Sex differences in the genetic regulation of the blood transcriptome response to glucocorticoid receptor activation

Multiomics Analysis of the Molecular Response to Glucocorticoids: Insights Into Shared Genetic Risk From Psychiatric to Medical Disorders

BACKGROUND

Alterations in the effects of glucocorticoids have been implicated in mediating some of the negative health effects associated with chronic stress, including increased risk for psychiatric disorders and cardiovascular and metabolic diseases. In this study, we investigated how genetic variants influence gene expression and DNA methylation in response to glucocorticoid receptor (GR) activation and their association with disease risk.

METHODS

We measured DNA methylation (n = 199) and gene expression (n = 297) in peripheral blood before and after GR activation with dexamethasone, with matched genotype data available for all samples. A comprehensive molecular quantitative trait locus (QTL) analysis was conducted, mapping GR-response methylation (me)QTLs, GR-response expression (e)QTLs, and GR-response expression quantitative trait methylation (eQTMs). A multilevel network analysis was employed to map the complex relationships between the transcriptome, epigenome, and genetic variation.

RESULTS

We identified 3772 GR-response meCpGs corresponding to 104,828 local GR-response meQTLs that did not strongly overlap with baseline meQTLs. eQTM and eQTL analyses revealed distinct genetic influences on gene expression and DNA methylation. Multilevel network analysis uncovered GR-response network trio QTLs, characterized by SNP-CpG-transcript combinations where meQTLs act as both eQTLs and eQTMs. GR-response trio variants were enriched in a genome-wide association study for psychiatric, respiratory, autoimmune, and cardiovascular diseases and conferred a higher relative heritability per SNP than GR-response meQTL and baseline QTL SNPs.

CONCLUSIONS

Genetic variants modulating the molecular effects of glucocorticoids are associated with psychiatric as well as medical diseases and not uncovered in baseline QTL analyses.

Reactivation of latent HIV-1 by the glucocorticoid receptor modulator AZD9567

One key determinant of HIV-1 latency reversal is the activation of the viral long terminal repeat (LTR) by cellular transcription factors such as NF-κB and AP-1. Interestingly, the activity of these two transcription factors can be modulated by glucocorticoid receptors (GRs). Furthermore, the HIV-1 genome contains multiple binding sites for GRs. We therefore hypothesized that glucocorticoids and other GR modulators may influence HIV-1 latency and reactivation. To investigate how GR signaling affects latent HIV-1 reservoirs, we assembled a representative panel of GR modulators including natural steroidal agonists, selective and non-selective GR modulators, and clinically approved GR-modulating drugs. The effects of these compounds on HIV-1 reactivation were assessed using latently HIV-1-infected cell lines and primary cells, as well as reporter assays that monitored GR and LTR activities. We found that AZD9567 (Mizacorat), a non-steroidal partial GR agonist, reactivates latent HIV-1 in both lymphoid and myeloid cell lines and primary CD4+ T cells. Conversely, the GR antagonist mifepristone suppresses HIV-1 LTR-driven gene expression. Mechanistic analyses revealed that AZD9567-mediated reactivation partially depends on both GR and AP-1 binding sites in the LTR. In summary, we, here, identify the GR modulator AZD9567 as novel latency-reversing agent that activates LTR-driven gene expression, which may aid in advancing current shock-and-kill approaches in the treatment of HIV-1 infection.IMPORTANCELatently infected cells of people living with HIV are constantly exposed to fluctuating levels of glucocorticoid hormones such as cortisol. In addition, many HIV-infected individuals regularly take corticosteroids as anti-inflammatory drugs. Although corticosteroids are known to affect the activity of the viral long terminal repeat (LTR) promoter and influence ongoing HIV-1 replication, relatively little is known about the effect of corticosteroid hormones and other glucocorticoid receptor (GR) modulators on latent HIV-1. By systematically comparing natural and synthetic GR modulators, we, here, identify a first first-in-class, oral, partial GR agonist that reactivates latent HIV-1 from different cell types. This drug, AZD9567, was previously tested in clinical trials for rheumatoid arthritis. Mutational analyses shed light on the underlying mode of action and revealed transcription factor binding sites in the HIV-1 LTR that determine responsiveness to AZD9567.

