DNA methylation of HPA-axis genes and the onset of major depressive disorder in adolescent girls: a prospective analysis

The relationship of the methylation status and polymorphism of glucocorticoid receptor gene (NR3C1) with attempted suicide or non-suicidal self-injury patients in schizophrenia

We aim to investigate the methylation of NR3C1 gene promotor and NR3C1 BclI polymorphism in schizophrenia (SCZ) patients with attempted suicide or non-suicidal self-injury (NSSI). A sample of 112 patients with SCZ was included in the study. Structured Clinical Interview for Diagnostic and Statistical Manual-Fourth Edition Axis I Disorders was used to confirm the diagnosis according to The Diagnostic and Statistical Manual of Mental Disorders, fourth edition, text revision criteria. The patients were evaluated by data forms that had sociodemographic, suicidal behavior, and NSSI information. Methylation-specific polymerase chain reaction (PCR) was used to identify the methylation of the NR3C1 gene. The analysis of the BclI polymorphism of the NR3C1 gene was evaluated by using the PCR restriction fragment length polymorphism. Our results revealed that although the NR3C1 gene methylation was not statistically significantly different, there was a significant difference in NR3C1 genotype distribution among the SCZ groups with and without attempted suicide. SCZ patients carrying the CC genotype had a lower risk of attempted suicide (Odds Ratio [OR]: 0.421; 95% Confidence Interval [CI]: 0.183-0.970; p = 0.040), while having the GG genotype in SCZ patients was associated with a higher risk of attempted suicide (OR: 3.785; 95% Cl: 1.107-12.945; p = 0.042). Additionally, due to NSSI in SCZ patients, there were no significant differences in NR3C1 gene methylation and NR3C1 genotype distribution among the groups. We propose that the NR3C1 BclI polymorphism may be associated with attempted suicide in Turkish patients diagnosed with SCZ.

Early life adversity drives sex-dependent changes in 5-mC DNA methylation of parvalbumin cells in the prefrontal cortex in rats

Early life adversity (ELA) can result in increased risk for developing affective disorders, such as anxiety or depression, later in life, with women showing increased risk. Interactions between an individual's genes and their environment play key roles in producing, as well as mitigating, later life neuropathology. Our current understanding of the underlying epigenomic drivers of ELA associated anxiety and depression are limited, and this stems in part from the complexity of underlying biochemical processes associated with how early experiences shapes later life behavior. Epigenetic alterations, or experience-driven modifications to DNA, can be leveraged to understand the interplay between genes and the environment. The present study characterized DNA methylation patterning, assessed via evaluation of 5-methylcytosine (5-mC), following ELA in a Sprague Dawley rat model of ELA induced by early caregiver deprivation. This study utilized maternal separation to investigate sex- and age-specific outcomes of ELA on epigenetic patterning in parvalbumin (PV)-containing interneurons in the prefrontal cortex (PFC), a subpopulation of inhibitory neurons which are associated with ELA and affective dysfunction. While global analysis of 5-mC methylation and CpG site specific pyrosequencing of the PV promoter, Pvalb, showed no obvious effects of ELA, when analyses were restricted to assessing 5-mC intensity in colocalized PV cells, there were significant sex and age dependent effects. We found that ELA leads sex-specific changes in PV cell counts, and that cell counts can be predicted by 5-mC intensity, with males and females showing distinct patterns of methylation and PV outcomes. ELA also produced sex-specific effects in corticosterone reactivity, with juvenile females showing a blunted stress hormone response compared to controls. Overall, ELA led to a sex-specific developmental shift in PV profile, which is comparable to profiles that are seen at a later developmental timepoint, and this shift may be mediated in part by epigenomic alterations driven by altered DNA methylation.

DNA Methylation of POMC and NR3C1-1F and Its Implication in Major Depressive Disorder and Electroconvulsive Therapy

INTRODUCTION

Precision medicine in psychiatry is still in its infancy. To establish patient-tailored treatment, adequate indicators predicting treatment response are required. Electroconvulsive therapy (ECT) is considered one of the most effective options for pharmacoresistant major depressive disorder (MDD), yet remission rates were reported to be below 50%.

METHODS

Since epigenetics of the stress response system seem to play a role in MDD, we analyzed the DNA methylation (DNAm) of genes encoding the glucocorticoid receptor (NR3C1) and proopiomelanocortin (POMC) through Sanger Sequencing. For analysis, blood was taken before and after the first and last ECT from MDD patients (n=31), unmedicated depressed controls (UDC; n=19, baseline), and healthy controls (HC; n=20, baseline).

