Blood-based gene expression signatures of medication-free outpatients with major depressive disorder: integrative genome-wide and candidate gene analyses

Gene expression and epigenetic changes in post-traumatic stress disorder, depression, and anxiety in first responders: A systematic review

OBJECTIVE

Police, firefighters, dispatchers, and emergency medical technicians-collectively known as first responders-are a unique population frequently exposed to chronic, traumatic incidents. This exposure results in a high prevalence of PTSD, depression, and anxiety, posing a substantial public health concern. Genetic predispositions and epigenetic modifications that regulate gene expression are significant contributors to trauma-related pathologies. This systematic review aims to summarize current data on epigenetic and gene expression changes in first responders related to three post-trauma pathologies: PTSD, depression, and anxiety. We also explore genetic pathways across these disorders to identify potential commonalities and therapeutic targets.

METHODS

Following PRISMA guidelines, databases were searched from July to October 2023, yielding 1103 studies, 12 of which met the inclusion criteria (total N = 6943).

RESULTS

Of the included studies, 11 examined PTSD, consistently implicating stress-response genes, such as those in the hypothalamic-pituitary-adrenal axis (e.g., FKBP5, NR3C1), and genes related to inflammation and immune responses. Three studies focused on depression-related genetic biomarkers but reported no significant genome-wide methylation differences between responders with current versus no major depressive disorder (MDD). No studies addressed epigenetic or gene expression changes linked to anxiety.

CONCLUSION

This review identified novel genes and pathways related to trauma as potential targets for future research and pharmacological therapy. It also highlights a significant gap in the literature, emphasizing the need for broader research to investigate the genetic underpinnings of trauma exposure in first responders, aiming to identify relevant pathways and therapeutic targets.

Identification and experimental validation of hub genes underlying depressive-like behaviors induced by chronic social defeat stress

Introduction: Major depressive disorder (MDD), characterized by severe neuropsychiatric symptoms and significant cognitive deficits, continues to present both etiological and therapeutic challenges. However, the specific underlying mechanisms and therapeutic targets remain unclear. Methods: We analyzed human postmortem dorsolateral prefrontal cortex (dlPFC) samples from MDD patients using datasets GSE53987 and GSE54568, identifying three key genes: AGA, FBXO38, and RGS5. To model depressive-like behavior, we employed chronic social defeat stress (CSDS) and subsequently measured the expression of AGA, FBXO38, and RGS5 in the dlPFC using qPCR and Western blot analysis following CSDS exposure. Results: CSDS significantly induced depressive-like behavior, and both the protein and transcriptional expression levels of AGA, FBXO38, and RGS5 in the dlPFC of mice were markedly reduced after stress, consistent with findings from datasets GSE53987 and GSE54568. Conclusion: Our research suggests that AGA, FBXO38, and RGS5 are potential biomarkers for MDD and could serve as valuable targets for MDD risk prediction.

Intron retention as an excellent marker for diagnosing depression and for discovering new potential pathways for drug intervention

Background

Peripheral inflammation is often associated with depressive disorders, and immunological biomarkers of depression remain a focus of investigation.

Methods

We performed RNA-seq analysis of RNA transcripts of human peripheral blood mononuclear cells from a case-control study including subjects with self-reported depression in the pre-symptomatic state of major depressive disorder and analyzed differentially expressed genes (DEGs) and the frequency of intron retention (IR) using rMATS.

Results

Among the statistically significant DEGs identified, the 651 upregulated DEGs were particularly enriched in the term "bacterial infection and phagocytosis", whereas the 820 downregulated DEGs were enriched in the terms "antigen presentation" and "T-cell proliferation and maturation". We also analyzed 158 genes for which the IR was increased (IncIR) and 211 genes for which the IR was decreased (DecIR) in the depressed subjects. Although the Gene Ontology terms associated with IncIR and DecIR were very similar to those of the up- and downregulated genes, respectively, IR genes appeared to be particularly enriched in genes with sensor functions, with a preponderance of the term "ciliary assembly and function". The observation that IR genes specifically interact with innate immunity genes suggests that immune-related genes, as well as cilia-related genes, may be excellent markers of depression. Re-analysis of previously published RNA-seq data from patients with MDD showed that common IR genes, particularly our predicted immune- and cilia-related genes, are commonly detected in populations with different levels of depression, providing validity for using IR to detect depression.

Conclusion

Depression was found to be associated with activation of the innate immune response and relative inactivation of T-cell signaling. The DEGs we identified reflect physiological demands that are controlled at the transcriptional level, whereas the IR results reflect a more direct mechanism for monitoring protein homeostasis. Accordingly, an alteration in IR, namely IncIR or DecIR, is a stress response, and intron-retained transcripts are sensors of the physiological state of the cytoplasm. The results demonstrate the potential of relative IR as a biomarker for the immunological stratification of depressed patients and the utility of IR for the discovery of novel pathways involved in recovery from depression.

