly reviewed recent epigenetic advancements in depression with suicide ideation (DSI) according to studies based on human tissue. Furthermore, we discussed the significance and potential of minimally-invasive peripheral epigenetic molecules to identify potential suicidal biomarkers for DSI, aiming to promote early identification and therapeutic evaluation of DSI.

A perspective on epigenomic aging processes in the human brain and their plasticity in patients with mental disorders - a systematic review

The debate surrounding nature versus nurture remains a central question in neuroscience, psychology, and in psychiatry, holding implications for both aging processes and the etiology of mental illness. Epigenetics can serve as a bridge between genetic predisposition and environmental influences, thus offering a potential avenue for addressing these questions. Epigenetic clocks, in particular, offer a theoretical framework for measuring biological age based on DNA methylation signatures, enabling the identification of disparities between biological and chronological age. This structured review seeks to consolidate current knowledge regarding the relationship between mental disorders and epigenetic age within the brain. Through a comprehensive literature search encompassing databases such as EBSCO, PubMed, and ClinicalTrials.gov, relevant studies were identified and analyzed. Studies that met inclusion criteria were scrutinized, focusing on those with large sample sizes, analyses of both brain tissue and blood samples, investigation of frontal cortex markers, and a specific emphasis on schizophrenia and depressive disorders. Our review revealed a paucity of significant findings, yet notable insights emerged from studies meeting specific criteria. Studies characterized by extensive sample sizes, analysis of brain tissue and blood samples, assessment of frontal cortex markers, and a focus on schizophrenia and depressive disorders yielded particularly noteworthy results. Despite the limited number of significant findings, these studies shed light on the complex interplay between epigenetic aging and mental illness. While the current body of literature on epigenetic aging in mental disorders presents limited significant findings, it underscores the importance of further research in this area. Future studies should prioritize large sample sizes, comprehensive analyses of brain tissue and blood samples, exploration of specific brain regions such as the frontal cortex, and a focus on key mental disorders. Such endeavors will contribute to a deeper understanding of the relationship between epigenetic aging and mental illness, potentially informing novel diagnostic and therapeutic approaches.

Investigating the Epigenetic Landscape of Major Depressive Disorder: A Genome-Wide Meta-Analysis of DNA Methylation Data, Including New Insights into Stochastic Epigenetic Mutations and Epivariations

Background/Objectives: Major depressive disorder (MDD) is a mental health condition that can severely impact patients' social lives, leading to withdrawal and difficulty in maintaining relationships. Environmental factors such as trauma and stress can worsen MDD by interacting with genetic predispositions. Epigenetics, which examines changes in gene expression influenced by the environment, may help identify patterns linked to depression. This study aimed to explore the epigenetic mechanisms behind MDD by analysing six public datasets (n = 1125 MDD cases, 398 controls in blood; n = 95 MDD cases, 96 controls in brain tissues) from the Gene Expression Omnibus. Methods: As an innovative approach, two meta-analyses of DNA methylation patterns were conducted alongside an investigation of stochastic epigenetic mutations (SEMs), epigenetic age acceleration, and rare epivariations. Results: While no significant global methylation differences were observed between MDD cases and controls, hypomethylation near the SHF gene (brain-specific probe cg25801113) was consistently found in MDD cases. SEMs revealed a gene-level burden in MDD, though epigenetic age acceleration was not central to the disorder. Additionally, 51 rare epivariations were identified in blood tissue and 1 in brain tissue linked to MDD. Conclusions: The study emphasises the potential role of rare epivariations in MDD's epigenetic regulation but calls for further research with larger, more diverse cohorts to confirm these findings.

Functional magnetic resonance imaging alternations in suicide attempts individuals and their association with gene expression

BACKGROUND

Functional Magnetic Resonance Imaging (fMRI) has shown brain activity alterations in individuals with a history of attempted suicide (SA) who are diagnosed with depression disorder (DD) or bipolar disorder (BD). However, patterns of spontaneous brain activity and their genetic correlations need further investigation.

METHODS

A voxel-based meta-analysis of 19 studies including 26 datasets, involving 742 patients with a history of SA and 978 controls (both nonsuicidal patients and healthy controls) was conducted. We examined fMRI changes in SA patients and analyzed the association between these changes and gene expression profiles using data from the Allen Human Brain Atlas by partial least squares regression analysis.

RESULTS

SA patients demonstrated increased spontaneous brain activity in several brain regions including the bilateral inferior temporal gyrus, hippocampus, fusiform gyrus, and right insula, and decreased activity in areas like the bilateral paracentral lobule and inferior frontal gyrus. Additionally, 5,077 genes were identified, exhibiting expression patterns associated with SA-related fMRI alterations. Functional enrichment analyses demonstrated that these SA-related genes were enriched for biological functions including glutamatergic synapse and mitochondrial structure. Concurrently, specific expression analyses showed that these genes were specifically expressed in the brain tissue, in neurons cells, and during early developmental periods.

CONCLUSION

Our findings suggest a neurobiological basis for fMRI abnormalities in SA patients with DD or BD, potentially guiding future genetic and therapeutic research.

Methylation of SSTR4 promoter region in multiple mental health disorders

The existence of a shared genetic basis for mental disorders has long been documented, yet research on whether acquired epigenetic modifications exhibit common alterations across diseases is limited. Previous studies have found that abnormal methylation of cg14631053 at the SSTR4 promoter region mediates the onset of alcohol use disorder. However, whether aberrant methylation of the SSTR4 gene promoter is involved in other mental health disorders remains unclear. In this study, leveraging publicly available data, we identified that changes in methylation of cg14631053 from the SSTR4 promoter region are involved in the development of bipolar disorder and schizophrenia. Furthermore, the direction of methylation changes in the SSTR4 promoter region is disease-specific: hypomethylation is associated with the onset of bipolar disorder and schizophrenia, rather than major depressive disorder. Methylation levels of cg14631053 correlate with chronological age, a correlation that can be disrupted in patients with mental health disorders including schizophrenia and bipolar disorder. In conclusion, SSTR4 promoter methylation may serve as a marker for identifying bipolar disorder and schizophrenia, providing insights into a transdiagnostic mechanism for precision medicine in the future.

MDDOmics: multi-omics resource of major depressive disorder

Major depressive disorder (MDD) is a pressing global health issue. Its pathogenesis remains elusive, but numerous studies have revealed its intricate associations with various biological factors. Consequently, there is an urgent need for a comprehensive multi-omics resource to help researchers in conducting multi-omics data analysis for MDD. To address this issue, we constructed the MDDOmics database (Major Depressive Disorder Omics, (https://www.csuligroup.com/MDDOmics/), which integrates an extensive collection of published multi-omics data related to MDD. The database contains 41 222 entries of MDD research results and several original datasets, including Single Nucleotide Polymorphisms, genes, non-coding RNAs, DNA methylations, metabolites and proteins, and offers various interfaces for searching and visualization. We also provide extensive downstream analyses of the collected MDD data, including differential analysis, enrichment analysis and disease-gene prediction. Moreover, the database also incorporates multi-omics data for bipolar disorder, schizophrenia and anxiety disorder, due to the challenge in differentiating MDD from similar psychiatric disorders. In conclusion, by leveraging the rich content and online interfaces from MDDOmics, researchers can conduct more comprehensive analyses of MDD and its similar disorders from various perspectives, thereby gaining a deeper understanding of potential MDD biomarkers and intricate disease pathogenesis. Database URL: https://www.csuligroup.com/MDDOmics/.