RESULTS

Baseline DNAm in NR3C1 was significantly lower in UDCs compared to both other groups (UDC: 0.014(±0.002), ECT: 0.031(±0.001), HC: 0.024(±0.002); p<0.001), whereas regarding POMC, ECT patients had the highest DNAm levels (ECT: 0.252(±0.013), UDC: 0.156(±0.015), HC: 0.162(±0.014); p<0.001). NR3C1m and POMCm decreased after the first ECT (NR3C1: p<0.001; POMC: p=0.001), and responders were less methylated compared to non-responders in NR3C1(p<0.001).

DISCUSSION

Our findings indicate that both genes might play a role in the chronification of depression and NR3C1 may be relevant for ECT response prediction.

Late-life depression: Epidemiology, phenotype, pathogenesis and treatment before and during the COVID-19 pandemic

Late-life depression (LLD) is one of the most common mental disorders among the older adults. Population aging, social stress, and the COVID-19 pandemic have significantly affected the emotional health of older adults, resulting in a worldwide prevalence of LLD. The clinical phenotypes between LLD and adult depression differ in terms of symptoms, comorbid physical diseases, and coexisting cognitive impairments. Many pathological factors such as the imbalance of neurotransmitters, a decrease in neurotrophic factors, an increase in β-amyloid production, dysregulation of the hypothalamic-pituitary-adrenal axis, and changes in the gut microbiota, are allegedly associated with the onset of LLD. However, the exact pathogenic mechanism underlying LLD remains unclear. Traditional selective serotonin reuptake inhibitor therapy results in poor responsiveness and side effects during LLD treatment. Neuromodulation therapies and complementary and integrative therapies have been proven safe and effective for the treatment of LLD. Importantly, during the COVID-19 pandemic, modern digital health intervention technologies, including socially assistive robots and app-based interventions, have proven to be advantageous in providing personal services to patients with LLD.

Biomarkers in Child and Adolescent Depression

Despite the significant prevalence of Major Depressive Disorder in the pediatric population, the pathophysiology of this condition remains unclear, and the treatment outcomes poor. Investigating tools that might aid in diagnosing and treating early-onset depression seems essential in improving the prognosis of the future disease course. Recent studies have focused on searching for biomarkers that constitute biochemical indicators of MDD susceptibility, diagnosis, or treatment outcome. In comparison to increasing evidence of possible biomarkers in adult depression, the studies investigating this subject in the youth population are lacking. This narrative review aims to summarize research on molecular and biochemical biomarkers in child and adolescent depression in order to advocate future directions in the research on this subject. More studies on depression involving the youth population seem vital to comprehend the natural course of the disease and identify features that may underlie commonly observed differences in treatment outcomes between adults and children.

Multi-level predictors of depression symptoms in the Adolescent Brain Cognitive Development (ABCD) study

BACKGROUND

While identifying risk factors for adolescent depression is critical for early prevention and intervention, most studies have sought to understand the role of isolated factors rather than across a broad set of factors. Here, we sought to examine multi-level factors that maximize the prediction of depression symptoms in US children participating in the Adolescent Brain and Cognitive Development (ABCD) study.

METHODS

A total of 7,995 participants from ABCD (version 3.0 release) provided complete data at baseline and 1-year follow-up data. Depression symptoms were measured with the Child Behavior Checklist. Predictive features included child demographic, environmental, and structural and resting-state fMRI variables, parental depression history and demographic characteristics. We used linear (elastic net regression, EN) and non-linear (gradient-boosted trees, GBT) predictive models to identify which set of features maximized prediction of depression symptoms at baseline and, separately, at 1-year follow-up.

RESULTS

Both linear and non-linear models achieved comparable results for predicting baseline (EN: MAE = 3.757; R2  = 0.156; GBT: MAE = 3.761; R2  = 0.147) and 1-year follow-up (EN: MAE = 4.255; R2  = 0.103; GBT: MAE = 4.262; R2  = 0.089) depression. Parental history of depression, greater family conflict, and shorter child sleep duration were among the top predictors of concurrent and future child depression symptoms across both models. Although resting-state fMRI features were relatively weaker predictors, functional connectivity of the caudate was consistently the strongest neural feature associated with depression symptoms at both timepoints.

CONCLUSIONS

Consistent with prior research, parental mental health, family environment, and child sleep quality are important risk factors for youth depression. Functional connectivity of the caudate is a relatively weaker predictor of depression symptoms but may represent a biomarker for depression risk.

The association of FKBP5 gene methylation, adolescents' sex, and depressive symptoms among Chinese adolescents: a nested case-control study

BACKGROUND

Depressive symptoms among adolescents are a serious health concern around the world. Altered DNA methylation in the FK506 binding protein 5 (FKBP5) gene has been reported to regulate stress response, which has been reported to be closely associated with depressive symptoms. However, most of the contributing studies have been conducted among adults and relatively few studies have considered the effect of disparate social influences and sex differences on the DNA methylation of FKBP5 in persons with depressive symptoms. The present study aimed to test the associations of FKBP5 DNA methylation and depressive symptoms among adolescents and explore possible sex differences in the foregoing associations.