Meningeal neutrophil immune signaling influences behavioral adaptation following threat

Social creatures must attend to threat signals from conspecifics and respond appropriately, both behaviorally and physiologically. In this work, we show in mice a threat-sensitive immune mechanism that orchestrates psychological processes and is amenable to social modulation. Repeated encounters with socially cued threats triggered meningeal neutrophil (MN) priming preferentially in males. MN activity was correlated with attenuated defensive responses to cues. Canonical neutrophil-specific activation marker CD177 was upregulated after social threat cueing, and its genetic ablation abrogated male behavioral phenotypes. CD177 signals favored meningeal T helper (Th)1-like immune bias, which blunted neural response to threatening stimuli by enhancing intrinsic GABAergic inhibition within the prelimbic cortex via interferon-gamma (IFN-γ). MN signaling was sensitized by negative emotional states and governed by socially dependent androgen release. This male-biased hormone/neutrophil regulatory axis is seemingly conserved in humans. Our findings provide insights into how immune responses influence behavioral threat responses, suggesting a possible neuroimmune basis of emotional regulation.

Short-term aerobic exercise prevents development of glucocorticoid myopathic features in aged skeletal muscle in a sex-dependent manner

Older adults are vulnerable to glucocorticoid-induced muscle atrophy and weakness, with sex potentially influencing their susceptibility to those effects. Aerobic exercise can reduce glucocorticoid-induced muscle atrophy in young rodents. However, it is unknown whether aerobic exercise can prevent glucocorticoid myopathy in aged muscle. The objectives of this study were to define the extent to which sex influences the development of glucocorticoid myopathy in aged muscle, and to determine the extent to which aerobic exercise training protects against myopathy development. Twenty-four-month-old female (n = 30) and male (n = 33) mice were randomized to either sedentary or aerobic exercise groups. Within their respective groups, mice were randomized to either daily treatment with dexamethasone (DEX) or saline. Upon completing treatments, the contractile properties of the triceps surae complex were assessed in situ. DEX marginally lowered muscle mass and soluble protein content in both sexes, which was attenuated by aerobic exercise only in females. DEX increased sub-tetanic force and rate of force development only in females, which was not influenced by aerobic exercise. Muscle fatigue was higher in both sexes following DEX, but aerobic exercise prevented fatigue induction only in females. The sex-specific differences to muscle function in response to DEX treatment coincided with sex-specific changes to the content of proteins related to calcium handling, mitochondrial quality control, reactive oxygen species production, and glucocorticoid receptor in muscle. These findings define several important sexually dimorphic changes to aged skeletal muscle physiology in response to glucocorticoid treatment and define the capacity of short-term aerobic exercise to protect against those changes. KEY POINTS: There are sexually dimorphic effects of glucocorticoids on aged skeletal muscle physiology. Glucocorticoid-induced changes to aged muscle contractile properties coincide with sex-specific differences in the content of calcium handling proteins. Aerobic exercise prevents glucocorticoid-induced fatigue only in aged females and coincides with differences in the content of mitochondrial quality control proteins and glucocorticoid receptors.

BMI Interacts with the Genome to Regulate Gene Expression Globally, with Emphasis in the Brain and Gut

Genome-wide association studies identify common genomic variants associated with disease across a population. Individual environmental effects are often not included, despite evidence that environment mediates genomic regulation of higher order biology. Body mass index (BMI) is associated with complex disorders across clinical specialties, yet has not been modeled as a genomic environment. Here, we tested for expression quantitative trait (eQTL) loci that contextually regulate gene expression across the BMI spectrum using an interaction approach. We parsed the impact of cell type, enhancer interactions, and created novel BMI-dynamic gene expression predictor models. We found that BMI main effects associated with endocrine gene expression, while interactive variant-by-BMI effects impacted gene expression in the brain and gut. Cortical BMI-dynamic loci were experimentally dysregulated by inflammatory cytokines in an in vitro system. Using BMI-dynamic models, we identify novel genes in nitric oxide signaling pathways in the nucleus accumbens significantly associated with depression and smoking. While neither genetics nor BMI are sufficient as standalone measures to capture the complexity of downstream cellular consequences, including environment powers disease gene discovery.

