The relationship of tryptophan hydroxylase-2 methylation to early-life stress and its impact on short-term antidepressant treatment response

Epigenetic aging in major depressive disorder: Clocks, mechanisms and therapeutic perspectives

Depression, a chronic mental disorder characterized by persistent sadness, loss of interest, and difficulty in daily tasks, impacts millions globally with varying treatment options. Antidepressants, despite their long half-life and minimal effectiveness, leave half of patients undertreated, highlighting the need for new therapies to enhance well-being. Epigenetics, which studies genetic changes in gene expression or cellular phenotype without altering the underlying Deoxyribonucleic Acid (DNA) sequence, is explored in this article. This article delves into the intricate relationship between epigenetic mechanisms and depression, shedding light on how environmental stressors, early-life adversity, and genetic predispositions shape gene expression patterns associated with depression. We have also discussed Histone Deacetylase (HDAC) inhibitors, which enhance cognitive function and mood regulation in depression. Non-coding RNAs, (ncRNAs) such as Long Non-Coding RNAs (lncRNAs) and micro RNA (miRNAs), are highlighted as potential biomarkers for detecting and monitoring major depressive disorder (MDD). This article also emphasizes the reversible nature of epigenetic modifications and their influence on neuronal growth processes, underscoring the dynamic interplay between genetics, environment, and epigenetics in depression development. It explores the therapeutic potential of targeting epigenetic pathways in treating clinical depression. Additionally, it examines clinical findings related to epigenetic clocks and their role in studying depression and biological aging.

No association between peripheral serotonin-gene-related DNA methylation and brain serotonin neurotransmission in the healthy and depressed state

BACKGROUND

Methylation of serotonin-related genes has been proposed as a plausible gene-by-environment link which may mediate environmental stress, depressive and anxiety symptoms. DNA methylation is often measured in blood cells, but little is known about the association between this peripheral epigenetic modification and brain serotonergic architecture. Here, we evaluated the association between whole-blood-derived methylation of four CpG sites in the serotonin transporter (SLC6A4) and six CpG sites of the tryptophan hydroxylase 2 (TPH2) gene and in-vivo brain levels of serotonin transporter (5-HTT) and serotonin 4 receptor (5-HT4) in a cohort of healthy individuals (N = 254) and, for 5-HT4, in a cohort of unmedicated patients with depression (N = 90). To do so, we quantified SLC6A4/TPH2 methylation using bisulfite pyrosequencing and estimated brain 5-HT4 and 5-HTT levels using positron emission tomography. In addition, we explored the association between SLC6A4 and TPH2 methylation and measures of early life and recent stress, depressive and anxiety symptoms on 297 healthy individuals.

RESULTS

We found no statistically significant association between peripheral DNA methylation and brain markers of serotonergic neurotransmission in patients with depression or in healthy individuals. In addition, although SLC6A4 CpG2 (chr17:30,236,083) methylation was marginally associated with the parental bonding inventory overprotection score in the healthy cohort, statistical significance did not remain after accounting for blood cell heterogeneity.

CONCLUSIONS

We suggest that findings on peripheral DNA methylation in the context of brain serotonin-related features should be interpreted with caution. More studies are needed to rule out a role of SLC6A4 and TPH2 methylation as biomarkers for environmental stress, depressive or anxiety symptoms.

Leveraging DNA methylation to predict treatment response in major depressive disorder: A critical review