Quantifying the proportion of different cell types in the human cortex using DNA methylation profiles

BACKGROUND

Due to interindividual variation in the cellular composition of the human cortex, it is essential that covariates that capture these differences are included in epigenome-wide association studies using bulk tissue. As experimentally derived cell counts are often unavailable, computational solutions have been adopted to estimate the proportion of different cell types using DNA methylation data. Here, we validate and profile the use of an expanded reference DNA methylation dataset incorporating two neuronal and three glial cell subtypes for quantifying the cellular composition of the human cortex.

RESULTS

We tested eight reference panels containing different combinations of neuronal- and glial cell types and characterised their performance in deconvoluting cell proportions from computationally reconstructed or empirically derived human cortex DNA methylation data. Our analyses demonstrate that while these novel brain deconvolution models produce accurate estimates of cellular proportions from profiles generated on postnatal human cortex samples, they are not appropriate for the use in prenatal cortex or cerebellum tissue samples. Applying our models to an extensive collection of empirical datasets, we show that glial cells are twice as abundant as neuronal cells in the human cortex and identify significant associations between increased Alzheimer's disease neuropathology and the proportion of specific cell types including a decrease in NeuNNeg/SOX10Neg nuclei and an increase of NeuNNeg/SOX10Pos nuclei.

CONCLUSIONS

Our novel deconvolution models produce accurate estimates for cell proportions in the human cortex. These models are available as a resource to the community enabling the control of cellular heterogeneity in epigenetic studies of brain disorders performed on bulk cortex tissue.

Obesity and Depression: Common Link and Possible Targets

Depression is among the main causes of disability, and its protracted manifestations could make it even harder to treat metabolic diseases. Obesity is linked to episodes of depression, which is closely correlated to abdominal adiposity and impaired food quality. The present review is aimed at studying possible links between obesity and depression along with targets to disrupt it. Research output in Pubmed and Scopus were referred for writing this manuscript. Obesity and depression are related, with the greater propensity of depressed people to gain weight, resulting in poor dietary decisions and a sedentary lifestyle. Adipokines, which include adiponectin, resistin, and leptin are secretory products of the adipose tissue. These adipokines are now being studied to learn more about the connection underlying obesity and depression. Ghrelin, a gut hormone, controls both obesity and depression. Additionally, elevated ghrelin levels result in anxiolytic and antidepressant-like effects. The gut microbiota influences the metabolic functionalities of a person, like caloric processing from indigestible nutritional compounds and storage in fatty tissue, that exposes an individual to obesity, and gut microorganisms might connect to the CNS through interconnecting pathways, including neurological, endocrine, and immunological signalling systems. The alteration of brain activity caused by gut bacteria has been related to depressive episodes. Monoamines, including dopamine, serotonin, and norepinephrine, have been widely believed to have a function in emotions and appetite control. Emotional signals stimulate arcuate neurons in the hypothalamus that are directly implicated in mood regulation and eating. The peptide hormone GLP-1(glucagon-like peptide- 1) seems to have a beneficial role as a medical regulator of defective neuroinflammation, neurogenesis, synaptic dysfunction, and neurotransmitter secretion discrepancy in the depressive brain. The gut microbiota might have its action in mood and cognition regulation, in addition to its traditional involvement in GI function regulation. This review addressed the concept that obesity-related low-grade mild inflammation in the brain contributes to chronic depression and cognitive impairments.

Anti-inflammatory Drugs in the Treatment of Depression

The last two decades have seen a flourishing of research into the immunobiology of psychiatric phenotypes, in particular major depressive disorder. Both preclinical and clinical data have highlighted pathways and possible mechanisms that might link changes in immunobiology, most especially inflammation, to clinically relevant behaviour. From a therapeutics perspective, a major impetus has been the action of Biologics, often monoclonal antibodies, that target specific cytokines acting as "molecular scalpels" helping to uncover the actions of those proteins. These interventions have been associated with improvements in mood and related symptoms. There are now enough studies and participants to permit meta-analytic analyses of the actions of these and other anti-inflammatory agents.In this chapter, the focus is on the evidence for the role of inflammation biology in depression and the meta-analytic data from trials. The putative mechanisms that might underpin the antidepressant effect of anti-inflammatory drugs are also explored. Lastly, I describe the more stubborn difficulties around heterogeneity, deep phenotyping and stratification as well as improved animal models and greater understanding of the biology that might be addressed by future studies.

Integrative Analyses of scRNA-seq, Bulk mRNA-seq, and DNA Methylation Profiling in Depressed Suicide Brain Tissues

BACKGROUND

Suicidal behaviors have become a serious public health concern globally due to the economic and human cost of suicidal behavior to individuals, families, communities, and society. However, the underlying etiology and biological mechanism of suicidal behavior remains poorly understood.

METHODS

We collected different single omic data, including single-cell RNA sequencing (scRNA-seq), bulk mRNA-seq, DNA methylation microarrays from the cortex of Major Depressive Disorder (MDD) in suicide subjects' studies, as well as fluoxetine-treated rats brains. We matched subject IDs that overlapped between the transcriptome dataset and the methylation dataset. The differential expression genes and differentially methylated regions were calculated with a 2-group comparison analysis. Cross-omics analysis was performed to calculate the correlation between the methylated and transcript levels of differentially methylated CpG sites and mapped transcripts. Additionally, we performed a deconvolution analysis for bulk mRNA-seq and DNA methylation profiling with scRNA-seq as the reference profiles.

RESULTS

Difference in cell type proportions among 7 cell types. Meanwhile, our analysis of single-cell sequence from the antidepressant-treated rats found that drug-specific differential expression genes were enriched into biological pathways, including ion channels and glutamatergic receptors.

CONCLUSIONS

This study identified some important dysregulated genes influenced by DNA methylation in 2 brain regions of depression and suicide patients. Interestingly, we found that oligodendrocyte precursor cells (OPCs) have the most contributors for cell-type proportions related to differential expression genes and methylated sites in suicidal behavior.

Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation

Introduction

The human brain comprises heterogeneous cell types whose composition can be altered with physiological and pathological conditions. New approaches to discern the diversity and distribution of brain cells associated with neurological conditions would significantly advance the study of brain-related pathophysiology and neuroscience. Unlike single-nuclei approaches, DNA methylation-based deconvolution does not require special sample handling or processing, is cost-effective, and easily scales to large study designs. Existing DNA methylation-based methods for brain cell deconvolution are limited in the number of cell types deconvolved.

Methods

Using DNA methylation profiles of the top cell-type-specific differentially methylated CpGs, we employed a hierarchical modeling approach to deconvolve GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells.

Results

We demonstrate the utility of our method by applying it to data on normal tissues from various brain regions and in aging and diseased tissues, including Alzheimer's disease, autism, Huntington's disease, epilepsy, and schizophrenia.

Discussion

We expect that the ability to determine the cellular composition in the brain using only DNA from bulk samples will accelerate understanding brain cell type composition and cell-type-specific epigenetic states in normal and diseased brain tissues.