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

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

Molecular evidence of altered stress responsivity related to neuroinflammation in the schizophrenia midbrain

Stress and inflammation are risk factors for schizophrenia. Chronic psychosocial stress is associated with subcortical hyperdopaminergia, a core feature of schizophrenia. Hyperdopaminergia arises from midbrain neurons, leading us to hypothesise that changes in stress response pathways may occur in this region. To identify whether transcriptional changes in glucocorticoid and mineralocorticoid receptors (NR3C1/GR, NR3C2/MR) or other stress signalling molecules (FKBP4, FKBP5) exist in schizophrenia midbrain, we measured gene expression in the human brain (N = 56) using qRT-PCR. We assessed whether alterations in these mRNAs were related to previously identified high/low inflammatory status. We investigated relationships between stress-related transcripts themselves, and between FKBP5 mRNA, dopaminergic, and glial cell transcripts in diagnostic and inflammatory subgroups. Though unchanged by diagnosis, GR mRNA levels were reduced in high inflammatory compared to low inflammatory schizophrenia cases (p = 0.026). We found no effect of diagnosis or inflammation on MR mRNA. FKBP4 mRNA was decreased and FKBP5 mRNA was increased in schizophrenia (p < 0.05). FKBP5 changes occurred in high inflammatory (p < 0.001), whereas FKBP4 changes occurred in low inflammatory schizophrenia cases (p < 0.05). The decrease in mRNA encoding the main stress receptor (GR), as well as increased transcript levels of the stress-responsive negative regulator (FKBP5), may combine to blunt the midbrain response to stress in schizophrenia when neuroinflammation is present. Negative correlations between FKBP5 mRNA and dopaminergic transcripts in the low inflammatory subgroup suggest higher levels of FKBP5 mRNA may also attenuate dopaminergic neurotransmission in schizophrenia even when inflammation is absent. We report alterations in GR-mediated stress signalling in the midbrain in schizophrenia.

Cohort profile: BioMD-Y (biopsychosocial factors of major depression in youth) - a biobank study on the molecular genetics and environmental factors of depression in children and adolescents in Munich

PURPOSE

BioMD-Y is a comprehensive biobank study of children and adolescents with major depression (MD) and their healthy peers in Germany, collecting a host of both biological and psychosocial information from the participants and their parents with the aim of exploring genetic and environmental risk and protective factors for MD in children and adolescents.

PARTICIPANTS

Children and adolescents aged 8-18 years are recruited to either the clinical case group (MD, diagnosis of MD disorder) or the typically developing control group (absence of any psychiatric condition).

FINDINGS TO DATE

To date, four publications on both genetic and environmental risk and resilience factors (including FKBP5, glucocorticoid receptor activation, polygenic risk scores, psychosocial and sociodemographic risk and resilience factors) have been published based on the BioMD-Y sample.

FUTURE PLANS

Data collection is currently scheduled to continue into 2026. Research questions will be further addressed using available measures.

Sex differences in a corticosterone-induced depression model in mice: Behavioral, neurochemical, and molecular insights

Depression is characterized by a significant sex disparity, with higher rates observed in women compared to men. This study aimed to investigate the impact of sex on depressive behaviors and explore the underlying mechanisms using a corticosterone (CORT)-induced depression model in mice. Behavioral tests, Nissl staining, UPLC-MS/MS, and Western blot analysis were performed to assess behavioral changes, as well as neuronal alterations, neurotransmitter levels, and protein expressions in the hippocampus. The mice in the model group exhibited sex-specific anxiety- and depression-like behaviors. Nissl staining revealed structural abnormalities in the CA3 region of the hippocampus in females. Neurotransmitter analysis indicated decreased serotonin and norepinephrine levels in both sexes, while glutamate levels were elevated in females. Furthermore, female mice demonstrated elevated serum CORT levels. Western blot analysis revealed sex-specific alterations in specific protein expression. Female mice exhibited downregulated glucocorticoid receptor and brain-derived neurotrophic factor expression, whereas male mice showed minimal changes. Additionally, female mice displayed reduced phosphorylated AKT, phosphorylated PI3K, and phosphorylated mTOR levels. These findings enhance our understanding of sex-specific differences in the CORT-induced depression model and provide insights into the underlying mechanisms of depression. This research emphasizes sex in depression studies and supports tailored interventions.