Major depressive disorder (MDD) is a debilitating and prevalent mental disorder with a high disease burden. Despite a wide array of different treatment options, many patients do not respond to initial treatment attempts. Selection of the most appropriate treatment remains a significant clinical challenge in psychiatry, highlighting the need for the development of biomarkers with predictive utility. Recently, the epigenetic modification DNA methylation (DNAm) has emerged to be of great interest as a potential predictor of MDD treatment outcomes. Here, we review efforts to date that seek to identify DNAm signatures associated with treatment response in individuals with MDD. Searches were conducted in the databases PubMed, Scopus, and Web of Science with the concepts and keywords MDD, DNAm, antidepressants, psychotherapy, cognitive behavior therapy, electroconvulsive therapy, transcranial magnetic stimulation, and brain stimulation therapies. We identified 32 studies implicating DNAm patterns associated with MDD treatment outcomes. The majority of studies (N = 25) are focused on selected target genes exploring treatment outcomes in pharmacological treatments (N = 22) with a few studies assessing treatment response to electroconvulsive therapy (N = 3). Additionally, there are few genome-scale efforts (N = 7) to characterize DNAm patterns associated with treatment outcomes. There is a relative dearth of studies investigating DNAm patterns in relation to psychotherapy, electroconvulsive therapy, or transcranial magnetic stimulation; importantly, most existing studies have limited sample sizes. Given the heterogeneity in both methods and results of studies to date, there is a need for additional studies before existing findings can inform clinical decisions.

Negative association between DNA methylation in brain-derived neurotrophic factor exon VI and left superior parietal gyrification in major depressive disorder

OBJECTIVE

We have recently reported significantly higher DNA methylation in brain-derived neurotrophic factor (BDNF) exon VI in major depressive disorder (MDD). This study aimed to investigated cortical changes and their associations with DNA methylations in BDNF exon VI in MDD.

METHODS

Data of 93 patients with MDD and 59 controls were involved in statistics. General linear regressions (GLM) were performed to analyze thickness and gyrification changes in MDD and their association with DNA methylation in BDNF exon VI in patients with MDD and controls.

RESULTS

Significantly decreased cortical thickness (CT) in left lateral orbitofrontal cortex (LOFC), left superior temporal lobe (ST) and right frontal pole (FP) and decreased local gyrification index (lGI) in left superior parietal lobe (SP) were found in MDD. The associations between DNA methylation in 3 CpG sites in BDNF exon VI and lGI in left SP were significantly different in patients and controls. DNA methylations in BDNF132 (β = -0.359, P < 0.001), BDNF137 (β = -0.214, P = 0.032), and BDNF151 (β = -0.223, P = 0.025) were significantly negatively associated with lGI in left SP in MDD.

CONCLUSION

The negative association between BDNF exon VI methylation and lGI in left SP might imply a potential epigenetic marker associated with cortical gyrification reduction in patients with MDD.

The associations between DNA methylation and depression: A systematic review and meta-analysis

BACKGROUND

Growing evidence suggests that epigenetic modification is vital in biological processes of depression. Findings from studies exploring the associations between DNA methylation and depression have been inconsistent.

METHODS

A systematical search of EMBASE, PubMed, Web of Science, and PsycINFO databases was conducted to include studies focusing on the associations between DNA methylation and depression (up to November 1st 2021) according to PRISMA guidelines with registration in PROSPERO (CRD42021288664).

RESULTS

A total of 47 studies met inclusion criteria and 31 studies were included in the meta-analysis. This meta-analysis found that genes hypermethylation, including BDNF (OR: 1.15, 95%CI: 1.01-1.32, I² = 90 %), and NR3C1 (OR: 1.43, 95%CI: 1.09-1.87, I² = 88 %) was associated with increased risk of depression. Significant association of SLC6A4 hypermethylation with depression was only found in the subgroup of using original data (OR: 1.09, 95%CI: 1.01-1.19, I² = 52 %). BDNF hypermethylation could increase the risk of depression only in the Asian population (OR: 1.18, 95%CI: 1.01-1.40, I² = 91 %), and significant associations of NR3C1 hypermethylation with depression were found in the group for depressive symptoms (OR: 1.34, 95%CI: 1.08-1.67, I² = 85 %), but not for depressive disorder (OR: 1.89, 95%CI: 0.54-6.55, I² = 94 %).

LIMITATIONS

More studies are needed to explore the factors that might influence the estimates owing to the contextual heterogeneity of the pooling of included studies.

CONCLUSIONS

It is noted that DNA hypermethylation, namely BDNF and NR3C1, is associated with increased risk of depression. The findings in this study could provide some material evidence for preventing and diagnosing of depression.