Autophagic Regulation of Adipogenesis Through TP53INP2: Insights from In Silico and In Vitro Analysis

Obesity is an epidemic disease associated with multimorbidity resulting in higher mortality risk. The imbalance between energy storage and expenditure is the prime factor in the prognosis of the disease. Specifically, excessive lipid storage through adipogenesis leads to obesity. Adipogenesis is the process that converts preadipocytes into mature adipocytes by regulating major transcription factors like PPARγ and C/EBPα, contributes to lipid storage in adipose tissue. On the contrary, autophagy is a self-degradative process that maintains homeostasis in adipose tissue by regulating adipogenesis and lipolysis. TP53INP2 is a key player that regulates the autophagy process, and it negatively regulates adipogenesis and lipid storage. The gene expression profile GSE93637 was retrieved from the GEO database and analyzed using an integrated bioinformatics approach. The differentially expressed genes (DEGs) were analyzed using R-Bioconductor for TP53INP2 knockdown microarray dataset of 3T3L1 cells, and the DEGs were analyzed for the functional enrichment analysis. Further, the genes involved in the potential biological and molecular functions were evaluated for pathway enrichment analysis by KEGG (Kyoto Encyclopedia of Genes and Genomes). A total of 726 DEGs were found including 391 upregulated and 335 downregulated genes. Further, the functional and pathway enrichment analysis was employed to identify the highly interacting genes, and we identified a total of 56 genes that are highly interacting through a protein-protein interaction network. The DEGs mainly regulate the Peroxisome proliferator-activated receptor (PPAR) signaling pathway, lipolysis, and autophagy. Further, we investigated the associated Hub genes for enriched pathway genes and found the involvement of two autophagic genes ATG7 and sequestosome 1 (p62). In addition, in vitro studies of qRT-PCR (Quantitative real-time polymerase chain reaction) and Western blot analysis revealed that increased autophagy resulted in reduced lipid storage through down-regulation of the adipogenic gene. Moreover, increased expression of autophagic gene TP53INP2 and ATG7 facilitates the down-regulation of p62 and PPARγ gene resulting in lipolysis in mature adipocytes through autophagy. There is no specific treatment to reduce obesity other than a caloric diet and exercise. Hence, this study provides sufficient evidence to conclude that TP53INP2 negatively regulates adipogenesis and increases the degradation of lipids in mature adipocytes which is crucial for reducing obesity. Therefore, it is plausible to consider TP53INP2 as a promising therapeutic target for managing adipogenesis and obesity. However, further studies are necessary to validate their functional and molecular pathway analysis in the regulation of adipogenesis and obesity.

Blood mRNA expression levels of glucocorticoid receptors and FKBP5 are associated with depressive disorder and altered HPA axis

BACKGROUND

While depression has been associated with alterations in the hypothalamic-pituitary adrenal (HPA) axis function, there is still controversy regarding the nature and extent of the dysfunction, such as in the debate about hypercortisolism vs. hypocortisolism. It may therefore be necessary to understand whether and how HPA axis function in depression is linked to mRNA expression of key genes regulating this system.

METHODS

We studied 163 depressed outpatients, most of whom were chronically ill, and 181 healthy controls. Blood mRNA expression levels of NR3C1 (including GRα, GRβ, and GR-P isoforms), FKBP4, and FKBP5 were measured at baseline. HPA axis feedback sensitivity was measured by the dexamethasone (Dex)/corticotropin-releasing hormone (CRH) test. The association between mRNA expression levels and HPA axis feedback sensitivity was examined.

RESULTS

Compared to controls, patients showed significantly higher expression of GRα and lower expression of FKBP5, and higher post-Dex cortisol levels, even after controlling for age and sex. FKBP5 expression was significantly positively correlated with cortisol levels in patients, while GRα expression was significantly negatively correlated with cortisol levels in controls.

LIMITATIONS

Most patients were taking psychotropic medications. The large number of correlation tests may have caused type I errors.

CONCLUSIONS

The tripartite relationship between depression, mRNA expression of GR and FKBP5, and HPA axis function suggests that the altered gene expression affects HPA axis dysregulation and, as a result, impacts the development and/or illness course of depressive disorder. The combination of increased GRα expression and decreased FKBP5 expression may serve as a biomarker for chronic depression.

Glycosylation and behavioral symptoms in neurological disorders

Glycosylation, the addition of glycans or carbohydrates to proteins, lipids, or other glycans, is a complex post-translational modification that plays a crucial role in cellular function. It is estimated that at least half of all mammalian proteins undergo glycosylation, underscoring its importance in the functioning of cells. This is reflected in the fact that a significant portion of the human genome, around 2%, is devoted to encoding enzymes involved in glycosylation. Changes in glycosylation have been linked to various neurological disorders, including Alzheimer's disease, Parkinson's disease, autism spectrum disorder, and schizophrenia. Despite its widespread occurrence, the role of glycosylation in the central nervous system remains largely unknown, particularly with regard to its impact on behavioral abnormalities in brain diseases. This review focuses on examining the role of three types of glycosylation: N-glycosylation, O-glycosylation, and O-GlcNAcylation, in the manifestation of behavioral and neurological symptoms in neurodevelopmental, neurodegenerative, and neuropsychiatric disorders.