Large epigenome-wide association study identifies multiple novel differentially methylated CpG sites associated with suicidal thoughts and behaviors in veterans

Introduction

The U.S. suicide mortality rate has steadily increased during the past two decades, particularly among military veterans; however, the epigenetic basis of suicidal thoughts and behaviors (STB) remains largely unknown.

Methods

To address this issue, we conducted an epigenome-wide association study of DNA methylation (DNAm) of peripheral blood samples obtained from 2,712 U.S. military veterans.

Results

Three DNAm probes were significantly associated with suicide attempts, surpassing the multiple testing threshold (FDR q-value <0.05), including cg13301722 on chromosome 7, which lies between the genes SLC4A2 and CDK5; cg04724646 in PDE3A; and cg04999352 in RARRES3. cg13301722 was also found to be differentially methylated in the cerebral cortex of suicide decedents in a publicly-available dataset (p = 0.03). Trait enrichment analysis revealed that the CpG sites most strongly associated with STB in the present sample were also associated with smoking, alcohol consumption, maternal smoking, and maternal alcohol consumption, whereas pathway enrichment analysis revealed significant associations with circadian rhythm, adherens junction, insulin secretion, and RAP-1 signaling, each of which was recently associated with suicide attempts in a large, independent genome-wide association study of suicide attempts of veterans.

Discussion

Taken together, the present findings suggest that SLC4A2, CDK5, PDE3A, and RARRES3 may play a role in STB. CDK5, a member of the cyclin-dependent kinase family that is highly expressed in the brain and essential for learning and memory, appears to be a particularly promising candidate worthy of future study; however, additional work is still needed to replicate these finding in independent samples.

Epigenetic Changes Associated with Different Types of Stressors and Suicide

Stress is associated with various epigenetic changes. Some stress-induced epigenetic changes are highly dynamic, whereas others are associated with lasting marks on the epigenome. In our study, a comprehensive narrative review of the literature was performed by investigating the epigenetic changes that occur with acute stress, chronic stress, early childhood stress, and traumatic stress exposures, along with examining those observed in post-mortem brains or blood samples of suicide completers and attempters. In addition, the transgenerational effects of these changes are reported. For all types of stress studies examined, the genes Nr3c1, OXTR, SLC6A4, and BDNF reproducibly showed epigenetic changes, with some modifications observed to be passed down to subsequent generations following stress exposures. The aforementioned genes are known to be involved in neuronal development and hormonal regulation and are all associated with susceptibility to mental health disorders including depression, anxiety, personality disorders, and PTSD (post-traumatic stress disorder). Further research is warranted in order to determine the scope of epigenetic actionable targets in individuals suffering from the long-lasting effects of stressful experiences.

Epigenetic changes in the CYP2D6 gene are related to severity of suicide attempt: A cross-sectional study of suicide attempters

BACKGROUND

The ability to accurately estimate risk of suicide deaths on an individual level remains elusive.

METHODS

This study reports on a case-control study set-up from a well-characterized cohort of 88 predominantly female suicide attempters (SA), stratified into low- (n = 57) and high-risk groups (n = 31) based on reports of later death by suicide, as well as degree of intent-to-die and lethality of SA method. We perform an unbiased analysis of 12,930 whole-blood derived CpG-sites (Illumina Infinium EPIC BeadChip) previously demonstrated to be more conciliable with brain-derived variations. The candidate site was validated by pyrosequencing. External replication was performed in (1) relation to age at index suicide attempt in 97 women with emotionally unstable personality disorder (whole-blood) and (2) death by suicide in a mixed group of 183 prefrontal-cortex (PFC) derived samples who died by suicide or from non-psychiatric etiologies.

RESULTS

CYP2D6-coupled CpG-site cg07016288 was hypomethylated in severe suicidal behavior (p < 10E-06). Results were validated by pyrosequencing (p < 0.01). Replication analyses demonstrate hypomethylation of cg07016288 in relation to age at index SA in females (p < 0.05) and hypermethylation in PFC of male suicide completers (p < 0.05).

LIMITATIONS

Genotyping of CYP2D6 was not performed and CpG-site associations to gene expression were not explored.

CONCLUSIONS

CYP2D6-coupled epigenetic markers are hypomethylated in females in dependency of features known to confer increased risk of suicide deaths and hypermethylated in PFC of male suicide completers. Further elucidating the role of CYP2D6 in severe suicidality or suicide deaths hold promise to deduce clinically meaningful results.

Epidemiology of mental health comorbidity in patients with psoriasis: An analysis of trends from 1986 to 2019

BACKGROUND

The prevalence of mental disorders such as depression, anxiety, and suicide has increased in patients with psoriasis, although no study has systematically analyzed the epidemiology worldwide.

OBJECTIVE

To explore the prevalence and incidence of psoriasis with comorbid mental disorders (i.e., depression, anxiety, and suicide).

METHODS

Five databases from establishment through May 2022 were searched. Stata SE 15.1 was used for the data analysis. Subgroup, meta-regression, and sensitivity analyses were used to evaluate the heterogeneity of pooled studies.

RESULTS

We evaluated 56 studies in our research. The prevalence of depression, anxiety, and suicide in adults with psoriasis was 20%, 21%, and 0.77%. Patients with psoriasis in North America had a higher prevalence of depression and suicide, whereas those in South America had a higher prevalence of anxiety. The incidence of depression, anxiety, and suicide was 42.1, 24.7, and 2.6 per 1000 person-years in adults with psoriasis, respectively.

LIMITATIONS

All of the included studies were published in Chinese and English, causing a degree of selection bias.

CONCLUSION

These findings demonstrate the incidence and prevalence of comorbid mental disorders in patients with psoriasis, which may raise awareness among physicians and patients regarding the mental problems associated with psoriasis.

Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression

Depression is a multifactorial disorder representing a significant public health burden. Previous studies have linked multiple single nucleotide polymorphisms with depressive phenotypes and suicidal behavior. MAD1L1 is a mitosis metaphase checkpoint protein that has been linked to depression in GWAS. Using a longitudinal EWAS approach in an adolescent cohort at two time points (n = 216 and n = 154), we identified differentially methylated sites that were associated with depression-related genetic variants in MAD1L1. Three methylation loci (cg02825527, cg18302629, and cg19624444) were consistently hypomethylated in the minor allele carriers, being cross-dependent on several SNPs. We further investigated whether DNA methylation at these CpGs is associated with depressive psychiatric phenotypes in independent cohorts. The first site (cg02825527) was hypomethylated in blood (exp(β) = 84.521, p value ~ 0.003) in participants with severe suicide attempts (n = 88). The same locus showed increased methylation in glial cells (exp(β) = 0.041, p value ~ 0.004) in the validation cohort, involving 29 depressed patients and 29 controls, and showed a trend for association with suicide (n = 40, p value ~ 0.089) and trend for association with depression treatment (n = 377, p value ~ 0.075). The second CpG (cg18302629) was significantly hypomethylated in depressed participants (exp(β) = 56.374, p value ~ 0.023) in glial cells, but did not show associations in the discovery cohorts. The last methylation site (cg19624444) was hypomethylated in the whole blood of severe suicide attempters; however, this association was at the borderline for statistical significance (p value ~ 0.061). This locus, however, showed a strong association with depression treatment in the validation cohort (exp(β) = 2.237, p value ~ 0.003) with 377 participants. The direction of associations between psychiatric phenotypes appeared to be different in the whole blood in comparison with brain samples for cg02825527 and cg19624444. The association analysis between methylation at cg18302629 and cg19624444 and MAD1L1 transcript levels in CD¹⁴⁺ cells shows a potential link between methylation at these CpGs and MAD1L1 expression. This study suggests evidence that methylation at MAD1L1 is important for psychiatric health as supported by several independent cohorts.