Measuring childhood trauma in young adults with depression: A latent profile analysis

Childhood traumas are important risk factors for depression in young adults. However, the co-occurrence of childhood traumas is complex, and the specific effects of different types of childhood traumas on depression need further exploration. The aim of this study was to assess the co-occurrence of childhood traumas and the impact of different profiles of childhood trauma on depression. A total of 1053 young adults with depression in China participated. PHQ-9, SHAPS, GAD-7, CTQ-SF, and NLES were evaluated. Latent profile analysis (LPA) was conducted to identify profiles of childhood trauma. The effects of different childhood trauma profiles on depression, anxiety, and anhedonia were assessed using stepwise linear regression. LPA suggested three profiles: no or low childhood traumas, moderate childhood trauma with emotional abuse and childhood neglect, and high childhood trauma with high levels of all trauma types. Regression analyses suggested that high levels of emotional abuse and childhood neglect significantly affected anhedonia. Childhood adverse events cluster in young adults with depression, allowing grouping into three distinct profiles. Specific childhood trauma patterns predict anhedonia symptoms in adult depression.

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.

The interaction of P11 methylation and early-life stress impacts the antidepressant response in patients with major depressive disorder

PURPOSE

The present research investigates the influence of P11 gene DNA methylation combined with life stress on the response to antidepressants in the first two weeks.

METHODS

A total of 291 Han Chinese patients with major depressive disorder and 100 healthy controls were included. The Life Events Scale and the Childhood Trauma Questionnaire were used to assess stress. The primary endpoint was the Hamilton Depression Rating Scale-17 reduction rate after two weeks of treatment. The Illumina HiSeq Platform was used to detect the methylation of 74 CpG sites of the P11 gene in peripheral blood samples.

RESULTS

The mean methylation of all P11 CpG sites, as well as the methylation at 4 CpG sites (P11-2-169, P11-2-192, P11-2-202, P11-2-204), were significantly higher in patients with MDD than in healthy controls (FDR-corrected P < 0.05). The response to antidepressants was associated with the following interactions: the CTQ score and P11-3-185 site methylation (OR = 0.297, FDR-corrected P = 0.023), the CTQ physical neglect score and P11-2-117 site methylation (OR = 0.005, FDR-corrected P = 0.033), and the CTQ emotional abuse score and P11-3-185 site methylation (OR = 0.001, FDR-corrected P = 0.023).

CONCLUSIONS

The methylation of the P11 gene was significantly higher in patients with major depressive disorder. The interaction of P11 DNA methylation and early-life stress may influence the short-term antidepressant treatment response.

Epigenetic Mechanism of Early Life Stress-Induced Depression: Focus on the Neurotransmitter Systems

Depression has an alarmingly high prevalence worldwide. A growing body of evidence indicates that environmental factors significantly affect the neural development and function of the central nervous system and then induce psychiatric disorders. Early life stress (ELS) affects brain development and has been identified as a major cause of depression. It could promote susceptibility to stress in adulthood. Recent studies have found that ELS induces epigenetic changes that subsequently affect transcriptional rates of differentially expressed genes. The epigenetic modifications involved in ELS include histone modifications, DNA methylation, and non-coding RNA. Understanding of these genetic modifications may identify mechanisms that may lead to new interventions for the treatment of depression. Many reports indicate that different types of ELS induce epigenetic modifications of genes involved in the neurotransmitter systems, such as the dopaminergic system, the serotonergic system, the gamma-aminobutyric acid (GABA)-ergic system, and the glutamatergic system, which further regulate gene expression and ultimately induce depression-like behaviors. In this article, we review the effects of epigenetic modifications on the neurotransmitter systems in depression-like outcomes produced by different types of ELS in recent years, aiming to provide new therapeutic targets for patients who suffer from depression.