Co-expression network of mRNA and DNA methylation in first-episode and drug-naive adolescents with major depressive disorder

OBJECTIVE

We explored the DNA methylation and messenger RNA (mRNA) co-expression network and hub genes in first-episode, drug-naive adolescents with major depressive disorder (MDD). To preliminarily explore whether adolescent MDD has unique mechanisms compared with adult MDD.

METHODS

We compared DNA methylation and mRNA profiles of peripheral blood mononuclear cells from four first-episode and drug-naive adolescents with MDD and five healthy adolescent controls (HCs). We performed differential expression analysis, constructed co-expression network, and screened the hub genes. And enrichment analysis was performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We also downloaded DNA methylation and mRNA datasets of adults with MDD (GSE113725/GSE38206) from the GEO database, and performed differential expression and enrichment analysis.

RESULTS

Our clinical data showed that 3034 methylation sites and 4190 mRNAs were differentially expressed in first-episode, drug-naive adolescents MDD patients compared with HCs. 19 hub genes were screened out according to the high degree value in the co-expression network. The results from the GEO database showed that compared with adult HCs, there were 290 methylation sites and 127 mRNAs were differentially expressed in adult MDD patients.

CONCLUSION

Compared with adolescent HCs and adult MDD patients, the DNA methylation and mRNA expression patterns of first-episode, drug-naive adolescent MDD patients were different. The co-expression network of DNA methylation and mRNA and the screened hub genes may play an important role in the pathogenesis of MDD in first-episode, drug-naive adolescents. Compared with adult MDD, adolescent MDD is more enriched in metabolism in terms of function and pathways.

Structural variation and eQTL analysis in two experimental populations of chickens divergently selected for feather-pecking behavior

Feather pecking (FP) is a damaging nonaggressive behavior in laying hens with a heritable component. Its occurrence has been linked to the immune system, the circadian clock, and foraging behavior. Furthermore, dysregulation of miRNA biogenesis, disturbance of the gamma-aminobutyric acid (GABAergic) system, as well as neurodevelopmental deficiencies are currently under debate as factors influencing the propensity for FP behavior. Past studies, which focused on the dissection of the genetic factors involved in FP, relied on single nucleotide polymorphisms (SNPs) and short insertions and deletions < 50 bp (InDels). These variant classes only represent a certain fraction of the genetic variation of an organism. Hence, we reanalyzed whole-genome sequencing data from two experimental populations, which have been divergently selected for FP behavior for over more than 15 generations, performed variant calling for structural variants (SVs) as well as tandem repeats (TRs), and jointly analyzed the data with SNPs and InDels. Genotype imputation and subsequent genome-wide association studies, in combination with expression quantitative trait loci analysis, led to the discovery of multiple variants influencing the GABAergic system. These include a significantly associated TR downstream of the GABA receptor subunit beta-3 (GABRB3) gene, two microRNAs targeting several GABA receptor genes, and dystrophin (DMD), a direct regulator of GABA receptor clustering. Furthermore, we found the transcription factor ETV1 to be associated with the differential expression of 23 genes, which points toward a role of ETV1, together with SMAD4 and KLF14, in the disturbed neurodevelopment of high-feather pecking chickens.

Cellular and immunometabolic mechanisms of inflammation in depression: Preliminary findings from single cell RNA sequencing and a tribute to Bruce McEwen

Inflammation is associated with symptoms of anhedonia, a core feature of major depression (MD). We have shown that MD patients with high inflammation as measured by plasma C-reactive protein (CRP) and anhedonia display gene signatures of metabolic reprograming (e.g., shift to glycolysis) necessary to sustain cellular immune activation. To gain preliminary insight into the immune cell subsets and transcriptomic signatures that underlie increased inflammation and its relationship with behavior in MD at the single-cell (sc) level, herein we conducted scRNA-Seq on peripheral blood mononuclear cells from a subset of medically-stable, unmedicated MD outpatients. Three MD patients with high CRP (>3 mg/L) before and two weeks after anti-inflammatory challenge with the tumor necrosis factor antagonist infliximab and three patients with low CRP (≤3 mg/L) were studied. Cell clusters were identified using a Single Cell Wizard pipeline, followed by pathway analysis. CD14⁺ and CD16⁺ monocytes were more abundant in MD patients with high CRP and were reduced by 29% and 55% respectively after infliximab treatment. Within CD14⁺ and CD16⁺ monocytes, genes upregulated in high CRP patients were enriched for inflammatory (phagocytosis, complement, leukocyte migration) and immunometabolic (hypoxia-inducible factor [HIF]-1, aerobic glycolysis) pathways. Shifts in CD4⁺ T cell subsets included ∼30% and ∼10% lower abundance of CD4⁺ central memory (T_CM) and naïve cells and ∼50% increase in effector memory-like (T_EM-like) cells in high versus low CRP patients. T_CM cells of high CRP patients displayed downregulation of the oxidative phosphorylation (OXPHOS) pathway, a main energy source in this cell type. Following infliximab, changes in the number of CD14⁺ monocytes and CD4⁺ T_EM-like cells predicted improvements in anhedonia scores (r = 1.0, p < 0.001). In sum, monocytes and CD4⁺ T cells from MD patients with increased inflammation exhibited immunometabolic reprograming in association with symptoms of anhedonia. These findings are the first step toward determining the cellular and molecular immune pathways associated with inflammatory phenotypes in MD, which may lead to novel immunomodulatory treatments of psychiatric illnesses with increased inflammation.