METHODS

This study was conducted using a nested case-control design within a longitudinal cohort study from January 2019 to December 2019. Adolescents aged 12 to 17 years from 69 classes in 10 public high schools located in Guangdong province of China participated in this research. Students with persistent depressive symptoms that reported having depressive symptoms at both baseline and follow-up were treated as the case group, and those without depressive symptoms were randomly selected as the control group. Our study finally included 87 cases and 151 controls. Quantitative methylation analyses of the selected gene were carried out by MassARRAY platform System.

RESULTS

The overall DNA methylation trend of FKBP5 CpG sites in the case group was lower in comparison to the control group. Compared to healthy controls, lower methylation percentage of FKBP5-12 CpG 1 was observed in adolescents with persistent depressive symptoms after adjusting for covariates (case: 0.94 ± 2.00, control: 0.47 ± 0.92; F = 5.41, P = 0.021), although the statistical significance of the difference was lost after false discovery rate correction (q > 0.05). In addition, the hypomethylation of FKBP5-12 CpG 1 was approaching significance after adjustment for social-environmental factors (aOR = 0.77; P = 0.055), which indicated that no independent association was detected between hypomethylation of FKBP5 CpG sites and persistent depressive symptoms. Furthermore, in the present study, we were unable to identify sex differences in the association of FKBP5 gene methylation with depressive symptoms.

CONCLUSION

The decreased methylation level of FKBP5 was observed in adolescents with persistent depressive symptoms, albeit non-significant after correction for multiple testing. Our results presented here are preliminary and underscore the complex gene-environment interactions relevant to the risk for depressive symptoms.

DNA Methylation Pattern of Gene Promoters of MB-COMT, DRD2, and NR3C1 in Turkish Patients Diagnosed with Schizophrenia

OBJECTIVE

We aim to evaluate the methylation status of membrane-bound catechol-O-methyltransferase (MB-COMT) promotor, dopamine receptor D2 (DRD2), and nuclear receptor subfamily 3 group C member 1 (NR3C1) gene in pa- tients with SCZ by comparing healthy controls.

METHODS

A sample of 110 patients with SCZ and 100 age- and sex-matched healthy volunteers was included in the study. The interview was started by filling out data forms that included sociodemographic and clinical information. The Structured Clinical Interview for DSM-IV Axis I Disorders was used to confirming the diagnosis according to DSM-IV-TR criteria. Then the patients were evaluated with the Positive and Negative Symptoms Scale in terms of symp- tom severity. Methylation-specific polymerase chain reaction was used to determine the methylation status of MB-COMT promotor, DRD2 , and NR3C1 gene from DNA material.

RESULTS

When we compared the percentages of MB-COMT promotor, DRD2, and NR3C1 gene methylation status in SCZ patients with the healthy control group, the percentages of MB-COMT promotor (OR: 0.466; 95% CI: 0.268- 0.809; p = 0.006), DRD2 (OR: 0.439; 95% CI: 0.375-0.514; p < 0.001), and NR3C1 (OR: 0.003; 95% CI: 0.001- 0.011; p < 0.001) gene methylation status of SCZ was found to be significantly different from the control group. Whereas unmethylation of MB-COMT promotor and NR3C1 genes were associated with SCZ, the partial methylation of the DRD2 gene was related to the SCZ.

CONCLUSION

The MB-COMT promotor, DRD2, and NR3C1 gene methylation status may be associated with the SCZ in the Turkish population.

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.

Glucocorticoid Receptor Gene (NR3C1) Expression in the Pathogenesis of Depression in Cancer

Background

This study aimed to compare the NR3C1 expression among cancer patients with major depressive disorder (cancer depression), cancer patients without major depressive disorder (cancer non-depression), and major depressive disorder patients without cancer (general depression), as a preliminary investigation of epigenetic changes in the glucocorticoid receptor gene.

Methods

From May 2019 to November 2019, patients were recruited from the Department of Psychiatry, Cancer Center in Busan, Korea. For gene expression studies, primers were designed using the Primer3 web tool (http://frodo.wi.mit.edu/primer3), and amplification reactions were performed.

Results

Expression levels of NR3C1 were lower in cancer depression and general depression than in cancer non-depression group. Given that we observed downregulation of the NR3C1 gene expression in depressive patients regardless of cancer status, it appears that methylation changes in NR3C1 may contribute to the pathophysiology of depression.

Conclusion

The results of this study imply that the expression of NR3C1 may be decreased in major depressive disorder.