Sex Differences in Depression Caused by Early Life Stress and Related Mechanisms

Depression is a common psychiatric disease caused by various factors, manifesting with continuous low spirits, with its precise mechanism being unclear. Early life stress (ELS) is receiving more attention as a possible cause of depression. Many studies focused on the mechanisms underlying how ELS leads to changes in sex hormones, neurotransmitters, hypothalamic pituitary adrenocortical (HPA) axis function, and epigenetics. The adverse effects of ELS on adulthood are mainly dependent on the time window when stress occurs, sex and the developmental stage when evaluating the impacts. Therefore, with regard to the exact sex differences of adult depression, we found that ELS could lead to sex-differentiated depression through multiple mechanisms, including 5-HT, sex hormone, HPA axis, and epigenetics.

Combination of spontaneous regional brain activity and HTR1A/1B DNA methylation to predict early responses to antidepressant treatments in MDD

BACKGROUND

Antidepressant medications are suggested as the first-line treatment in patients with major depressive disorder (MDD). However, the drug therapy outcomes vary from person to person. The functional activity of the brain and DNA methylation levels correlate with the antidepressant efficacy. To predict the early antidepressant responses in MDD and establish the prediction framework, we aimed to apply multidimensional data based on the resting-state activity of the brain and HTR1A/1B methylation.

METHODS

The values of Amplitude of Low-Frequency Fluctuations (ALFF) and regional homogeneity (ReHo) were measured as variables in 116 brain regions along with 181 CpG sites in the promoter region of HTR1A/1B and 11 clinical characteristics. After performing the feature reduction step using the least absolute shrinkage and selection operator (LASSO) method, the selected variables were put into Support Vector Machines (SVM), Random Forest (RF), Naïve Bayes (NB), and logistic regression (LR), consecutively, to construct the prediction models. The models' performance was evaluated by the Leave-One-Out Cross-Validation.

RESULTS

The LR model composed of the selected multidimensional features reached a maximum performance of 78.57% accuracy and 0.8340 area under the ROC curve (AUC). The prediction accuracies based on multidimensional datasets were found to be higher than those obtained from the data based only on fMRI or methylation.

LIMITATIONS

A relatively small sample size potentially restricted the usage of our prediction framework in clinical applications.

CONCLUSION

Our study revealed that combining the data of brain imaging and DNA methylation could provide a complementary effect in predicting early-stage antidepressant outcomes.

Influence and interaction of resting state functional magnetic resonance and tryptophan hydroxylase-2 methylation on short-term antidepressant drug response

BACKGROUND

Most antidepressants have been developed on the basis of the monoamine deficiency hypothesis of depression, in which neuronal serotonin (5-HT) plays a key role. 5-HT biosynthesis is regulated by the rate-limiting enzyme tryptophan hydroxylase-2 (TPH2). TPH2 methylation is correlated with antidepressant effects. Resting-state functional MRI (rs-fMRI) is applied for detecting abnormal brain functional activity in patients with different antidepressant effects. We will investigate the effect of the interaction between rs-fMRI and TPH2 DNA methylation on the early antidepressant effects.

METHODS

A total of 300 patients with major depressive disorder (MDD) and 100 healthy controls (HCs) were enrolled, of which 60 patients with MDD were subjected to rs-fMRI. Antidepressant responses was assessed by a 50% reduction in 17-item Hamilton Rating Scale for Depression (HAMD-17) scores at baseline and after two weeks of medication. The RESTPlus software in MATLAB was used to analyze the rs-fMRI data. The amplitude of low-frequency fluctuation (ALFF), regional homogeneity (ReHo), fractional ALFF (fALFF), and functional connectivity (FC) were used, and the above results were used as regions of interest (ROIs) to extract the average value of brain ROIs regions in the RESTPlus software. Generalized linear model analysis was performed to analyze the association between abnormal activity found in rs-fMRI and the effect of TPH2 DNA methylation on antidepressant responses.

RESULTS

Two hundred ninety-one patients with MDD and 100 HCs were included in the methylation statistical analysis, of which 57 patients were included in the further rs-fMRI analysis (3 patients were excluded due to excessive head movement). 57 patients were divided into the responder group (n = 36) and the non-responder group (n = 21). Rs-fMRI results showed that the ALFF of the left inferior frontal gyrus (IFG) was significantly different between the two groups. The results showed that TPH2-1-43 methylation interacted with ALFF of left IFG to affect the antidepressant responses (p = 0.041, false discovery rate (FDR) corrected p = 0.149).