Differently sized drug-loaded mesoporous silica nanoparticles elicit differential gene expression in MCF-7 cancer cells

Aim: This study investigates the effects of different sized unmodified and chemo-responsive mesoporous silica nanocarriers on MCF-7 cancer cells. Materials & methods: Unmodified and thiol-functionalized large and small-sized mesoporous MCM-41 silica nanoparticles prepared using templated sol-gel process were characterized for their physicochemical properties and in vitro and in vivo anticancer efficacy. Microarray analysis was carried out to assess their differential effect on gene expression. Results: Thiol-functionalized nanoparticles displayed chemo responsive release and greater cytotoxicity to cancer cells when compared with unmodified carriers. Microarray studies showed distinct differences in genes differentially regulated by sMCM-41and lMCM-41 carriers when compared with the free drug. Conclusion: The small chemo-responsive carrier was more effective in suppressing oncogenes and genes involved in proliferation, invasion and survival while the large carrier mainly altered membrane-associated pathways.

Gene expression signatures differentiating major depressive disorder from subsyndromal symptomatic depression

Subsyndromal symptomatic depression (SSD) and major depressive disorder (MDD) have been classified as distinct diseases, due to their dissimilar gene expression profiles and responses to venlafaxine. To identify specific biomarkers of these two diseases, we conducted a secondary analysis of the gene expression signatures of SSD patients, MDD patients and healthy controls (n=8/group) from the study of Yi et al. Global, individual, specific, enrichment and co-expression analyses were used to compare the transcriptomic profiles of peripheral blood lymphocytes from the three groups. The global and individual analyses revealed that different genes were up- and downregulated in the SSD and MDD groups. Through our specific analysis, we identified 1719 and 3278 differentially expressed genes specifically associated with MDD and SSD, respectively. Enrichment and co-expression analyses demonstrated that the genes specific to MDD were enriched in pathways associated with hormone levels and immune responses, while those specific to SSD were associated with immune function. The specific hub gene for the MDD co-expression network was transmembrane protein 132B (TMEM132B), while the hub genes for SSD were actin-related protein 2/3 complex (ARPC2) and solute carrier family 5 member 5 (SLC5A5). This bioinformatic analysis has provided potential biomarkers that can distinguish SSD from MDD.

Depression patient-derived cortical neurons reveal potential biomarkers for antidepressant response

Major depressive disorder is highly prevalent worldwide and has been affecting an increasing number of people each year. Current first line antidepressants show merely 37% remission, and physicians are forced to use a trial-and-error approach when choosing a single antidepressant out of dozens of available medications. We sought to identify a method of testing that would provide patient-specific information on whether a patient will respond to a medication using in vitro modeling. Patient-derived lymphoblastoid cell lines from the Sequenced Treatment Alternatives to Relieve Depression study were used to rapidly generate cortical neurons and screen them for bupropion effects, for which the donor patients showed remission or non-remission. We provide evidence for biomarkers specific for bupropion response, including synaptic connectivity and morphology changes as well as specific gene expression alterations. These biomarkers support the concept of personalized antidepressant treatment based on in vitro platforms and could be utilized as predictors to patient response in the clinic.

Major Depressive Disorder Is Associated With Differential Expression of Innate Immune and Neutrophil-Related Gene Networks in Peripheral Blood: A Quantitative Review of Whole-Genome Transcriptional Data From Case-Control Studies

BACKGROUND

Whole-genome transcription has been measured in peripheral blood samples as a candidate biomarker of inflammation associated with major depressive disorder.

METHODS

We searched for all case-control studies on major depressive disorder that reported microarray or RNA sequencing measurements on whole blood or peripheral blood mononuclear cells. Primary datasets were reanalyzed, when openly accessible, to estimate case-control differences and to evaluate the functional roles of differentially expressed gene lists by technically harmonized methods.