Comorbidity of Novel CRHR2 Gene Variants in Type 2 Diabetes and Depression

The corticotropin-releasing hormone receptor 2 (CRHR2) gene encodes CRHR2, contributing to the hypothalamic–pituitary–adrenal stress response and to hyperglycemia and insulin resistance. CRHR2−/− mice are hypersensitive to stress, and the CRHR2 locus has been linked to type 2 diabetes and depression. While CRHR2 variants confer risk for mood disorders, MDD, and type 2 diabetes, they have not been investigated in familial T2D and MDD. In 212 Italian families with type 2 diabetes and depression, we tested 17 CRHR2 single nucleotide polymorphisms (SNPs), using two-point parametric-linkage and linkage-disequilibrium (i.e., association) analysis (models: dominant-complete-penetrance-D1, dominant-incomplete-penetrance-D2, recessive-complete-penetrance-R1, recessive-incomplete-penetrance-R2). We detected novel linkage/linkage-disequilibrium/association to/with depression (3 SNPs/D1, 2 SNPs/D2, 3 SNPs/R1, 3 SNPs/R2) and type 2 diabetes (3 SNPs/D1, 2 SNPs/D2, 2 SNPs/R1, 1 SNP/R2). All detected risk variants are novel. Two depression-risk variants within one linkage-disequilibrium block replicate each other. Two independent novel SNPs were comorbid while the most significant conferred either depression- or type 2 diabetes-risk. Although the families were primarily ascertained for type 2 diabetes, depression-risk variants showed higher significance than type 2 diabetes-risk variants, implying CRHR2 has a stronger role in depression-risk than type 2 diabetes-risk. In silico analysis predicted variants’ dysfunction. CRHR2 is for the first time linked to/in linkage-disequilibrium/association with depression-type 2 diabetes comorbidity and may underlie the shared genetic pathogenesis via pleiotropy.

Early developmental stage glucocorticoid exposure causes DNA methylation and behavioral defects in adult zebrafish

Post-traumatic stress disorder (PTSD) is a psychiatric disorder caused by genetic and environmental factors. It is closely related to a dysfunction of the hypothalamic-pituitary-adrenal (HPA) axis, in which the epigenetic modification of the nr3c1 plays an important role. It is well known that nr3c1 methylation in offspring is reportedly related to early adverse life experiences, prenatal stress response, and early nursing conditions; however, the methylation location and extent of the nr3c1 are not sufficiently elucidated. In order to study the internal mechanism of PTSD caused by early adverse life experience, we used zebrafish to construct a psychopathological model. We found that early developmental stage prednisolone exposure caused HPA axis negative feedback dysfunction and hormone secretion disorder in adult male zebrafish. By analyzing nr3c1 promoter, we found that cytosine-guanine island (CpGI) 2 was highly methylated in adult male zebrafish, which affected the expression of glucocorticoid receptor, resulting in abnormal behavior and anxiety like phenotype of adult male zebrafish. Therefore, we believed that an early exposure of zebrafish larvae to prednisolone may be recorded through a change of CpGI 2 methylation in the nr3c1 promoter region, causing abnormal adult male zebrafish behavior. Moreover, the establishment of the zebrafish psychopathological model may facilitate the study of the clinical management of patients with PTSD.

Basal and reactive cortisol: A systematic literature review of offspring of parents with depressive and bipolar disorders

One of the most consistent biological findings in the study of affective disorders is that those with depression commonly show abnormal cortisol response, which suggests dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis. Children of parents with mood disorders offer the opportunity to explore the biological pathways that may confer risk for psychopathology. This review explores basal and reactive cortisol in the offspring of parents who are currently depressed or have had a history of a depressive or bipolar disorder. Using PRISMA guidelines, search terms yielded 2002 manuscripts. After screening, 87 of these manuscripts were included. Results from the literature suggest that while the degree and direction of dysregulation varies, offspring of a parent with depression tend to show elevations in both basal (particularly morning and evening) and reactive (tentatively for social stressors) cortisol levels. There were few studies focused on offspring of parents with bipolar disorder. This review also discusses implications and recommendations for future research regarding the HPA axis in the intergenerational transmission of depressive disorders.

Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with global and local ancestries

Lack of diversity in human genomics limits our understanding of the genetic underpinnings of complex traits, hinders precision medicine, and contributes to health disparities. To map genetic effects on gene regulation in the underrepresented Indonesian population, we have integrated genotype, gene expression, and CpG methylation data from 115 participants across three island populations that capture the major sources of genomic diversity in the region. In a comparison with European datasets, we identify eQTLs shared between Indonesia and Europe as well as population-specific eQTLs that exhibit differences in allele frequencies and/or overall expression levels between populations. By combining local ancestry and archaic introgression inference with eQTLs and methylQTLs, we identify regulatory loci driven by modern Papuan ancestry as well as introgressed Denisovan and Neanderthal variation. GWAS colocalization connects QTLs detected here to hematological traits, and further comparison with European datasets reflects the poor overall transferability of GWAS statistics across diverse populations. Our findings illustrate how population-specific genetic architecture, local ancestry, and archaic introgression drive variation in gene regulation across genetically distinct and in admixed populations and highlight the need for performing association studies on non-European populations.

