DNA methylation and expression of stress related genes in PBMC of MDD patients with and without serious suicidal ideation

https://doi.org/10.1016/j.jpsychires.2017.02.005Get rights and content

Highlights

  • Stress associated genes are hypermethylated in MDD individuals.

  • The hypermethylation status of stress related genes are more prominent in MDD patients with significant suicidal ideation.

  • Stress related gene dysfunctionality in suicidal patient may be due to epigenetic modification via DNA methylation..

  • These genes may serve as predictive biomarker of suicidal behavior in MDD patients.

Abstract

Stress plays an important role in major depressive disorder (MDD) and is one of the state dependent factors in suicidal behavior. A dysfunctional hypothalamic-pituitary-adrenal axis is a common feature in this disorder. The involvement of environmental factors has added additional complexity to understanding depression or suicidal behavior. In this regard, epigenetic regulation has been considered a mechanistic interface between environmental stress stimuli and altered functioning of underlying gene network that may increase susceptibility to depression or suicidal behavior. The present study examined whether epigenetic modifications of stress related genes are associated with MDD and whether there are differences in these epigenetic marks between depressed individuals with and without serious suicidal ideation. Using MeDIP analysis in genomic DNA isolated from peripheral blood mononuclear cells (PBMC) of healthy controls (n = 20), MDD patients with (n = 14) or without serious suicidal ideation (n = 10), we studied methylation of the stress-associated genes, Brain Derived Neurotrophic Factor (BDNF), Nuclear Receptor Subfamily 3 Group C Member 1 (NR3C1), FK506 Binding Protein 5 (FKBP5), Corticotropin Releasing Hormone Binding Protein (CRHBP), and Corticotropin Releasing Hormone Receptor 1 (CRHR1). In addition, we determined their transcript levels in RNAs isolated from the same PBMC. We found that BDNF, FKBP5, CRHBP, and NR3C1 gene promoters were significantly hypermethylated in MDD patients with and without suicidal ideation. We also found concomitant reductions in expression of BDNF, FKBP5 transcript variants (1, 2 and 3), and NR3C1 genes in these patients, suggesting that promoter hypermethylation in these genes may functionally be associated with their observed downregulation in MDD patients. In a secondary analysis, methylation of these genes was compared between MDD patients with or without serious suicidal ideation and controls. The MDD with serious suicidal ideation were significantly different from controls while the MDD without were not, although MDD with or without suicidal ideation were not different from each other, likely owning to a relatively small sample size. Thus, our findings underline the importance of epigenetic modifications of stress-associated genes in depression and, possibly, suicidal behavior, which, in future, needs to be confirmed in a larger patient population.

Introduction

Suicide is a major public health concern. Approximately one million people commit suicide worldwide each year and 40,000 people commit suicide in the United States alone (CDC, 2014, WHO, 2012). In the U.S., the lifetime rate of suicidal ideation is estimated at 13.5%, suicidal plan at 3.9%, and suicide attempt at 4.6% (Kessler et al., 1999). Among adolescents, suicide is the 3rd leading cause of death after motor vehicle accidents and homicide (CDC (Centers for Disease Control and Prevention), 2013). Previously, most of the studies of suicidal behavior were focused on the role of psychosocial and sociocultural factors; however, these factors are of too little predictive value to be of clinically useful. Therefore, research on the biological perspective of suicide has gained momentum and is a promising approach for identifying biological risk factors associated with suicidal behavior (Dwivedi and Pandey, 2011).

The presence of psychopathology is a strong predictor of suicide; however, only a minority of people with such diagnoses commit suicide (Mann, 1998, Mann, 2002, Turecki, 2005). This is evident from studies suggesting that though MDD is a major risk factor in suicide, but only 9% of severely ill MDD patients commit suicide (Bostwick and Pankratz, 2000). Further, not all people who commit suicide are depressed. Thus, the existence of suicidal syndromes that are independent of psychiatric illnesses has been proposed (Mann, 2010, van Heeringen and Mann, 2014). According to this hypothesis, suicidal behavior is a function of the interplay between state-dependent factors, such as illness and life events, and trait-dependent factors, which include biological markers (Mann and Haghighi, 2010). One of the state-dependent factors in suicidal behavior is stress (Mann and Haghighi, 2010). Several clinical evidence show a strong association between hyperactive hypothalamic-pituitary-adrenal axis and suicidal behavior (Dumser et al., 1998, Lopez et al., 1992, Nemeroff et al., 1988, Szigethy et al., 1994). More recently, a number of environmental factors have been found to act as contributory factor in suicide vulnerability, including maternal stress, childhood maltreatment, traumatic events, and exposure to stress (Lopizzo et al., 2015). It has been argued that adverse life events such as early life stress or traumatic exposure can cause gene × environment interaction with a result in improper functioning of neuronal circuitry, which can lead to an early onset of MDD and can increase susceptibility to suicidal behavior (Brezo et al., 2008, Martin et al., 2004, Menke and Binder, 2014, Plunkett et al., 2001).