RESULTS

We found 10 eligible studies (N = 1754 depressed cases and N = 1145 healthy controls). Fifty-two genes were called significant by 2 of the primary studies (published overlap list). After harmonization of analysis across 8 accessible datasets (n = 1706 cases, n = 1098 controls), 272 genes were coincidentally listed in the top 3% most differentially expressed genes in 2 or more studies of whole blood or peripheral blood mononuclear cells with concordant direction of effect (harmonized overlap list). By meta-analysis of standardized mean difference across 4 studies of whole-blood samples (n = 1567 cases, n = 954 controls), 343 genes were found with false discovery rate <5% (standardized mean difference meta-analysis list). These 3 lists intersected significantly. Genes abnormally expressed in major depressive disorder were enriched for innate immune-related functions, coded for nonrandom protein-protein interaction networks, and coexpressed in the normative transcriptome module specialized for innate immune and neutrophil functions.

CONCLUSIONS

Quantitative review of existing case-control data provided robust evidence for abnormal expression of gene networks important for the regulation and implementation of innate immune response. Further development of white blood cell transcriptional biomarkers for inflamed depression seems warranted.

Epigenome-wide association study of depression symptomatology in elderly monozygotic twins

Depression is a severe and debilitating mental disorder diagnosed by evaluation of affective, cognitive and physical depression symptoms. Severity of these symptoms strongly impacts individual's quality of life and is influenced by a combination of genetic and environmental factors. One of the molecular mechanisms allowing for an interplay between these factors is DNA methylation, an epigenetic modification playing a pivotal role in regulation of brain functioning across lifespan. The aim of this study was to investigate if there are DNA methylation signatures associated with depression symptomatology in order to identify molecular mechanisms contributing to pathophysiology of depression. We performed an epigenome-wide association study (EWAS) of continuous depression symptomatology score measured in a cohort of 724 monozygotic Danish twins (346 males, 378 females). Through EWAS analyses adjusted for sex, age, flow-cytometry based blood cell composition, and twin relatedness structure in the data we identified depression symptomatology score to be associated with blood DNA methylation levels in promoter regions of neuropsin (KLK8, p-value = 4.7 × 10^-7) and DAZ associated protein 2 (DAZAP2, p-value = 3.13 × 10^-8) genes. Other top associated probes were located in gene bodies of MAD1L1 (p-value = 5.16 × 10^-6), SLC29A2 (p-value = 6.15 × 10^-6) and AKT1 (p-value = 4.47 × 10^-6), all genes associated before with development of depression. Additionally, the following three measures (a) DNAmAge (calculated with Horvath and Hannum epigenetic clock estimators) adjusted for chronological age, (b) difference between DNAmAge and chronological age, and (c) DNAmAge acceleration were not associated with depression symptomatology score in our cohort. In conclusion, our data suggests that depression symptomatology score is associated with DNA methylation levels of genes implicated in response to stress, depressive-like behaviors, and recurrent depression in patients, but not with global DNA methylation changes across the genome.

Involvement of inflammatory gene expression pathways in depressed patients with hyperphagia

The pathophysiology of major depressive disorder (MDD) is highly heterogeneous. Previous evidence at the DNA level as well as on the serum protein level suggests that the role of inflammation in MDD pathology is stronger in patients with hyperphagia during an active episode. Which inflammatory pathways differ in MDD patients with hyperphagia inflammatory pathways in terms of gene expression is unknown. We analyzed whole-blood gene expression profiles of 881 current MDD cases and 331 controls from the Netherlands Study of Depression and Anxiety (NESDA). The MDD patients were stratified according to patients with hyperphagia (characterized by increased appetite and/or weight, N = 246) or hypophagia (characterized by decreased appetite and/or weight, N = 342). Using results of differential gene expression analysis between controls and the MDD subgroups, enrichment of curated inflammatory pathways was estimated. The majority of the pathways were significantly (FDR < 0.1) enriched in the expression profiles of MDD cases with hyperphagia, including top pathways related to factors responsible for the onset of inflammatory response ('caspase', 'GATA3', 'NFAT', and 'inflammasomes' pathways). Only two pathways ('adaptive immune system' and 'IL-8- and CXCR2-mediated signaling') were enriched in the MDD with hypophagia subgroup, these were also enriched in the total current MDD group and the group with hyperphagia. This confirms the importance of inflammation in MDD pathology of patients with hyperphagia, and suggests that distinguishing more uniform MDD phenotypes can help in finding their pathophysiological basis.

Umbilical cord blood-based gene signatures related to prenatal major depressive disorder

BACKGROUND

Prenatal exposure to depression has been considered as a risk factor for adverse childhood, while it is accompanied by unknown molecular mechanisms. The aim of this study was to identify differentially expressed genes (DEGs) and associated biological processes between cord blood samples from neonates born to mothers who exposed to major depressive disorder (MDD) and healthy mothers.