Global and glucocorticoid receptor gene-specific (NR3C1) DNA methylation analysis in patients with cannabinoid or synthetic cannabinoid use disorder

This study investigates the relationship between cannabinoid use disorder (CUD) or synthetic cannabinoid use disorder (SCUD) and the global methylation, methylation of NR3C1 gene promotor, and NR3C1 BclI polymorphism, considering clinical parameters. Based on the DSM-5 criteria, 172 SCUD patients' and 44 CUD patients' diagnoses were confirmed with a positive urine test; 88 healthy volunteers were also included in the study. Global DNA methylation was measured using a 5-methylcytosine (5-mC) DNA ELISA Kit. Methylation-specific PCR was used to identify the methylation of the NR3C1 gene. The analysis of the BclI polymorphism of the NR3C1 gene was evaluated by using the PCR-RFLP. Our results demonstrated that the mean of 5-mC percentages of SCUD patients differed significantly from those of the control group. When comparing NR3C1 gene methylation and clinical parameters due to NR3C1 genotype distribution in patients, the genotype distribution was significantly different between the groups, due to the former polysubstance abuse. Additionally, there was a significantly positive correlation between the 5-mC percentages of SCUD patients and the reported durations of their disorders. In summary, whereas global DNA methylation may be associated with SCUD, the methylation of the NR3C1 gene and NR3C1 BclI polymorphism were not related to CUD or SCUD.

Structural brain correlates of serum and epigenetic markers of inflammation in major depressive disorder

Inflammatory processes are implicated in the aetiology of Major Depressive Disorder (MDD); however, the relationship between peripheral inflammation, brain structure and depression remains unclear, partly due to complexities around the use of acute/phasic inflammatory biomarkers. Here, we report the first large-scale study of both serological and methylomic signatures of CRP (considered to represent acute and chronic measures of inflammation respectively) and their associations with depression status/symptoms, and structural neuroimaging phenotypes (T1 and diffusion MRI) in a large community-based sample (Generation Scotland; NMDD cases = 271, Ncontrols = 609). Serum CRP was associated with overall MDD severity, and specifically with current somatic symptoms- general interest (β = 0.145, PFDR = 6 × 10-4) and energy levels (β = 0.101, PFDR = 0.027), along with reduced entorhinal cortex thickness (β = -0.095, PFDR = 0.037). DNAm CRP was significantly associated with reduced global grey matter/cortical volume and widespread reductions in integrity of 16/24 white matter tracts (with greatest regional effects in the external and internal capsules, βFA= -0.12 to -0.14). In general, the methylation-based measures showed stronger associations with imaging metrics than serum-based CRP measures (βaverage = -0.15 versus βaverage = 0.01 respectively). These findings provide evidence for central effects of peripheral inflammation from both serological and epigenetic markers of inflammation, including in brain regions previously implicated in depression. This suggests that these imaging measures may be involved in the relationship between peripheral inflammation and somatic/depressive symptoms. Notably, greater effects on brain morphology were seen for methylation-based rather than serum-based measures of inflammation, indicating the importance of such measures for future studies.

Integrated Analysis of Methylomic and Transcriptomic Data to Identify Potential Diagnostic Biomarkers for Major Depressive Disorder

Major depressive disorder (MDD) is a mental illness with high incidence and complex etiology, that poses a serious threat to human health and increases the socioeconomic burden. Currently, high-accuracy biomarkers for MDD diagnosis are urgently needed. This paper aims to identify novel blood-based diagnostic biomarkers for MDD. Whole blood DNA methylation data and gene expression data from the Gene Expression Omnibus database are downloaded. Then, differentially expressed/methylated genes (DEGs/DMGs) are identified. In addition, we made a systematic analysis of the DNA methylation on 5′-C-phosphate-G-3′ (CpGs) in all of the gene regions, as well as different gene regions, and then we defined a “dominant” region. Subsequently, integrated analysis is employed to identify the robust MDD-related blood biomarkers. Finally, a gene expression classifier and a methylation classifier are constructed using the random forest algorithm and the leave-one-out cross-validation method. Our results demonstrate that DEGs are mainly involved in the inflammatory response-associated pathways, while DMGs are primarily concentrated in the neurodevelopment- and neuroplasticity-associated pathways. Our integrated analysis identified 46 hypo-methylated and up-regulated (hypo-up) genes and 71 hyper-methylated and down-regulated (hyper-down) genes. One gene expression classifier and two DNA methylation classifiers, based on the CpGs in all of the regions or in the dominant regions are constructed. The gene expression classifier possessed the best predictive ability, followed by the DNA methylation classifiers, based on the CpGs in both the dominant regions and all of the regions. In summary, the integrated analysis of DNA methylation and gene expression has identified 46 hypo-up genes and 71 hyper-down genes, which could be used as diagnostic biomarkers for MDD.