Because of the complex genetic composition and overlapping molecular cross-talk, the current understanding of gene × environment interaction has opened new approaches to better understand the mechanisms that affect multiple genes involved in an abnormal behavior (Lesch, 2004, Tsuang et al., 2004). In this regard, modulation in neuronal functions mediated by epigenomic changes, which cause alteration in chromatin architecture without affecting the nucleotide sequence arrangements in DNA, have been identified as one of the major risk factors in several psychiatric illnesses including depression and suicidal behavior (Haghighi et al., 2014, Higuchi et al., 2011, Keller et al., 2010, Maussion et al., 2014, Numata et al., 2015, Zhang et al., 2014, Zhang et al., 2015). Interestingly, in suicidal patients, a few studies show that these epigenetic modifications can be independent of psychiatric illnesses such as depression (Kang et al., 2013, Kim et al., 2014). The present study was undertaken to further examine whether epigenetic modifications of stress related genes play a role in suicidal behavior and whether these modifications are common to or independent of depression. More specifically, we examined whether: 1) genes associated with stress show altered DNA methylation in their promoter regions in MDD patients, 2) changes in DNA methylation are associated with suicidal behavior independent of MDD diagnosis, and 3) changes in DNA methylation are associated with their functional response at gene transcript level. For this, we determined DNA methylation of stress-related genes such as Brain Derived Neurotrophic Factor (BDNF), Nuclear Receptor Subfamily 3 Group C Member 1 (NR3C1), FK506 Binding Protein 5 (FKBP5), Corticotropin Releasing Hormone Binding Protein (CRHBP), and Corticotropin Releasing Hormone Receptor 1 (CRHR1) in PBMC of healthy controls and MDD patients with and without serious suicidal ideation. We also determined the expression of these genes to examine the functional response of altered DNA methylation.

Section snippets

Subjects

The study was reviewed and approved by the Institutional Review Board of the University of Alabama at Birmingham (UAB) and written informed consent was obtained from all subjects prior to the study. The study was performed in 20 healthy controls and 24 MDD patients. Of 24 MDD patients, 14 had recent clinically significant suicidal ideation and 10 did not. Patients were recruited from UAB Department of Psychiatry clinics and the UAB Medical Center Emergency Department. All participants were

Demographic and clinical characteristics of MDD and healthy control subjects

The demographic and clinical characteristics of subjects are provided in Table 1. There was no significant difference in age between MDD patients and healthy controls (F(2,41) = 0.06, p = 0.94). The MDD-suicide group had a significantly higher MADRS score than the MDD-non-suicide group (t = 4.16, p < 0.001). This remained significant even after removing the suicide score from the MADRS total (t = 3.24, p < 0.005). The mean ± SEM of the MADRS in the MDD group was 36.3 ± 8.5, whereas in the MDD

Discussion

The primary objective of the study was to examine whether MDD was associated with epigenetic modifications in the genes that are critical in stress response. The exploratory objective was to test whether these modifications were specifically associated with serious suicidal ideation or whether they represented a general feature of MDD. Our data show a significant increase in DNA methylation of stress related genes including BDNF, NR3C1, FKBP5, and CRHBP in PBMC of total MDD patients (with and

Contributors

YD designed the study. RC managed the clinical study. BR conducted the biological and statistical analyses. RC conducted the statistical analyses. BR, RC, and YD co-wrote the manuscript. All authors have approved the final article.

Role of the funding source

The study was supported by grants from National Institute of Mental Health (R01MH082802; R21MH081099; 1R01MH101890; R01MH100616; 1R01MH107183), and American Foundation for Suicide Prevention (SRG-1-042-14) to Dr. Dwivedi and American Foundation for Suicide Prevention (2-SRG-xxx-00023) to Dr. Shelton. The authors declare no competing financial interests.

Statement of interest

The authors declare no competing financial or other conflicts of interests.

Acknowledgement

We would like to thank Dr. Birgit Ludwig for valuable comments.

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