METHODS

The microarray data GSE114852 were downloaded to analyze the mRNA expression profiles of umbilical cord blood with 31 samples exposed to prenatal MDD and 62 samples with healthy mothers. Kyoto Encyclopedia of Genes and Genomes pathway and Gene ontology enrichment analyses were conducted to identify associated biochemical pathways and functional categories of the DEGs. The protein-protein interaction network was constructed and the top 10 hub genes in the network were predicted.

RESULTS

The results showed several immunity related processes, such as "phagosome", "Epstein-Barr virus infection", "proteasome", "positive regulation of I-kappaB kinase/NF-kappaB signaling", "interferon-gamma-mediated signaling pathway", and "tumor necrosis factor" presented significant differences between two groups. Most of the hub genes (for example PSMD2, PSMD6, PSMB8, PSMB9) were also associated with immune pathways.

CONCLUSION

This bioinformatic analysis demonstrated immune-mediated mechanisms might play a fatal role in abnormalities in fetal gene expression profiles caused by prenatal MDD.

Intraday Activity Levels May Better Reflect the Differences Between Major Depressive Disorder and Bipolar Disorder Than Average Daily Activity Levels

It is important to establish an objective index to differentiate mood disorders (i.e., bipolar disorder; BD and major depressive disorder; MDD). The present study focused on the pattern of changes of physical activity in the amount of activity intraday, and examined the relationship between activity patterns and mood disorders. One hundred and eighteen inpatients with MDD or BD in a depressive state provided the activity data by using wearable activity trackers for 3 weeks. In order to illuminate the characteristic patterns of intraday activities, Principal Component Analysis (PCA) was adopted to extract the main components of intraday activity changes. We found that some of the PCs reflected the differences between the types of mood disorder. BD participants showed high activity pattern in the morning and low activity pattern in evenings. However, MDD showed the opposite. Our results suggest that activity tracking focused on daytime activity patterns may provide objective auxiliary diagnostic information.

Mitogen-stimulated cell proliferation and cytokine production in major depressive disorder patients

BACKGROUND

Major depressive disorder (MDD) is related to human's immune status, and immunological indicators such as mitogen stimulated cell proliferation and cytokines may become candidate biomarkers for disease diagnosis.

METHODS

One hundred diagnosed major depressive disorder subjects and 100 health controls were enrolled in this study. Phytohaemagglutinin and lipopolysaccharide stimulated cell proliferations and cytokine concentrations were detected in peripheral blood mononuclear cells from both groups. The corresponding stimulated responses were conducted and confirmed in chronic unpredictable mild stress (CUMS) mice.

RESULTS

Compared to the people in control group, there were lower cell proliferations and lower TNF-α produced in lipopolysaccharide stimulated peripheral blood mononuclear cells in depression patients, lower IL-2 and IL-10 produced in phytohaemagglutinin stimulated peripheral blood mononuclear cells in depression patients, higher IL-6, IL-10 and lower IL-2 secretions were detected in peripheral plasma in depression patients. In CUMS mice we found lower splenocyte proliferations, lower IL-1α productions and higher IL-6 secretions in lipopolysaccharide stimulated splenocytes. It seems lipopolysaccharide stimulated cell proliferation activities were inhibited in depressive states.

CONCLUSIONS

Lower lipopolysaccharide stimulated cell proliferation and phytohaemagglutinin stimulated or plasma cytokine IL-2 decreases should be potential monitoring indices in the depressive state assessment for major depressive disorder patients.

Integrated profiling of phenotype and blood transcriptome for stress vulnerability and depression

Etiology of depression and its vulnerability remains elusive. Using a latent profile analysis on dimensional personality traits, we previously identified 3 different phenotypes in the general population, namely stress-resilient, -vulnerable, and -resistant groups. Here we performed microarray-based blood gene expression profiling of these 3 groups (n = 20 for each group) in order to identify genes involved in stress vulnerability as it relates to the risk of depression. Identified differentially expressed genes among the groups were most markedly enriched in ribosome-related pathways. These ribosomal genes, which included ribosomal protein L17 (RPL17) and ribosomal protein L34 (RPL34), were upregulated in relation to the stress vulnerability. Protein-protein interaction and correlational co-expression analyses of the differentially expressed genes/non-coding RNAs consistently showed that functional networks involving ribosomes were affected. The significant upregulation of RPL17 and RPL34 was also observed in depressed patients compared to healthy controls, as confirmed in 2 independent case-control datasets by using pooled microarray data and qPCR experiments (total number of subjects was 122 and 166, respectively). Moreover, the upregulation of RPL17 and RPL34 was most marked in DSM-IV major depressive disorder, followed by in bipolar disorder, and then in schizophrenia, suggesting some diagnostic specificity of these markers as well as their general roles in stress vulnerability. These results suggest that ribosomal genes, particularly RPL17 and RPL34, can play integral roles in stress vulnerability and depression across nonclinical and clinical conditions. This study presents an opportunity to understand how multiple psychological traits and underlying molecular mechanisms interact to render individuals vulnerable to depression.