Precision Psychiatry: Biomarker-Guided Tailored Therapy for Effective Treatment and Prevention in Major Depression

Depression contributes greatly to global disability and is a leading cause of suicide. It has multiple etiologies and therefore response to treatment can vary significantly. By applying the concepts of personalized medicine, precision psychiatry attempts to optimize psychiatric patient care by better predicting which individuals will develop an illness, by giving a more accurate biologically based diagnosis, and by utilizing more effective treatments based on an individual's biological characteristics (biomarkers). In this chapter, we discuss the basic principles underlying the role of biomarkers in psychiatric pathology and then explore multiple biomarkers that are specific to depression. These include endophenotypes, gene variants/polymorphisms, epigenetic factors such as methylation, biochemical measures, circadian rhythm dysregulation, and neuroimaging findings. We also examine the role of early childhood trauma in the development of, and treatment response to, depression. In addition, we review how new developments in technology may play a greater role in the determination of new biomarkers for depression.

DNA methylation and regulation of gene expression: Guardian of our health

One of the most critical epigenetic signatures present in the genome of higher eukaryotes is the methylation of DNA at the C-5 position of the cytosine ring. Based on the sites of DNA methylation in a locus, it can serve as a repressive or activation mark for gene expression. In a crosstalk with histone modifiers, DNA methylation can consequently either inhibit binding of the transcription machinery or generate a landscape conducive for transcription. During developmental phases, the DNA methylation pattern in the genome undergoes alterations as a result of regulated balance between de novo DNA methylation and demethylation. Resultantly, differentiated cells inherit a unique DNA methylation pattern that fine tunes tissue-specific gene expression. Although apparently a stable epigenetic mark, DNA methylation is actually labile and is a complex reflection of interaction between epigenome, genome and environmental factors prior to birth and during progression of life. Recent findings indicate that levels of DNA methylation in an individual is a dynamic outcome, strongly influenced by the dietary environment during germ cell formation, embryogenesis and post birth exposures. Loss of balances in DNA methylation during developmental stages may result in imprinting disorders, while at any later stage may lead to increased predisposition to various diseases and abnormalities. This review aims to provide an outline of how our epigenome is uniquely guided by our lifetime of experiences beginning in the womb and how understanding it better holds future possibilities of improvised clinical applications.

A Load to Find Clinically Useful Biomarkers for Depression

Depression is heterogeneous and complex disease with diverse symptoms. Its neurobiological underpinning is still not completely understood. For now, there are still no validated, easy obtainable, clinically useful noninvasive biomarker(s) or biomarker panel that will be able to confirm a diagnosis of depression, its subtypes and improve diagnostic procedures. Future multimodal preclinical and clinical research that involves (epi)genetic, molecular, cellular, imaging, and other studies is necessary to advance our understanding of the role of monoamines, GABA, HPA axis, neurotrophins, metabolome, and glycome in the pathogenesis of depression and their potential as diagnostic, prognostic, and treatment response biomarkers. These studies should be focused to include the first-episode depression and antidepressant drug-naïve patients with large sample sizes to reduce variability in different biological and clinical parameters. At present, metabolomics study revealed with high precision that a neurometabolite panel consisting of plasma metabolite biomarkers (GABA, dopamine, tyramine, kynurenine) might represent clinically useful biomarkers of MDD.

Perinatal protein malnutrition results in genome-wide disruptions of 5-hydroxymethylcytosine at regions that can be restored to control levels by an enriched environment

Maternal malnutrition remains one of the major adversities affecting brain development and long-term mental health outcomes, increasing the risk to develop anxiety and depressive disorders. We have previously shown that malnutrition-induced anxiety-like behaviours can be rescued by a social and sensory stimulation (enriched environment) in male mice. Here, we expand these findings to adult female mice and profiled genome-wide ventral hippocampal 5hmC levels related to malnutrition-induced anxiety-like behaviours and their rescue by an enriched environment. This approach revealed 508 differentially hydroxymethylated genes associated with protein malnutrition and that several genes (N = 34) exhibited a restored 5hmC abundance to control levels following exposure to an enriched environment, including genes involved in neuronal functions like dendrite outgrowth, axon guidance, and maintenance of neuronal circuits (e.g. Fltr3, Itsn1, Lman1, Lsamp, Nav, and Ror1) and epigenetic mechanisms (e.g. Hdac9 and Dicer1). Sequence motif predictions indicated that 5hmC may be modulating the binding of transcription factors for several of these transcripts, suggesting a regulatory role for 5hmC in response to perinatal malnutrition and exposure to an enriched environment. Together, these findings establish a role for 5hmC in early-life malnutrition and reveal genes linked to malnutrition-induced anxious behaviours that are mitigated by an enriched environment.

miR-218 in Adolescence Predicts and Mediates Vulnerability to Stress

BACKGROUND

Adolescence is a period of increased vulnerability to psychiatric disorders, including depression. Discovering novel biomarkers to identify individuals who are at high risk is very much needed. Our previous work shows that the microRNA miR-218 mediates susceptibility to stress and depression in adulthood by targeting the netrin-1 guidance cue receptor gene Dcc in the medial prefrontal cortex (mPFC).