The cortisol switch between vulnerability and resilience

In concert with neuropeptides and transmitters, the end products of the hypothalamus-pituitary-adrenal (HPA) axis, the glucocorticoid hormones cortisol and corticosterone (CORT), promote resilience: i.e., the ability to cope with threats, adversity, and trauma. To exert this protective action, CORT activates mineralocorticoid receptors (MR) and glucocorticoid receptors (GR) that operate in a complementary manner -as an on/off switch- to coordinate circadian events, stress-coping, and adaptation. The evolutionary older limbic MR facilitates contextual memory retrieval and supports an on-switch in the selection of stress-coping styles at a low cost. The rise in circulating CORT concentration after stress subsequently activates a GR-mediated off-switch underlying recovery of homeostasis by providing the energy for restraining the primary stress reactions and promoting cognitive control over emotional reactivity. GR activation facilitates contextual memory storage of the experience to enable future stress-coping. Such complementary MR-GR-mediated actions involve rapid non-genomic and slower gene-mediated mechanisms; they are time-dependent, conditional, and sexually dimorphic, and depend on genetic background and prior experience. If coping fails, GR activation impairs cognitive control and promotes emotional arousal which eventually may compromise resilience. Such breakdown of resilience involves a transition to a chronic stress construct, where information processing is crashed; it leads to an imbalanced MR-GR switch and hence increased vulnerability. Novel MR-GR modulators are becoming available that may reset a dysregulated stress response system to reinstate the cognitive flexibility required for resilience.

Epigenetic clock analysis reveals increased plasma cystatin C levels based on DNA methylation in major depressive disorder

Major depressive disorder (MDD) is a common mental illness and a major public health concern worldwide. Depression is associated with epigenetic changes that regulate gene expression, and analyzing these changes may help elucidate the pathophysiology of MDD. Genome-wide DNA methylation (DNAm) profiles can function as 'epigenetic clocks' that can help estimate biological aging. Here, we assessed biological aging in patients with MDD using various DNAm-based indicators of epigenetic aging. We used a publicly available dataset containing data obtained from the whole blood samples of MDD patients (n = 489) and controls (n = 210). We analyzed five epigenetic clocks (HorvathAge, HannumAge, SkinBloodAge, PhenoAge, and GrimAge) and DNAm-based telomere length (DNAmTL). We also investigated seven DNAm-based age-predictive plasma proteins (including cystatin C) and smoking status, which are components of GrimAge. Following adjustment for confounding factors such as age and sex, patients with MDD showed no significant difference in epigenetic clocks and DNAmTL. However, DNAm-based plasma cystatin C levels were significantly higher in patients with MDD than controls. Our findings revealed specific DNAm changes predicting plasma cystatin C levels in MDD. These findings may help elucidate the pathophysiology of MDD, leading to the development of new biomarkers and medications.

Multi-omic modeling of antidepressant response implicates dynamic immune and inflammatory changes in individuals who respond to treatment

BACKGROUND

Major depressive disorder (MDD) is a leading cause of disability worldwide, and is commonly treated with antidepressant drugs (AD). Although effective, many patients fail to respond to AD treatment, and accordingly identifying factors that can predict AD response would greatly improve treatment outcomes. In this study, we developed a machine learning tool to integrate multi-omic datasets (gene expression, DNA methylation, and genotyping) to identify biomarker profiles associated with AD response in a cohort of individuals with MDD.

MATERIALS AND METHODS

Individuals with MDD (N = 111) were treated for 8 weeks with antidepressants and were separated into responders and non-responders based on the Montgomery-Åsberg Depression Rating Scale (MADRS). Using peripheral blood samples, we performed RNA-sequencing, assessed DNA methylation using the Illumina EPIC array, and performed genotyping using the Illumina PsychArray. To address this rich multi-omic dataset with high dimensional features, we developed integrative Geneset-Embedded non-negative Matrix factorization (iGEM), a non-negative matrix factorization (NMF) based model, supplemented with auxiliary information regarding gene sets and gene-methylation relationships. In particular, we factorize the subjects by features (i.e., gene expression or DNA methylation) into subjects-by-factors and factors-by-features. We define the factors as the meta-phenotypes as they represent integrated composite scores of the molecular measurements for each subject.

RESULTS

Using our model, we identified a number of meta-phenotypes which were related to AD response. By integrating geneset information into the model, we were able to relate these meta-phenotypes to biological processes, including a meta-phenotype related to immune and inflammatory functions as well as other genes related to depression or AD response. The meta-phenotype identified several genes including immune interleukin 1 receptor like 1 (IL1RL1) and interleukin 5 receptor (IL5) subunit alpha (IL5RA), AKT/PIK3 pathway related phosphoinositide-3-kinase regulatory subunit 6 (PIK3R6), and sphingomyelin phosphodiesterase 3 (SMPD3), which has been identified as a target of AD treatment.

CONCLUSIONS

The derived meta-phenotypes and associated biological functions represent both biomarkers to predict response, as well as potential new treatment targets. Our method is applicable to other diseases with multi-omic data, and the software is open source and available on Github (https://github.com/li-lab-mcgill/iGEM).