CONCLUSIONS

Our study demonstrated that the differences in the ALFF of left IFG between the two groups and its association with TPH2 methylation affect short-term antidepressant drug responses.

The impact of HTR1A and HTR1B methylation combined with stress/genotype on early antidepressant efficacy

AIMS

Antidepressants are effective in the treatment of major depressive disorder (MDD), while many patients fail to respond to antidepressants. Both 5-HT1A (HTR1A) and 5-HT1B (HTR1B) receptors play an important role in antidepressant activity. Meanwhile, DNA methylation is associated with MDD and antidepressant efficacy. In this study we investigate the influence of HTR1A and HTR1B methylation combined with stress/genotype on antidepressant efficacy.

METHODS

A total of 291 MDD patients and 100 healthy controls received the Life Events Scale (LES) and the Childhood Trauma Questionnaire (CTQ) as stress assessment. Eight single nucleotide polymorphisms (SNPs) of HTR1A and HTR1B involved in antidepressant mechanisms were tested. Methylation status in 181 cytosine-phosphate-guanine (CpG) sites of HTR1A and HTR1B were assessed. All MDD patients were divided into response (RES) and non-response (NRES) after 2 weeks of antidepressant treatment. Logistic regression was conducted for interactions between methylation, NLES/CTQ score and genotype.

RESULTS

Low HTR1A-2-143 methylation is connected with better antidepressant efficacy in subgroup. Low HTR1A-2-143 methylation combined with low CTQ score is related to better antidepressant efficacy. The interaction between high HTR1B methylation with the rs6298 AA/AG genotype affects better antidepressant efficacy.

CONCLUSIONS

HTR1A and HTR1B methylation combined with stress/genotype is associated with antidepressant efficacy.

Meta-analysis of association between TPH2 single nucleotide poiymorphism and depression

Tryptophan hydroxylase 2 (TPH2) plays a crucial role in the human brain. Although the association between the TPH2 gene and depression has been suggested in previous meta-analyses, studies based on Chinese subjects are often neglected. Therefore, we included some previous studies based on Chinese subjects to explore the relationship between TPH2 polymorphisms and depression via conducting an extensive meta-analysis. We reviewed 40 research papers that included data on TPH2 gene single nucleotide polymorphisms (SNPs) from 5766 patients with depression and 5988 healthy subjects. The analysis showed an association between polymorphisms in the TPH2 gene and depression, and some results were significant in 24 studies that included Chinese Han study participants. The results of our meta-analysis showed that rs4570625, rs17110747, rs120074175, rs4290270, rs120074175, and rs4290270 may be significantly associated with depression, and that rs11178997 (A/A genotype) may be a significant risk factor for depression in the Chinese subjects. Based on the results of this study, biological experiments should be performed in the future to explore how different SNPs affect depression.

Identifying patients with major depressive disorder based on tryptophan hydroxylase-2 methylation using machine learning algorithms

OBJECTIVES

This study aimed to identify patients with major depressive disorder (MDD) by developing different machine learning (ML) models based on tryptophan hydroxylase-2 (TPH2) methylation and environmental stress.

METHODS

The data were collected from 291 patients with MDD and 100 healthy control participants: individual basic information, the Negative Life Events Scale (NLES) scores, the Childhood Trauma Questionnaire (CTQ) scores and the methylation level at 38 CpG sites in TPH2. Information gain was used to select critical input variables. Support vector machine (SVM), back propagation neural network (BPNN) and random forest (RF) algorithms were used to build recognition models, which were evaluated by the 10-fold cross-validation. SHapley Additive exPlanations (SHAP) method was used to evaluate features importance.

RESULTS

Gender, NLES scores, CTQ scores and 13 CpG sites in TPH2 gene were considered as predictors in the models. Three ML algorithms showed satisfactory performance in predicting MDD and the BPNN model indicated best prediction effects.

