Major depressive disorder (MDD) is associated with complex metabolic alterations. In this study, we applied a multiplatform metabolomics approach (GC-MS and LC-MS) to characterize the plasma extracellular vesicle (EV) metabolome in healthy controls (N = 50), responsive MDD patients (N = 60), and patients with treatment-resistant depression (TRD; N = 65). Longitudinal analyses were performed following 8-week treatment with duloxetine (N = 30), bright-light therapy (BLT; N = 30), or esketamine (N = 35). A total of 230 metabolites were identified, with the most pronounced metabolic alterations observed in TRD patients, particularly in lipid, amino acid, and energy metabolism pathways. Elevated lysophospholipids and fatty acids in TRD suggested dysregulated lipid metabolism and inflammatory processes. All treatments resulted in clinical improvement, accompanied by partial normalization of metabolic profiles. Duloxetine treatment was associated with modulation of amino acid and glycerophospholipid metabolism, including increases in tryptophan-related metabolites and normalization of specific lipid species. BLT primarily reduced lysophospholipids and mannose levels, while esketamine modulated metabolites related to lipid turnover, short-chain fatty acids, carbohydrate metabolism, and neuroendocrine function, including increased thyrotropin-releasing hormone levels. These findings support the concept that TRD represents a biologically distinct and more metabolically dysregulated subtype of depression and highlight EV-based metabolomics as a promising approach for elucidating disease and treatment mechanisms.

Background /Objectives: Suicide is a significant public health concern with a multifactorial etiology. The biological background of suicide is not sufficiently explored, which encumbers suicide prevention. Epigenetic mechanisms may mediate environmental influences on suicide risk. Recent studies have suggested that protein aggregation occurs in the brains of patients with chronic psychiatric disorders and suicidality, which may influence disease trajectory. However, the intersection between epigenetics and proteinopathy in suicide remains unexplored. Our pilot study investigated whether aggregation-related genes show epigenetic and transcriptional alterations in the post-mortem brains of individuals who had died by suicide. Methods: Brain tissue from 69 male subjects (32 suicide by hanging, 37 sudden cardiac death controls) was collected at autopsy. Genome-wide hippocampal DNA methylation data from our previous reduced representation bisulfite sequencing (RRBS) study were reanalyzed to identify differentially methylated cytosines (DMCs) in candidate aggregation-related genes. The expression of nine candidate and three reference genes in the hippocampus and Brodmann area 46 was assessed by qPCR. Statistical analyses were performed using Student’s t-test or Mann–Whitney U test (p < 0.05 was considered significant). Results: Reanalysis revealed hypomethylation in suicide cases within CRMP1, DISC1, MAPT, SOD1, PRKN, GABARAPL1, GRIN2A, and GRIN2B. In the hippocampus, suicides exhibited increased expression of CRMP1, SOD1, PRKN, GABARAPL1, and GRIN2A, and decreased MAPT expression. The GRIN2A/GRIN2B ratio was significantly elevated. In Brodmann area 46, altered expression was limited to increased GRIN2A and decreased DISC1. Conclusions: This is the first study to implicate epigenetic and transcriptional dysregulation of protein aggregation-associated genes in suicide. The findings suggest a possible role for proteostasis disturbances in suicidality, particularly within the hippocampal pathways related to stress response and synaptic signaling. Validation in larger cohorts and protein-level studies are warranted to determine the functional significance of these findings.

Brain disorders are among the most debilitating, costly and therapeutically challenging conditions worldwide. Therefore, there is a growing need for identification of biomarkers to support diagnostic, prognostic and therapeutic procedures. Technological advances are enabling increasingly precise, high-throughput profiling of epigenetic modifications, and the potential reversibility of epigenetic marks makes them a promising target for therapeutic intervention. Recent research on in-vitro models, post-mortem brain samples and peripheral tissues from living individuals has suggested that epigenetic mechanisms are involved in the pathogenesis of chronic mental illnesses, functioning as distal or proximal risk factors and mediating the long-term effects of environmental stressors on brain function. In brain cancers, including the highly lethal glioblastoma, epigenetic dysregulation (especially DNA methylation patterns) is already implicated in tumor classification as it contributes to cellular heterogeneity and may drive tumor progression. This review examines the multifaceted role of epigenomic regulation of brain gene expression, focusing on psychiatric disorders and primary brain malignancies such as glioblastoma. We summarize the technological advances that have enabled high-throughput and high-resolution exploration of the epigenome. Furthermore, we present the current knowledge of epigenomic signatures that may contribute to brain pathology and discuss their potential for biomarker discovery and the advancement of personalized medicine.

Suicide is a major public health concern and cause of death worldwide. While progress has been made in understanding molecular pathways involved in suicide, much more work is needed to identify clinically useful biomarkers of suicidality. Disturbed cellular proteostasis and aggregation of specific misfolded proteins are established pathological factors of neurodegenerative diseases. Increasing evidence also suggests that such aggregates often occur in patients with chronic mental illnesses. Recently, genes related to disturbed proteostasis showed differential methylation in individuals who died by suicide compared to controls. These include five genes encoding proteins that aggregate in neurodegenerative and/or mental illness: CRMP1 (also called DPYSL1), DISC1, MAPT (encoding the Tau protein), PRKN (also called PARK2, encoding Parkin), and SOD1. Given the possibility that altered methylation in these genes could affect expression of the proteins they encode, we aimed to review evidence for whether disturbed proteostasis may be a point of overlap between suicidality, neurodegenerative disease, and/or mental illnesses. Epigenetic changes in most of these genes also occur in other neurological disorders. Autophagy, and, to a lesser extent, the ubiquitin–proteasome system, are emerging as potentially impaired in individuals with suicidal tendencies and individuals who died by suicide. Based on this accumulated data, we hypothesise that disturbed proteostasis is likely to be a pathological component of suicidality. It is also plausible that this may lead to the accumulation of aggregated proteins in a similar manner to, and potentially overlapping with, those seen in major mental illnesses. If true, this would have consequences for potential identification of biomarkers for suicidality and should be a priority for future research in the field.