DNA Methylation in Depression and Depressive-Like Phenotype: Biomarker or Target of Pharmacological Intervention?

Major depressive disorder (MDD) is a debilitating psychiatric disorder, the third leading global cause of disability. Regarding aetiopathogenetic mechanisms involved in the onset of depressive disorders, the interaction between genetic vulnerability traits and environmental factors is believed to play a major role. Although much is still to be elucidated about the mechanisms through which the environment can interact with genetic background shaping the disease risk, there is a general agreement about a key role of epigenetic marking. In this narrative review, we focused on the association between changes in DNA methylation patterns and MDD or depressive-like phenotype in animal models, as well as mechanisms of response to antidepressant drugs. We discussed studies presenting DNA methylation changes at specific genes of interest and profiling analyses in both patients and animal models of depression. Overall, we collected evidence showing that DNA methylation could not only be considered as a promising epigenetic biomarker of pathology but could also help in predicting antidepressant treatment efficacy. Finally, we discussed the hypothesis that specific changes in DNA methylation signature could play a role in aetiopathogenetic processes as well as in the induction of antidepressant effect.

Genetics and epigenetics of self-injurious thoughts and behaviors: Systematic review of the suicide literature and methodological considerations

Suicide is a multifaceted and poorly understood clinical outcome, and there is an urgent need to advance research on its phenomenology and etiology. Epidemiological studies have demonstrated that suicidal behavior is heritable, suggesting that genetic and epigenetic information may serve as biomarkers for suicide risk. Here we systematically review the literature on genetic and epigenetic alterations observed in phenotypes across the full range of self-injurious thoughts and behaviors (SITB). We included 577 studies focused on genome-wide and epigenome-wide associations, candidate genes (SNP and methylation), noncoding RNAs, and histones. Convergence of specific genes is limited across units of analysis, although pathway-based analyses do indicate nervous system development and function and immunity/inflammation as potential underlying mechanisms of SITB. We provide suggestions for future work on the genetic and epigenetic correlates of SITB with a specific focus on measurement issues.

Epigenome-wide associations between observed maternal sensitivity and offspring DNA methylation: a population-based prospective study in children

BACKGROUND

Experimental work in animals has shown that DNA methylation (DNAm), an epigenetic mechanism regulating gene expression, is influenced by typical variation in maternal care. While emerging research in humans supports a similar association, studies to date have been limited to candidate gene and cross-sectional approaches, with a focus on extreme deviations in the caregiving environment.

METHODS

Here, we explored the prospective association between typical variation in maternal sensitivity and offspring epigenome-wide DNAm, in a population-based cohort of children (N = 235). Maternal sensitivity was observed when children were 3- and 4-years-old. DNAm, quantified with the Infinium 450 K array, was extracted at age 6 (whole blood). The influence of methylation quantitative trait loci (mQTLs), DNAm at birth (cord blood), and confounders (socioeconomic status, maternal psychopathology) was considered in follow-up analyses.

RESULTS

Genome-wide significant associations between maternal sensitivity and offspring DNAm were observed at 13 regions (p < 1.06 × 10^-07), but not at single sites. Follow-up analyses indicated that associations at these regions were in part related to genetic factors, confounders, and baseline DNAm levels at birth, as evidenced by the presence of mQTLs at five regions and estimate attenuations. Robust associations with maternal sensitivity were found at four regions, annotated to ZBTB22, TAPBP, ZBTB12, and DOCK4.

CONCLUSIONS

These findings provide novel leads into the relationship between typical variation in maternal caregiving and offspring DNAm in humans, highlighting robust regions of associations, previously implicated in psychological and developmental problems, immune functioning, and stress responses.

Differential Methylation Analysis of Suicidal Ideation Severity in Schizophrenia with the Illumina MethylationEPIC Array

There is a multitude of factors that makes difficult to identify those at risk for suicide, especially among schizophrenia patients. Suicide cannot be explained by genetics alone, therefore epigenetic mechanisms including DNA methylation are thought to play a role. DNA methylation could be a valuable tool in helping predict those at-risk individuals. This cross-sectional study comprised 112 subjects diagnosed with schizophrenia spectrum disorders, and were grouped according to the current suicidal ideation severity. DNA methylation across the genome was measured with the Infinium® MethylationEPIC BeadChip. We utilized the dmpFinder and bumphunter functions within the Bioconductor minfi package to identify differentially methylated positions (DMPs) and differentially methylated regions (DMRs), respectively. Following quality control, we removed one sample from the analysis and reported the most significant DMPs and DMRs associated with suicidal ideation severity. All positions and regions identified in this analysis were only found to have suggestive levels of significance at the genome-wide level. The present study was one of the first to investigate genome-wide methylation and suicidal ideation severity. While there were many strengths of our study, including investigating both differentially methylated positions and regions, further larger-scale studies are necessary to replicate, support, and validate our findings presented here.

Immune targets for therapeutic development in depression: towards precision medicine

Over the past two decades, compelling evidence has emerged indicating that immune mechanisms can contribute to the pathogenesis of major depressive disorder (MDD) and that drugs with primary immune targets can improve depressive symptoms. Patients with MDD are heterogeneous with respect to symptoms, treatment responses and biological correlates. Defining a narrower patient group based on biology could increase the treatment response rates in certain subgroups: a major advance in clinical psychiatry. For example, patients with MDD and elevated pro-inflammatory biomarkers are less likely to respond to conventional antidepressant drugs, but novel immune-based therapeutics could potentially address their unmet clinical needs. This article outlines a framework for developing drugs targeting a novel patient subtype within MDD and reviews the current state of neuroimmune drug development for mood disorders. We discuss evidence for a causal role of immune mechanisms in the pathogenesis of depression, together with targets under investigation in randomized controlled trials, biomarker evidence elucidating the link to neural mechanisms, biological and phenotypic patient selection strategies, and the unmet clinical need among patients with MDD.

Effects of Personality Characteristics of Different Genders and Quality of Life Analysis on Risk Factors for Suicide in Depressive Patients

Objective

The study was to explore the roles of personality characteristics of different genders and analyze the risk factors of quality of life (QOL) analysis in suicide among depressive patients.

Methods

One hundred and eighty-six depressive patients from January 2018 to March 2019 in the Department of Psychiatry of our hospital were enrolled and divided into Groups A and B considering whether they had a suicidal tendency or not. Among them, 90 in Group A had a suicidal tendency and consisted of 42 males and 48 females, while 96 in Group B had no suicidal tendency and consisted of 44 males and 52 females. Forward and backward selection and then backward selection were performed on all the variables of gender characteristic factors and QOL factors that may cause suicide, on which stepwise regression was finally conducted. Next, univariate logistic regression analysis was first performed to select important variables from the related risk factors that may cause suicide, and then, the multivariate logistic regression model was used to select important independent risk factors. Results and Conclusion. The age of onset, degree of anxiety, moral support, positive mental attitude, and family independence were the independent risk factors that may cause a suicidal tendency for male depressive patients. The age of onset, degree of anxiety, negative life events, moral support, positive mental attitude, family intimacy, psychoticism, and neuroticism were the independent risk factors for female depressive patients. Physiological function, role physical, bodily pain, social function, and emotional role in QOL may be the independent risk factors for a suicidal tendency.