Blood plasma/IgG N-glycome biosignatures associated with major depressive disorder symptom severity and the antidepressant response

While N-linked glycosylation has been extensively studied in the context of inflammatory and metabolic disorders, its relationship with major depressive disorder (MDD) and antidepressant treatment response has not been investigated. In our exploratory study, we analysed N-glycan profiles in blood plasma samples collected from MDD patients (n = 18) and found gender-dependent correlations with severity of depressive symptoms prior to initiating antidepressant treatment. In addition, several N-glycosylation traits showed gender-dependent associations with clinical antidepressant response. Follow up proteomics analysis in peripheral blood mononuclear cells (PBMCs) collected from MDD patients (n = 20) identified baseline and post-antidepressant treatment pathway differences between responder and non-responder patients. Reactome data analysis further delineated potential biological reaction differences between responder and non-responder patients. Our preliminary results suggest that specific glycosylation traits are associated with depressive symptom severity and antidepressant response and may be of use as biomarkers.

The NCAM1 gene set is linked to depressive symptoms and their brain structural correlates in healthy individuals

Depressive symptoms exist on a continuum, the far end of which is found in depressive disorders. Utilizing the continuous spectrum of depressive symptoms may therefore contribute to the understanding of the biological underpinnings of depression. Gene set enrichment analysis (GSEA) is an important tool for the identification of gene groups linked to complex traits, and was applied in the present study on genome-wide association study (GWAS) data of depression scores and their brain-level structural correlates in healthy young individuals. On symptom level (i.e. depression scores), robust enrichment was identified for two gene sets: NCAM1 Interactions and Collagen Formation. Depression scores were also associated with decreased fractional anisotropy (FA) - a brain white matter property - within the forceps minor and the left superior temporal longitudinal fasciculus. Within each of these tracts, mean FA value of depression score-associated voxels was used as a phenotype in a subsequent GSEA. The NCAM1 Interactions gene set was significantly enriched in these tracts. By linking the NCAM1 Interactions gene set to depression scores and their structural brain correlates in healthy participants, the current study contributes to the understanding of the molecular underpinnings of depressive symptomatology.

Identification of commonly altered genes between in major depressive disorder and a mouse model of depression

The heterogeneity of depression (due to factors such as varying age of onset) may explain why biological markers of major depressive disorder (MDD) remain uncertain. We aimed to identify gene expression markers of MDD in leukocytes using microarray analysis. We analyzed gene expression profiles of patients with MDD (age ≥50, age of depression onset <50) (N = 10, depressed state; N = 13, remitted state). Seven-hundred and ninety-seven genes (558 upregulated, 239 downregulated when compared to those of 30 healthy subjects) were identified as potential markers for MDD. These genes were then cross-matched to microarray data obtained from a mouse model of depression (676 genes, 148 upregulated, 528 downregulated). Of the six common genes identified between patients and mice, five genes (SLC35A3, HIST1H2AL, YEATS4, ERLIN2, and PLPP5) were confirmed to be downregulated in patients with MDD by quantitative real-time polymerase chain reaction. Of these genes, HIST1H2AL was significantly decreased in a second set of independent subjects (age ≥20, age of onset <50) (N = 18, subjects with MDD in a depressed state; N = 19, healthy control participants). Taken together, our findings suggest that HIST1H2AL may be a biological marker of MDD.

Genome-wide expression profiling establishes novel modulatory roles of vitamin C in THP-1 human monocytic cell line

Background

Vitamin C (vit C) is an essential dietary nutrient, which is a potent antioxidant, a free radical scavenger and functions as a cofactor in many enzymatic reactions. Vit C is also considered to enhance the immune effector function of macrophages, which are regarded to be the first line of defence in response to any pathogen. The THP-1 cell line is widely used for studying macrophage functions and for analyzing host cell-pathogen interactions.

Results

We performed a genome-wide temporal gene expression and functional enrichment analysis of THP-1 cells treated with 100 μM of vit C, a physiologically relevant concentration of the vitamin. Modulatory effects of vitamin C on THP-1 cells were revealed by differential expression of genes starting from 8 h onwards. The number of differentially expressed genes peaked at the earliest time-point i.e. 8 h followed by temporal decline till 96 h. Further, functional enrichment analysis based on statistically stringent criteria revealed a gamut of functional responses, namely, ‘Regulation of gene expression’, ‘Signal transduction’, ‘Cell cycle’, ‘Immune system process’, ‘cAMP metabolic process’, ‘Cholesterol transport’ and ‘Ion homeostasis’. A comparative analysis of vit C-mediated modulation of gene expression data in THP-1cells and human skin fibroblasts disclosed an overlap in certain functional processes such as ‘Regulation of transcription’, ‘Cell cycle’ and ‘Extracellular matrix organization’, and THP-1 specific responses, namely, ‘Regulation of gene expression’ and ‘Ion homeostasis’. It was noteworthy that vit C modulated the ‘Immune system’ process throughout the time-course.