METHODS

Here, we investigated whether miR-218 regulates Dcc expression in adolescence and could serve as an early predictor of lifetime stress vulnerability in male mice.

RESULTS

miR-218 expression in the mPFC increases from early adolescence to adulthood and correlates negatively with Dcc levels. In blood, postnatal miR-218 expression parallels changes occurring in the mPFC. Notably, circulating miR-218 levels in adolescence associate with vulnerability to social defeat stress in adulthood, with high levels associated with social avoidance severity. Indeed, downregulation of miR-218 in the mPFC in adolescence promotes resilience to stress in adulthood.

CONCLUSIONS

miR-218 expression in adolescence may serve both as a marker of risk and as a target for early interventions.

Psychological and physical condition of Japan maritime self-defense force personnel who performed disaster-relief missions after the 2011 great east Japan earthquake

The Great East Japan Earthquake, which occurred on March 11, 2011, was the most powerful earthquake ever recorded in Japan. In the present study, we examine personnel from the Japan Maritime Self-Defense Force who performed disaster relief in the earthquake's aftermath, focusing on the associated psychological and physical impacts. Overall, 8733 personnel were examined. In both July-August 2011 (M1) and July 2012 (M2), these personnel answered the Impact of Events Scale-Revised, the Kessler Psychological Distress Scale, and the Disaster Relief Questionnaire. We also analyzed the sample's physical examination records for the periods before and after the earthquake, using as controls a sample of peers who were not dispatched to the disaster area (N = 32,270). The psychological examinations showed that, in M1, holding the rank of private/sergeant (odds ratio [OR] = 2.13), performing body-recovery duties (OR = 1.94), and having disaster-affected family members (OR = 2.13) were significant risk factors for high post-traumatic stress response (PTSR). In M2, performing body-recovery duties (OR = 1.45) and having disaster-affected family members (OR = 2.60) were significant risk factors for high PTSR. Also, being woman (OR = 2.18) and having disaster-affected family members (OR = 1.68) were significant risk factors for high general psychological distress. For the physical examinations, the mean alanine transaminase in the dispatched group (31.73 ± 25.21) was significantly higher than that in the non-dispatched group (29.56 ± 21.03). These findings suggest that personnel involved in disaster relief experience psychological impacts in the subacute stage, but that these impacts attenuate one year after the event.

COVID-19 and Women's Health: A Low- and Middle-Income Country Perspective

Corona Virus Disease (COVID-19), a contagious disease, is a global pandemic affecting the lives and health of individuals across borders, genders and races. Much of what is known about the effects of natural disasters and disease outbreaks on women's health in particular, is based on studies conducted in high-income countries. The evolving evidence suggests that COVID-19 has a profound negative impact on the perinatal mental health of women. It is also clear that global pandemics such as COVID-19 disproportionately affect the less affluent, including individuals living in low- and middle-income countries. The purpose of this review is to summarize and critically discuss extant knowledge on COVID-19 as it relates to the perinatal health of women in low and middle-income countries, using Pakistan as a case example. We specifically highlight the effects on perinatal mental health, preterm birth, and timing of the COVID-19 exposure. Our review suggests that it is essential to consider the effects of COVID-19 within this cultural context and that findings from high-income countries do not necessarily translate to the situation in low and middle-income countries.

Sex-dependent association of mineralocorticoid receptor gene (NR3C2) DNA methylation and schizophrenia

Schizophrenia is a complex disease caused by genetic and environmental factors. Epigenetic regulation mediates gene-environment interactions by modulating gene expression. Abnormal activation of the hypothalamic-pituitary-adrenal (HPA) axis has been widely reported in schizophrenia patients. The DNA methylation levels of critical genes are associated with HPA axis activity, which is linked to schizophrenia pathogenesis. The mineralocorticoid receptor gene NR3C2 regulates HPA axis activity. However, how NR3C2 methylation affects the development of schizophrenia remains unknown. Here, we investigated the DNA methylation state of NR3C2, including the promoter P1 (NR3C2-1, NR3C2-2 and NR3C2-3) and exon 1α and its downstream sequence (NR3C2-4), in schizophrenia. Peripheral blood DNA from 80 schizophrenia patients and 128 healthy controls was used to assess NR3C2 DNA methylation via sodium bisulfite treatment and the MethylTarget method. NR3C2-4 region was hypermethylated in schizophrenia patients compared with healthy controls in the female group. Specific CpG sites in P1 and NR3C2-4 region were associated with schizophrenia, with sex-specific effects. These findings showed a relationship between NR3C2 DNA methylation and schizophrenia, revealing that epigenetic processes may mediate schizophrenia pathophysiology. Further research should address the potential epigenetic mechanisms of the relationship between NR3C2 and schizophrenia.