Epigenetic studies in suicidal ideation and behavior

Most psychiatric disorders are associated with an elevated risk of suicide. Suicidal behavior is the product of the interaction of many risk factors, such as genetics and environmental factors. Hence, epigenetics research may help to understand the mechanisms leading to suicidal ideation and behavior. This review will discuss epigenetic studies in both suicidal ideation and behavior. Epigenetic modifications are likely to be important in both suicidal ideation and behavior. Most of the reviewed studies found significant epigenetic modifications linked with suicidal behavior rather than ideation. Although sizable research has been carried out on this topic, most studies have been done on small-scale samples, and future research is required in larger samples with better clinical characterization of suicide phenotypes to investigate these epigenetic modifications further.

Exon and intron sharing in opposite direction-an undocumented phenomenon in human genome-between Pou5f1 and Tcf19 genes

BACKGROUND

Overlapping genes share same genomic regions in parallel (sense) or anti-parallel (anti-sense) orientations. These gene pairs seem to occur in all domains of life and are best known from viruses. However, the advantage and biological significance of overlapping genes is still unclear. Expressed sequence tags (ESTs) analysis enabled us to uncover an overlapping gene pair in the human genome.

RESULTS

By using in silico analysis of previous experimental documentations, we reveal a new form of overlapping genes in the human genome, in which two genes found on opposite strands (Pou5f1 and Tcf19), share two exons and one intron enclosed, at the same positions, between OCT4B3 and TCF19-D splice variants.

CONCLUSIONS

This new form of overlapping gene expands our previous perception of splicing events and may shed more light on the complexity of gene regulation in higher organisms. Additional such genes might be detected by ESTs analysis also of other organisms.

Epigenetic marks in suicide: a review

Suicide is a complex phenomenon and a global public health problem that involves several biological factors that could contribute to the pathophysiology of suicide. There is evidence that epigenetic factors influence some psychiatric disorders, suggesting a predisposition to suicide or suicidal behavior. Here, we review studies of molecular mechanisms of suicide in an epigenetic perspective in the postmortem brain of suicide completers and peripheral blood cells of suicide attempters. Besides, we include studies of gene-specific DNA methylation, epigenome-wide association, histone modification, and interfering RNAs as epigenetic factors. This review provides an overview of the epigenetic mechanisms described in different biological systems related to suicide, contributing to an understanding of the genetic regulation in suicide. We conclude that epigenetic marks are potential biomarkers in suicide, and they could become attractive therapeutic targets due to their reversibility and importance in regulating gene expression.

Mediating effect of genome-wide DNA methylation on suicidal ideation induced by perceived stress

Stress is an important risk factor for suicidal ideation, but the mechanisms that link stress, suicidal ideation and neurobiology remain unclear. Epigenetic mechanisms are involved in both vulnerability to suicidal behavior and stress. This is a pilot study of 60 patients with schizophrenia spectrum disorders (36 men and 24 women), with an average age of 43.75 ± 12.24 years. We analyzed the effects of (1) perceived stress and (2) the mediation of genome-wide methylation (~450 000 CpG sites) on suicidal ideation severity. The top CpG site mediating the effect of stress on suicidal ideation was the cg10782349 located in the ZNF701 gene on chromosome 19, facilitating the effect through DNA hypermethylation. These preliminary results indicate that DNA methylation in peripheral tissues can clarify the complex relationship between stress and suicidal ideation in schizophrenia.

Analysis of the Potential Genetic Links between Psoriasis and Cardiovascular Risk Factors

Cardiovascular risk factors are one of the most common comorbidities in psoriasis. A higher prevalence of hypertension, insulin resistance and type 2 diabetes, dyslipidemia, obesity, metabolic syndrome, depression, as well as cardiovascular disease was confirmed in psoriatic patients in comparison to the general population. Data suggest that psoriasis and systemic inflammatory disorders may originate from the pleiotropic interactions with many genetic pathways. In this review, the authors present the current state of knowledge on the potential genetic links between psoriasis and cardiovascular risk factors. The understanding of the processes linking psoriasis with cardiovascular risk factors can lead to improvement of psoriasis management in the future.

Integrative DNA Methylation and Gene Expression Analysis in the Prefrontal Cortex of Mexicans Who Died by Suicide

BACKGROUND

Suicide represents a major health concern, especially in developing countries. While many demographic risk factors have been proposed, the underlying molecular pathology of suicide remains poorly understood. A body of evidence suggests that aberrant DNA methylation and expression is involved. In this study, we examined DNA methylation profiles and concordant gene expression changes in the prefrontal cortex of Mexicans who died by suicide.

METHODS

In collaboration with the coroner's office in Mexico City, brain samples of males who died by suicide (n = 35) and age-matched sudden death controls (n = 13) were collected. DNA and RNA were extracted from prefrontal cortex tissue and analyzed with the Infinium Methylation480k and the HumanHT-12 v4 Expression Beadchips, respectively.

RESULTS

We report evidence of altered DNA methylation profiles at 4430 genomic regions together with 622 genes characterized by differential expression in cases vs controls. Seventy genes were found to have concordant methylation and expression changes. Metacore-enriched analysis identified 10 genes with biological relevance to psychiatric phenotypes and suicide (ADCY9, CRH, NFATC4, ABCC8, HMGA1, KAT2A, EPHA2, TRRAP, CD22, and CBLN1) and highlighted the association that ADCY9 has with various pathways, including signal transduction regulated by the cAMP-responsive element modulator, neurophysiological process regulated by the corticotrophin-releasing hormone, and synaptic plasticity. We therefore went on to validate the observed hypomethylation of ADCY9 in cases vs control through targeted bisulfite sequencing.

CONCLUSION

Our study represents the first, to our knowledge, analysis of DNA methylation and gene expression associated with suicide in a Mexican population using postmortem brain, providing novel insights for convergent molecular alterations associated with suicide.

Hard wiring of normal tissue-specific chromosome-wide gene expression levels is an additional factor driving cancer type-specific aneuploidies

Background

Many carcinomas have recurrent chromosomal aneuploidies specific to the tissue of tumor origin. The reason for this specificity is not completely understood.

Methods

In this study, we looked at the frequency of chromosomal arm gains and losses in different cancer types from the The Cancer Genome Atlas (TCGA) and compared them to the mean gene expression of each chromosome arm in corresponding normal tissues of origin from the Genotype-Tissue Expression (GTEx) database, in addition to the distribution of tissue-specific oncogenes and tumor suppressors on different chromosome arms.

Results

This analysis revealed a complex picture of factors driving tumor karyotype evolution in which some recurrent chromosomal copy number reflect the chromosome arm-wide gene expression levels of the their normal tissue of tumor origin.