Impact of duration of critical illness and level of systemic glucocorticoid availability on tissue-specific glucocorticoid receptor expression and actions: A prospective, observational, cross-sectional human and two translational mouse studies

Background

Reduced glucocorticoid-receptor (GR) expression in blood suggested that critically ill patients become glucocorticoid-resistant necessitating stress-doses of glucocorticoids. We hypothesised that critical illness evokes a tissue-specific, time-dependent expression of regulators of GR-action which adaptively guides glucocorticoid action to sites of need.

Methods

We performed a prospective, observational, cross-sectional human study and two translational mouse studies. In freshly-isolated neutrophils and monocytes and in skeletal muscle and subcutaneous adipose tissue of 137 critically ill patients and 20 healthy controls and in skeletal muscle and adipose tissue as well as in vital tissues (heart, lung, diaphragm, liver, kidney) of 88 septic and 26 healthy mice, we quantified gene expression of cortisone-reductase 11β-HSD1, glucocorticoid-receptor-isoforms GRα and GRβ, GRα-sensitivity-regulating-co-chaperone FKBP51, and GR-action-marker GILZ. Expression profiles were compared in relation to illness-duration and systemic-glucocorticoid-availability.

Findings

In patients’ neutrophils, GRα and GILZ were substantially suppressed (p≤0·05) throughout intensive care unit (ICU)-stay, while in monocytes low/normal GRα coincided with increased GILZ (p≤0·05). FKBP51 was increased transiently (neutrophils) or always (monocytes,p≤0·05). In patients’ muscle, 11β-HSD1 and GRα were low-normal (p≤0·05) and substantially suppressed in adipose tissue (p≤0·05); FKBP51 and GILZ were increased in skeletal muscle (p≤0·05) but normal in adipose tissue. GRβ was undetectable. Increasing systemic glucocorticoid availability in patients independently associated with further suppressed muscle 11β-HSD1 and GRα, further increased FKBP51 and unaltered GILZ (p≤0·05). In septic mouse heart and lung, 11β-HSD1, FKBP51 and GILZ were always high (p≤0·01). In heart, GRα was suppressed (p≤0·05), while normal or high in lung (all p≤0·05). In diaphragm, 11β-HSD1 was high/normal, GRα low/normal and FKBP51 and GILZ high (p≤0·01). In kidney, 11β-HSD1 transiently increased but decreased thereafter, GRα was normal and FKBP51 and GILZ high (p≤0·01). In liver, 11β-HSD1 was suppressed (p≤0·01), GRα normal and FKBP51 high (p≤0·01) whereas GILZ was transiently decreased but elevated thereafter (p≤0·05). Only in lung and diaphragm, treatment with hydrocortisone further increased GILZ.

Interpretation

Tissue-specific, time-independent adaptations to critical illness guided GR-action predominantly to vital tissues such as lung, while (partially) protecting against collateral harm in other cells and tissues, such as neutrophils. These findings argue against maladaptive generalised glucocorticoid-resistance necessitating glucocorticoid-treatment.

Funding

Research-Foundation-Flanders, Methusalem-Program-Flemish-Government, European-Research-Council, European-Respiratory-Society.

Sex-Specific Brain Transcriptional Signatures in Human MDD and Their Correlates in Mouse Models of Depression

Major depressive disorder (MDD) is amongst the most devastating psychiatric conditions affecting several millions of people worldwide every year. Despite the importance of this disease and its impact on modern societies, still very little is known about the etiological mechanisms. Treatment strategies have stagnated over the last decades and very little progress has been made to improve the efficiency of current therapeutic approaches. In order to better understand the disease, it is necessary for researchers to use appropriate animal models that reproduce specific aspects of the complex clinical manifestations at the behavioral and molecular levels. Here, we review the current literature describing the use of mouse models to reproduce specific aspects of MDD and anxiety in males and females. We first describe some of the most commonly used mouse models and their capacity to display unique but also shared features relevant to MDD. We then transition toward an integral description, combined with genome-wide transcriptional strategies. The use of these models reveals crucial insights into the molecular programs underlying the expression of stress susceptibility and resilience in a sex-specific fashion. These studies performed on human and mouse tissues establish correlates into the mechanisms mediating the impact of stress and the extent to which different mouse models of chronic stress recapitulate the molecular changes observed in depressed humans. The focus of this review is specifically to highlight the sex differences revealed from different stress paradigms and transcriptional analyses both in human and animal models.