The link between parental psychological control, depressive symptoms and epigenetic changes in the glucocorticoid receptor gene (NR3C1)

AIMS

This paper examines the relationship between parental Psychological Control (PC) and depressive symptoms in adolescents and assesses whether this relationship was mediated by DNA methylation, focusing on the glucocorticoid receptor gene (NR3C1), which plays a crucial role in HPA-axis functioning and is linked to environmental stress and depression. This is among the very few studies that looked at the relation between DNA methylation, environmental stress and depression in family trios.

METHODS

The study cohort consisted of 250 families: father, mother and a biologically related adolescent (adolescents (48.9% boys), mean age: 15.14, SD= 1.9; mean age mothers: 45.83, SD= 4.2; mean age fathers: 47.77, SD= 4.7). Depressive symptoms and PC were measured in adolescents and in both parents. DNA methylation levels in NR3C1 were examined in all participants.

RESULTS

Depressive symptoms in adolescents were predicted by PC of both mothers and fathers. Moreover, maternal depressive symptoms were associated with maternal PC, and fathers' depressive symptoms and PC. In fathers, only the level of their self-reported PC was associated with their depressive symptoms. There was no relation between adolescents' DNA methylation and depressive symptoms or the level of parental PC. Yet, there was a significant association between maternal depressive symptoms and maternal epigenetic patterns in NR3C1.

CONCLUSIONS

These findings highlight the need for more research in order to better understand the biological and contextual mechanisms through which parenting and parental emotional well-being is related to the development of psychopathology.

An epigenome-wide association study of early-onset major depression in monozygotic twins

Major depression (MD) is a debilitating mental health condition with peak prevalence occurring early in life. Genome-wide examination of DNA methylation (DNAm) offers an attractive complement to studies of allelic risk given it can reflect the combined influence of genes and environment. The current study used monozygotic twins to identify differentially and variably methylated regions of the genome that distinguish twins with and without a lifetime history of early-onset MD. The sample included 150 Caucasian monozygotic twins between the ages of 15 and 20 (73% female; Mage = 17.52 SD = 1.28) who were assessed during a developmental stage characterized by relatively distinct neurophysiological changes. All twins were generally healthy and currently free of medications with psychotropic effects. DNAm was measured in peripheral blood cells using the Infinium Human BeadChip 450 K Array. MD associations with early-onset MD were detected at 760 differentially and variably methylated probes/regions that mapped to 428 genes. Genes and genomic regions involved neural circuitry formation, projection, functioning, and plasticity. Gene enrichment analyses implicated genes related to neuron structures and neurodevelopmental processes including cell-cell adhesion genes (e.g., PCDHA genes). Genes previously implicated in mood and psychiatric disorders as well as chronic stress (e.g., NRG3) also were identified. DNAm regions associated with early-onset MD were found to overlap genetic loci identified in the latest Psychiatric Genomics Consortium meta-analysis of depression. Understanding the time course of epigenetic influences during emerging adulthood may clarify developmental phases where changes in the DNA methylome may modulate individual differences in MD risk.

Current status of development of methylation biomarkers for in vitro diagnostic IVD applications

A significant volume of research clearly shows that disease-related methylation changes can be used as biomarkers at all stages of clinical disease management, including risk assessment and predisposition screening through early diagnostics to personalization of patient care and monitoring of the relapse and chronic disease. Thus disease-related methylation changes are an attractive source of the biomarkers that can have significant impact on precision medicine. However, the translation of the research findings in methylation biomarkers field to clinical practice is at the very least not satisfactory. That is mainly because the evidence generated in research studies indicating the utility of the disease-related methylation change to predict clinical outcome is in majority of the cases not sufficient to postulate the diagnostic use of the biomarker. The research studies need to be followed by well-designed and systematic investigations of clinical utility of the biomarker that produce data of sufficient quality to meet regulatory approval for the test to be used to make clinically valid decision. In this review, we describe methylation-based IVD tests currently approved for IVD use or at the advanced stages of the development for the diagnostic use. For each of those tests, we analyze the technologies that the test utilizes for methylation detection as well as describe the types of the clinical studies that were performed to show clinical validity of the test and warrant regulatory approval. The examples reviewed here should help with planning of clinical investigations and delivery of the clinical evidence required for the regulatory approval of potential methylation biomarker based IVD tests.

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.