Conclusions

We conclude that the cancer type-specific distribution of chromosomal arm gains and losses is potentially “hardwiring” gene expression levels characteristic of the normal tissue of tumor origin, in addition to broadly modulating the expression of tissue-specific tumor driver genes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13073-021-00905-y.

Global DNA methylation in suicidal ideation and suicide attempt in schizophrenia

Suicidal behavior is influenced by many risk factors such as childhood trauma, stressful life events, genetic factors, and severe mental illnesses. Suicidal ideation is present in 50% of schizophrenia patients and is associated with an elevated risk of suicide attempt. Studies have shown that epigenetic mechanisms are associated with suicidal behavior in schizophrenia. Although several studies have suggested the importance of epigenetic factors in suicidal ideation and behavior, no studies have investigated global methylation in association with these two phenotypes. This study investigated global methylation level/change in association with current and emergent suicidal ideation and also with suicide attempt. Forty-seven schizophrenia patients were assessed for the association between global methylation and suicide attempt, and a subsample of these patients (n = 27) was assessed for current suicidal ideation. Afterwards, we performed a longitudinal analysis in which global methylation changes during a 3-month follow-up were compared between patients with and without emergent suicidal ideation. This methylation analysis did not find evidence for a significant association between global methylation and suicidal ideation or suicide attempt. To date, there are no robust biomarkers predicting suicidal ideation or behavior in psychotic patients. This study is the first to investigate global methylation in predicting suicidal ideation and behavior. Although we did not find evidence for an association between global methylation and these phenotypes, our findings may offer novel insights into the molecular mechanisms linked to suicide. Future investigation may measure global methylation in association with suicidal ideation or behavior in larger samples.

Modeling heritability of temperamental differences, stress reactivity, and risk for anxiety and depression: Relevance to research domain criteria (RDoC)

Animal models provide important tools to study biological and environmental factors that shape brain function and behavior. These models can be effectively leveraged by drawing on concepts from the National Institute of Mental Health Research Domain Criteria (RDoC) Initiative, which aims to delineate molecular pathways and neural circuits that underpin behavioral anomalies that transcend psychiatric conditions. To study factors that contribute to individual differences in emotionality and stress reactivity, our laboratory utilized Sprague-Dawley rats that were selectively bred for differences in novelty exploration. Selective breeding for low versus high locomotor response to novelty produced rat lines that differ in behavioral domains relevant to anxiety and depression, particularly the RDoC Negative Valence domains, including acute threat, potential threat, and loss. Bred Low Novelty Responder (LR) rats, relative to their High Responder (HR) counterparts, display high levels of behavioral inhibition, conditioned and unconditioned fear, avoidance, passive stress coping, anhedonia, and psychomotor retardation. The HR/LR traits are heritable, emerge in the first weeks of life, and appear to be driven by alterations in the developing amygdala and hippocampus. Epigenomic and transcriptomic profiling in the developing and adult HR/LR brain suggest that DNA methylation and microRNAs, as well as differences in monoaminergic transmission (dopamine and serotonin in particular), contribute to their distinct behavioral phenotypes. This work exemplifies ways that animal models such as the HR/LR rats can be effectively used to study neural and molecular factors driving emotional behavior, which may pave the way toward improved understanding the neurobiological mechanisms involved in emotional disorders.

Network-based approach to identify molecular signatures in the brains of depressed suicides

BACKGROUND

Suicide is a serious and global health problem that has a strong association with major depressive disorder (MDD). Weighted gene co-expression network analysis (WGCNA) was performed for the construction of a co-expression network to get important gene modules associated with depressed suicide.

METHODS

Transcriptome sequencing data from dorsolateral prefrontal cortex was used, which included 29 non-psychiatric controls (CON), 21 MDD suicides (MDD-S) and 9 MDD non-suicides (MDD-NS) of medication-free sudden death individuals.

RESULTS

The highest correlation in the module-traits relationship was discovered between the black module and suicide (r = -0.30, p = 0.024) as well as MDD (r = -0.34, p = 0.010).Furthermore, the expression levels of genes decreased progressively across the three groups (CON>MDD-NS>MDD-S). Therefore, the genes in the black module was selected for subsequent analyses. Protein-Protein Interaction Network found that the top 10 hub genes were somehow involved in depressed suicide including JUN, FOS, ATF3, MYC, EGR1, FOSB, DUSP1, NFKBIA, TLR2, NR4A1. Most of the GO terms were enriched in cell death and apoptosis and KEGG was mainly enriched in MAPK pathway. Cell Type-Specific Analysis found these genes were significantly enriched in endothelial and microglia (p<0.000) cell types. In addition, 92 genes in this module had at least one highly significant differentially methylated positions between MDD-S and controls.

CONCLUSION

Cell death and apoptosis may participate in the interplay between depressed suicide and neuro-inflammation system.

Epigenetic landscape of stress surfeit disorders: Key role for DNA methylation dynamics

Chronic exposure to stress throughout lifespan alters brain structure and function, inducing a maladaptive response to environmental stimuli, that can contribute to the development of a pathological phenotype. Studies have shown that hypothalamic-pituitary-adrenal (HPA) axis dysfunction is associated with various neuropsychiatric disorders, including major depressive, alcohol use and post-traumatic stress disorders. Downstream actors of the HPA axis, glucocorticoids are critical mediators of the stress response and exert their function through specific receptors, i.e., the glucocorticoid receptor (GR), highly expressed in stress/reward-integrative pathways. GRs are ligand-activated transcription factors that recruit epigenetic actors to regulate gene expression via DNA methylation, altering chromatin structure and thus shaping the response to stress. The dynamic interplay between stress response and epigenetic modifiers suggest DNA methylation plays a key role in the development of stress surfeit disorders.

Epigenetic marks and their relationship with BDNF in the brain of suicide victims

Background

Suicide is a common phenomenon affecting people of all ages. There is a strong relationship between suicidal ideation and depressive disorders. Increasing number of studies suggest that epigenetic modifications in certain brain areas are the main mechanism through which environmental and genetic factors interact with each other contributing to the development of mental disorders. To verify this hypothesis, some epigenetic marks: H3K9/14ac, HDAC2/3, H3K27me2 and Sin3a, as well as p-S421-MeCP2/MeCP2 were examined. On the other hand, BDNF protein level were studied.

Materials and methods

Western blot analysis were performed in the frontal cortex (FCx) and hippocampus (HP) of suicide victims (n = 14) and non-suicidal controls (n = 8). The differences between groups and correlations between selected proteins were evaluated using Mann-Whitney U-test and Spearman’s rank correlation.

Results

Statistically significant decrease in H3K9/14ac (FCx:↓~23%;HP:↓~33%) combined with increase in HDAC3 (FCx:↑~103%;HP:↑~85% in HP) protein levels in suicides compared to the controls was shown. These alterations were accompanied by an increase in H3K27me2 (FCx:↑45%;HP:↑~59%) and Sin3a (HP:↑50%) levels and decrease in p-S421-MeCP2/MeCP2 protein ratio (HP:↓~55%;FCx:↓~27%). Moreover, reduced BDNF protein level (FCx:↓~43%;HP:↓~28%) in suicides was observed. On the other hand, some significant correlations (e.g. between H3K9/14ac and HDAC2 or between BDNF and p-S421-MeCP2/MeCP2) were demonstrated.