Conclusions

This study reveals the genome-wide effects of physiological levels of vit C on THP-1 gene expression. The multitude of effects impacted by vit C in macrophages highlights its role in maintaining homeostasis of several cellular functions. This study provides a rational basis for the use of the Vitamin C- THP-1 cell model, to study biochemical and cellular responses to stresses, including infection with M. tuberculosis and other intracellular pathogens.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3635-4) contains supplementary material, which is available to authorized users.

Genetic Contributions of Inflammation to Depression

This paper describes the effects of immune genes genetic variants and mRNA expression on depression's risk, severity, and response to antidepressant treatment, through a systematic review on all papers published between 2000 and 2016. Our results, based largely on case-control studies, suggest that common genetic variants and gene-expression pathways are involved in both immune activation and depression. The most replicated and relevant genetic variants include polymorphisms in the genes for interleukin (IL)-1β, IL-6, IL-10, monocyte chemoattractant protein-1, tumor necrosis factor-alpha, C-reactive protein, and phospholipase A2. Moreover, increased blood cytokines mRNA expression (especially of IL-1β) identifies patients that are less likely to respond to conventional antidepressants. However, even for the most replicated findings there are inconsistent results, not only between studies, but also between the immune effects of the genetic variants and the resulting effects on depression. We find evidence that these discrepant findings may be explained, at least in part, by the heterogeneity of the depression immunophenotype, by environmental influences and gene × environment interactions, and by the complex interfacing of genetic variants with gene expression. Indeed, some of the most robust findings have been obtained in patients developing depression in the context of treatment with interferon-alpha, a widely used model to mimic depression in the context of inflammation. Further 'omics' approaches, through GWAS and transcriptomics, will finally shed light on the interaction between immune genes, their expression, and the influence of the environment, in the pathogenesis of depression.

Transcript levels of plastin 3 and neuritin 1 modifier genes in spinal muscular atrophy siblings

BACKGROUND

In single gene disorders, patients with the same genotype may have variations in severity. One of the main factors affecting disease severity is modifier genes. Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by degeneration of alpha motor neurons. Plastin 3 (PLS3) is a phenotypic modifier of SMA, and neuritin 1 (NRN1) has also been suggested as a possible modifier gene. The aim of the present study was therefore to analyze PLS3 and NRN1 expression in SMA siblings in four families.

METHODS

The study group consisted of four SMA families with seven with discordant phenotype and two affected siblings. Total RNA was isolated from whole blood. PLS3 and NRN1 expression was analyzed on quantitative real-time polymerase chain reaction.

RESULTS

In family 1 only NRN1 expression was increased in the mildly affected sister. In family 2 only PLS3 had a modifier effect. Family 3, which had type III siblings with identical clinical phenotypes, had similar PLS3 expression between the siblings but no NRN1 expression. In family 4, neither PLS3 nor NRN1 had any correlation with severity.

CONCLUSION

On analysis of the expression of NRN1 in SMA patients for the first time, NRN1 could be a potential modifier gene. PLS3 expression does not always modify SMA phenotype. In patients with no modifier effect of known genes, genome sequencing and transcriptome analysis are promising for the identification of novel modifiers and understanding of SMA pathophysiology.

Gene expression alterations in the medial prefrontal cortex and blood cells in a mouse model of depression during menopause

Aims

The prevalence of major depressive disorder (MDD) is higher in women than in men, and this may be due to the decline in estrogen levels that occurs during the menopausal transition. We studied the biological alterations in the medial prefrontal cortex (mPFC), which is a region that is highly implicated in the neurobiology of MDD, and the blood cells (BCs) of ovariectomized (OVX) mice subjected to chronic mild stress (CMS), which represents a mouse model of depression during menopause.

Main methods

The mPFC and the BCs were obtained from the same individuals. Gene expression levels were analyzed by microarray. The data were used for the Ingenuity Pathway Analysis and the Gene Ontology analysis.

Key findings

The gene expression alterations (GEAs) induced by OVX were mainly associated with ribosomal and mitochondrial functions in both the mPFC and the BCs. Rapamycin-insensitive companion of mTOR (RICTOR) was identified as a possible upstream regulator of the OVX-induced GEAs in both tissues. The CMS-induced GEAs were associated with retinoic acid receptor signaling, inflammatory cytokines and post-synaptic density in the mPFC, but not in the BCs.

Significance

OVX and CMS independently affect biological pathways in the mPFC, which is involved in the development of the depression-like phenotype. Because a subset of the OVX-induced GEAs in the mPFC also occurred in the BCs, the GEAs in the BCs might be a useful probe to predict biological pathways in the corresponding brain tissue under specific conditions such as OVX in females.