CONCLUSION

ML models with TPH2 methylation and environmental stress were identified to possess great performance in identifying patients with MDD, which provided precious experience for artificial intelligence to assist traditional diagnostic methods in the future.

DNA methylations of brain-derived neurotrophic factor exon VI are associated with major depressive disorder and antidepressant-induced remission in females

BACKGROUND

Brain-derived neurotrophic factor (BDNF) has been suggested to play important roles in major depressive disorder (MDD) and antidepressant treatment. The main purpose of this study was to evaluate the association of DNA methylation changes in the BDNF gene with MDD and antidepressant treatment.

METHODS

A total of 291 MDD patients and 100 healthy controls were included and followed up for 6 weeks. The Hamilton Depression Rating Scale-17 (HDRS-17) was used to measure treatment improvement. The life events scales (LES) and childhood trauma questionnaire (CTQ) were used to rate recent and early life stress. DNA methylation levels of CpG sites in the BDNF gene were measured.

RESULTS

Two CpG sites in BDNF exon VI (BDNF133 and BDNF134) were demonstrated to have significantly higher methylation in MDD patients than in controls (both FDR-adjusted P = 0.001). A logistics regression model indicated that the interaction between the hypermethylation of BDNF133 and negative subscore of LES was associated to MDD (OR=0.0075, P<0.001). Methylation of BDNF140 at baseline was significantly elevated in remitters (FDR-adjusted P = 0.046) at week 6. In subgroup analyses, these findings could be replicated in females, but not in males.

LIMITATIONS

The methylation status of BDNF after 6 weeks of antidepressant treatment was not measured and the DNA methylation were detected in peripheral blood cells.

CONCLUSIONS

These findings highlight gender-specific alteration of methylation at several CpG sites in BDNF exon VI as a promising candidate indicator of MDD and antidepressant-induced remission.

Epigenetics of childhood trauma: Long term sequelae and potential for treatment

Childhood trauma (CT) can have persistent effects on the brain and is one of the major risk factors for neuropsychiatric diseases in adulthood. Recent advances in the field of epigenetics suggest that epigenetic factors such as DNA methylation and histone modifications, as well as regulatory processes involving non-coding RNA are associated with the long-term sequelae of CT. This narrative review summarizes current knowledge on the epigenetic basis of CT and describes studies in animal models and human subjects examining how the epigenome and transcriptome are modified by CT in the brain. It discusses psychological and pharmacological interventions that can counteract epigenetic changes induced by CT and the need to establish longitudinal assessment after CT for developing more effective diagnostics and treatment strategies based on epigenetic targets.

The Importance of Epigenetics in Diagnostics and Treatment of Major Depressive Disorder

Recent studies imply that there is a tight association between epigenetics and a molecular mechanism of major depressive disorder (MDD). Epigenetic modifications, i.e., DNA methylation, post-translational histone modification and interference of microRNA (miRNA) or long non-coding RNA (lncRNA), are able to influence the severity of the disease and the outcome of the therapy. This article summarizes the most recent literature data on this topic, i.e., usage of histone deacetylases as therapeutic agents with an antidepressant effect and miRNAs or lncRNAs as markers of depression. Due to the noteworthy potential of the role of epigenetics in MDD diagnostics and therapy, we have gathered the most relevant data in this area.

Genetic and Epigenetic Consequence of Early-Life Social Stress on Depression: Role of Serotonin-Associated Genes

Early-life adversity caused by poor social bonding and deprived maternal care is known to affect mental wellbeing and physical health. It is a form of chronic social stress that persists because of a negative environment, and the consequences are long-lasting on mental health. The presence of social stress during early life can have an epigenetic effect on the body, possibly resulting in many complex mental disorders, including depression in later life. Here, we review the evidence for early-life social stress-induced epigenetic changes that modulate juvenile and adult social behavior (depression and anxiety). This review has a particular emphasis on the interaction between early-life social stress and genetic variation of serotonin associate genes including the serotonin transporter gene (5-HTT; also known as SLC6A4), which are key molecules involved in depression.