Conclusions

Our findings confirm the role of epigenetic component and BDNF protein in suicidal behavior. Lowered BDNF protein level in suicides is probably due to decrease in histone acetylation and increased level of factors related with deacetylation and methylation processes, including MeCP2 factor, which may operate bidirectionally (an activator or inhibitor of transcription).

The Epigenetic Overlap between Obesity and Mood Disorders: A Systematic Review

(1) Background: Obesity and mood disorders are considered as the most prevalent morbidities in many countries. We suppose that epigenetic mechanisms may induce higher rates of obesity in subjects who suffer from mood disorders. In this systematic review, we focused on the potential roles of DNA methylation on mood disorders and obesity development. (2) Methods: This systematic review was conducted in accordance with the PRISMA statement and registered in Prospero. A systematic search was conducted in MEDLINE, Scopus, Web of Science, Cochrane Central database, EMBASE, and CINHAL. We also conducted a Grey literature search, such as Google Scholar. (3) Results: After deduplication, we identified 198 potentially related citations. Finally, ten unique studies met our inclusion criteria. We have found three overlap genes that show significant DNA methylation changes, both in obesity and depression. Pathway analysis interaction for TAPBP, BDNF, and SORBS2 confirmed the relation of these genes in both obesity and mood disorders. (4) Conclusions: While mechanisms linking both obesity and mood disorders to epigenetic response are still unknown, we have already known chronic inflammation induces a novel epigenetic program. As the results of gene enrichment, pathways analysis showed that TAPBP, BDNF, and SORBS2 linked together by inflammatory pathways. Hypermethylation in these genes might play a crucial rule in the co-occurrence of obesity and mood disorders.

Methylome profiling of young adults with depression supports a link with immune response and psoriasis

BACKGROUND

Currently the leading cause of global disability, clinical depression is a heterogeneous condition characterised by low mood, anhedonia and cognitive impairments. Its growing incidence among young people, often co-occurring with self-harm, is of particular concern. We recently reported very high rates of depression among first year university students in Northern Ireland, with over 25% meeting the clinical criteria, based on DSM IV. However, the causes of depression in such groups remain unclear, and diagnosis is hampered by a lack of biological markers. The aim of this exploratory study was to examine DNA methylation patterns in saliva samples from individuals with a history of depression and matched healthy controls.

RESULTS

From our student subjects who showed evidence of a total lifetime major depressive event (MDE, n = 186) we identified a small but distinct subgroup (n = 30) with higher risk scores on the basis of co-occurrence of self-harm and attempted suicide. Factors conferring elevated risk included being female or non-heterosexual, and intrinsic factors such as emotional suppression and impulsiveness. Saliva samples were collected and a closely matched set of high-risk cases (n = 16) and healthy controls (n = 16) similar in age, gender and smoking status were compared. These showed substantial differences in DNA methylation marks across the genome, specifically in the late cornified envelope (LCE) gene cluster. Gene ontology analysis showed highly significant enrichment for immune response, and in particular genes associated with the inflammatory skin condition psoriasis, which we confirmed using a second bioinformatics approach. We then verified methylation gains at the LCE gene cluster at the epidermal differentiation complex and at MIR4520A/B in our cases in the laboratory, using pyrosequencing. Additionally, we found loss of methylation at the PSORSC13 locus on chromosome 6 by array and pyrosequencing, validating recent findings in brain tissue from people who had died by suicide. Finally, we could show that similar changes in immune gene methylation preceded the onset of depression in an independent cohort of adolescent females.

CONCLUSIONS

Our data suggests an immune component to the aetiology of depression in at least a small subgroup of cases, consistent with the accumulating evidence supporting a relationship between inflammation and depression. Additionally, DNA methylation changes at key loci, detected in saliva, may represent a valuable tool for identifying at-risk subjects.

Methylome-wide association findings for major depressive disorder overlap in blood and brain and replicate in independent brain samples

We present the first large-scale methylome-wide association studies (MWAS) for major depressive disorder (MDD) to identify sites of potential importance for MDD etiology. Using a sequencing-based approach that provides near-complete coverage of all 28 million common CpGs in the human genome, we assay methylation in MDD cases and controls from both blood (N = 1132) and postmortem brain tissues (N = 61 samples from Brodmann Area 10, BA10). The MWAS for blood identified several loci with P ranging from 1.91 × 10^-8 to 4.39 × 10^-8 and a resampling approach showed that the cumulative association was significant (P = 4.03 × 10^-10) with the signal coming from the top 25,000 MWAS markers. Furthermore, a permutation-based analysis showed significant overlap (P = 5.4 × 10^-3) between the MWAS findings in blood and brain (BA10). This overlap was significantly enriched for a number of features including being in eQTLs in blood and the frontal cortex, CpG islands and shores, and exons. The overlapping sites were also enriched for active chromatin states in brain including genic enhancers and active transcription start sites. Furthermore, three loci located in GABBR2, RUFY3, and in an intergenic region on chromosome 2 replicated with the same direction of effect in the second brain tissue (BA25, N = 60) from the same individuals and in two independent brain collections (BA10, N = 81 and 64). GABBR2 inhibits neuronal activity through G protein-coupled second-messenger systems and RUFY3 is implicated in the establishment of neuronal polarity and axon elongation. In conclusion, we identified and replicated methylated loci associated with MDD that are involved in biological functions of likely importance to MDD etiology.

Suicide epigenetics, a review of recent progress

BACKGROUND

Suicide results in over 800,000 deaths every year, making it a major public health concern worldwide. It is highly complex, with genetic and environmental influences. Epigenetic mechanisms, including DNA methylation, miRNA, and histone modifications, could explain the complex interplay of environmental risk factors with genetic risk factors in the emergence of suicidal behavior.

METHODS

Here, we review the literature on suicide epigenetics over the past 10 years.

RESULTS

There has been significant progress in the field of suicide epigenetics, with emerging findings in the brain-derived neurotrophic factor and hypothalamic-pituitary-adrenal axis genes.

LIMITATIONS

Studying patient subgroups is needed in order to extract more comparable and reproducible epigenetic findings in suicide.

CONCLUSIONS

It is crucial to consider suicidal patients or suicide victims' distal and proximal past history e.g., early-life adversity and psychiatric disorder in epigenetic studies of suicidality.

Accelerated extrinsic epigenetic aging and increased natural killer cells in blood of suicide completers

BACKGROUND

Studies suggest aberrant DNA methylation in victims of suicide. Recently, DNA methylation profiles have been developed for determining "epigenetic age," which is the most accurate estimate of biological age. Subsequently, two refined measures of epigenetic age acceleration have been expanded for blood samples as intrinsic and extrinsic epigenetic age acceleration (IEAA and EEAA, respectively). IEAA involves pure epigenetic aging independent of blood cell composition, whereas EEAA involves immunosenescence in association with blood cell composition.

METHODS

We investigated epigenetic age acceleration using two independent DNA methylation datasets: a brain dataset from 16 suicide completers and 15 non-psychiatric controls and a blood dataset compiled using economical DNA pooling technique from 56 suicide completers and 60 living healthy controls. In the blood dataset, we considered IEAA and EEAA, as well as DNA methylation-based blood cell composition.

RESULTS

There was no significant difference in universal epigenetic age acceleration between suicide completers and controls in both brain and blood datasets. Blood of suicide completers exhibited an increase in EEAA, but not in IEAA. We additionally found that suicide completers had more natural killer cells but fewer granulocytes compared to controls.

CONCLUSION

This study provides novel evidence for accelerated extrinsic epigenetic aging in suicide completers and for the potential application of natural killer cells as a biomarker for suicidal behavior.

Cell Type-Specific Methylome-wide Association Studies Implicate Neurotrophin and Innate Immune Signaling in Major Depressive Disorder

BACKGROUND

We sought to characterize methylation changes in brain and blood associated with major depressive disorder (MDD). As analyses of bulk tissue may obscure association signals and hamper the biological interpretation of findings, these changes were studied on a cell type-specific level.

METHODS

In 3 collections of human postmortem brain (n = 206) and 1 collection of blood samples (N = 1132) of MDD cases and controls, we used epigenomic deconvolution to perform cell type-specific methylome-wide association studies within subpopulations of neurons/glia for the brain data and granulocytes/T cells/B cells/monocytes for the blood data. Sorted neurons/glia from a fourth postmortem brain collection (n = 58) were used for validation purposes.

RESULTS

Cell type-specific methylome-wide association studies identified multiple findings in neurons/glia that were detected across brain collections and were reproducible in physically sorted nuclei. Cell type-specific analyses in blood samples identified methylome-wide significant associations in T cells, monocytes, and whole blood that replicated findings from a past methylation study of MDD. Pathway analyses implicated p75 neurotrophin receptor/nerve growth factor signaling and innate immune toll-like receptor signaling in MDD. Top results in neurons, glia, bulk brain, T cells, monocytes, and whole blood were enriched for genes supported by genome-wide association studies for MDD and other psychiatric disorders.

CONCLUSIONS

We both replicated and identified novel MDD-methylation associations in human brain and blood samples at a cell type-specific level. Our results provide mechanistic insights into how the immune system may interact with the brain to affect MDD susceptibility. Importantly, our findings involved associations with MDD in human samples that implicated many closely related biological pathways. These disease-linked sites and pathways represent promising new therapeutic targets for MDD.

Genome-wide DNA methylation meta-analysis in the brains of suicide completers

Suicide is the second leading cause of death globally among young people representing a significant global health burden. Although the molecular correlates of suicide remains poorly understood, it has been hypothesised that epigenomic processes may play a role. The objective of this study was to identify suicide-associated DNA methylation changes in the human brain by utilising previously published and unpublished methylomic datasets. We analysed prefrontal cortex (PFC, n = 211) and cerebellum (CER, n = 114) DNA methylation profiles from suicide completers and non-psychiatric, sudden-death controls, meta-analysing data from independent cohorts for each brain region separately. We report evidence for altered DNA methylation at several genetic loci in suicide cases compared to controls in both brain regions with suicide-associated differentially methylated positions enriched among functional pathways relevant to psychiatric phenotypes and suicidality, including nervous system development (PFC) and regulation of long-term synaptic depression (CER). In addition, we examined the functional consequences of variable DNA methylation within a PFC suicide-associated differentially methylated region (PSORS1C3 DMR) using a dual luciferase assay and examined expression of nearby genes. DNA methylation within this region was associated with decreased expression of firefly luciferase but was not associated with expression of nearby genes, PSORS1C3 and POU5F1. Our data suggest that suicide is associated with DNA methylation, offering novel insights into the molecular pathology associated with suicidality.

Large epigenome-wide association study of childhood ADHD identifies peripheral DNA methylation associated with disease and polygenic risk burden

Epigenetic variation in peripheral tissues is being widely studied as a molecular biomarker of complex disease and disease-related exposures. To date, few studies have examined differences in DNA methylation associated with attention-deficit hyperactivity disorder (ADHD). In this study, we profiled genetic and methylomic variation across the genome in saliva samples from children (age 7-12 years) with clinically established ADHD (N = 391) and nonpsychiatric controls (N = 213). We tested for differentially methylated positions (DMPs) associated with both ADHD diagnosis and ADHD polygenic risk score, by using linear regression models including smoking, medication effects, and other potential confounders in our statistical models. Our results support previously reported associations between ADHD and DNA methylation levels at sites annotated to VIPR2, and identify several novel disease-associated DMPs (p < 1e-5), although none of them were genome-wide significant. The two top-ranked, ADHD-associated DMPs (cg17478313 annotated to SLC7A8 and cg21609804 annotated to MARK2) are also significantly associated with nearby SNPs (p = 1.2e-46 and p = 2.07e-59), providing evidence that disease-associated DMPs are under genetic control. We also report a genome-wide significant association between ADHD polygenic risk and variable DNA methylation at a site annotated to the promoter of GART and SON (p = 6.71E-8). Finally, we show that ADHD-associated SNPs colocalize with SNPs associated with methylation levels in saliva. This is the first large-scale study of DNA methylation in children with ADHD. Our results represent novel epigenetic biomarkers for ADHD that may be useful for patient stratification, reinforce the importance of genetic effects on DNA methylation, and provide plausible molecular mechanisms for ADHD risk variants.

The Role of Epigenetic Dysregulation in Suicidal Behaviors

Suicidal behaviors have been associated with both heritable genetic variables and environmental risk factors. Epigenetic processes, such as DNA methylation, have important roles in mediating the effects of the environment on behavior. Dysregulation of these processes has been observed in many psychiatric disorders, and evidence suggests that they may also be involved in suicidal behaviors. Herein, we have summarized candidate gene and epigenome-wide studies which have investigated DNA methylation in relation to suicidal behaviors, as well as discussed some of the limitations of the field to date.

Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression

Unrecognized depression during adolescence can result in adult suicidal behaviour. The aim of this study was to identify, replicate and characterize DNA methylation (DNAm) shifts in depression aetiology, using a longitudinal, multi-tissue (blood and brain) and multi-layered (genetics, epigenetics, transcriptomics) approach. We measured genome-wide blood DNAm data at baseline and one-year follow-up, and imputed genetic variants, in 59 healthy adolescents comprising the discovery cohort. Depression and suicidal symptoms were determined using the Development and Well-Being Assessment (DAWBA) depression band, Montgomery-Åsberg Depression Rating Scale-Self (MADRS-S) and SUicide Assessment Scale (SUAS). DNAm levels at follow-up were regressed against depression scores, adjusting for sex, age and the DNAm residuals at baseline. Higher methylation levels of 5% and 13% at cg24627299 within the MET gene were associated with higher depression scores (p_raw<1e-4) and susceptibility for suicidal symptoms (p_adj.<0.005). The nearby rs39748 was discovered to be a methylation and expression quantitative trait locus in blood cells. mRNA levels of hepatocyte growth factor (HGF) expression, known to strongly interact with MET, were inversely associated with methylation levels at cg24627299, in an independent cohort of 1180 CD14+ samples. In an open-access dataset of brain tissue, lower methylation at cg24627299 was found in 45 adults diagnosed with major depressive disorder compared with matched controls (p_adj.<0.05). Furthermore, lower MET expression was identified in the hippocampus of depressed individuals compared with controls in a fourth, independent cohort. Our findings reveal methylation changes at MET in the pathology of depression, possibly involved in downregulation of HGF/c-MET signalling the hippocampal region.