| Literature DB >> 31428135 |
Duan Zeng1, Shen He1, Changlin Ma2, Yi Wen2, Ying Xie3, Nan Zhao4, Xirong Sun4, Dongxiang Wang1, Yifeng Shen1, Yimin Yu1, Huafang Li1,5,6.
Abstract
Major depressive disorder (MDD) is a leading cause of disability worldwide, although its etiology and mechanism remain unknown. The aim of our study was to identify hub genes associated with MDD and to illustrate the underlying mechanisms. A weighted gene co-expression network analysis (WGCNA) was performed to identify significant gene modules and hub genes associated with MDD in peripheral blood mononuclear cells (PBMCs) (n = 45). In the blue module (R 2 = 0.95), five common hub genes in both co-expression network and protein-protein interaction (PPI) network were regarded as "real" hub genes. In another independent dataset, GSE52790, four genes were still significantly down-regulated in PBMCs from MDD patients compared with the controls. Furthermore, these four genes were validated by quantitative real-time polymerase chain reaction (qRT-PCR) in PBMCs from 33 MDD patients and 41 healthy controls. The qRT-PCR analysis showed that ATP synthase membrane subunit c locus 1 (ATP5G1) was significantly down-regulated in samples from MDD patients than in control samples (t = -2.89, p-value = 0.005). Moreover, this gene was significantly differentially expressed between patients and controls in the prefrontal cortex (z = -2.83, p-value = 0.005). Highly significant differentially methylated positions were identified in the Brodmann area 25 (BA25), with probes in the ATP5G1 gene being significantly associated with MDD: cg25495775 (t = 2.82, p-value = 0.008), cg25856120 (t = -2.23, p-value = 0.033), and cg23708347 (t = -2.24, p-value = 0.032). These findings indicate that the ATP5G1 gene is associated with the pathogenesis of MDD and that it could serve as a peripheral biomarker for MDD.Entities:
Keywords: ATP5G1; biomarker; major depressive disorder; oxidative stress; weighted gene co-expression network analysis
Year: 2019 PMID: 31428135 PMCID: PMC6688554 DOI: 10.3389/fgene.2019.00703
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.599
Figure 1Flow diagram of the data processing, analysis, and validation procedures performed in this study. DEGs, differentially expressed genes; PPI, protein–protein interaction; PBMCs, peripheral blood mononuclear cells; qPCR, quantitative real-time polymerase chain reaction; BA25, Brodmann area 25.
Basic information about the datasets used in our study.
| Series | Sample size | Tissue type | Type | |
|---|---|---|---|---|
| MDD | Control | |||
| GSE39653 | 21 | 24 | PBMCs | Gene expression |
| GSE52790 | 10 | 12 | PBMCs | |
| GSE87610 | 19 | 19 | L3 pyramidal neurons in the dorsolateral prefrontal cortex | |
| GSE88890 | 20 | 20 | Cortical brain region (BA25) | Methylation levels |
MDD, major depressive disorder; PBMCs, peripheral blood mononuclear cells; BA25, Brodmann area 25.
Figure 2Determination of soft-thresholding power in the weighted gene co-expression network analysis. (A) Analysis of the scale-free fit index for different soft-thresholding powers (β). Numbers in the plots represent the corresponding soft-thresholding powers. The approximate scale-free topology can be obtained at a soft-thresholding power of 4. (B) Analysis of the mean connectivity for different soft-thresholding powers. (C) Histogram of connectivity distribution when β = 4. (D) Checking the scale-free topology when β = 4.
Figure 3Identification of modules associated with major depressive disorder (MDD) and Gene Ontology analysis. (A) Dendrogram of all differentially expressed genes clustered based on a dissimilarity measure (1-TOM). (B) Heatmap of the correlation between module eigengenes and the disease status (MDD vs. control). Each cell contains the corresponding correlation and p-value. (C) Gene Ontology analysis of genes in the blue module.
Figure 4Protein–protein interaction network of genes in the blue module. The color intensity in each node is proportional to the number of edges for the node. The nodes with a bold circle indicate hub genes identified by the PPI network.
Figure 5Hub gene detection and validation. (A) Selection of real hub genes in the PPI network and co-expression network. (B) The expression levels of the four genes (VHL, ATP5G1, COX4I1, and DDOST) were correlated with MDD (based on microarray data of GSE52790). (C) Relative expression levels of the four genes (VHL, ATP5G1, COX4I1, and DDOST) determined by real-time PCR. ATP5G1 was significantly down-regulated in samples from MDD patients compared with the control samples (p = 0.005). PCR, polymerase chain reaction. (D) The expression levels of ATP5G1 in L3 pyramidal neurons in the dorsolateral prefrontal cortex (DLPFC) (based on microarray data of GSE87610) and the methylation levels in BA25 (based on microarray data of GSE88890).
Demographic and clinical characteristics of the participants in the qPCR experiment.
| MDD ( | Controls ( |
|
| |
|---|---|---|---|---|
| Sex (M/F) | 15/18 | 15/26 | 0.597 | 0.482a |
| Age (years) | 38.48 ± 14.92 | 33.98 ± 11.60 | 1.443 | 0.153b |
| BMI | 22.25 ± 3.55 | 22.43 ± 2.94 | −0.231 | 0.818b |
| Duration of current episode (months) | 33.43 ± 60.29 | |||
| Duration of illness (months) | 77.94 ± 83.60 | |||
| Baseline HAMD-17 scores (mean ± SD) | 16.12 ± 6.34 | |||
| The expression level of | 2.47 ± 0.63 | 3.06 ± 1.10 |
|
|
| The expression level of | 2.17 ± 0.67 | 2.65 ± 1.07 | −1.90 | 0.058c |
| The expression level of | 2.19 ± 0.62 | 2.19 ± 0.71 | 0.02 | 0.988b |
| The expression level of | 5.08 ± 2.73 | 6.59 ± 4.52 | −0.60 | 0.550c |
Bold number represents significant p-value.
qPCR, quantitative real-time polymerase chain reaction; MDD, major depressive disorder; BMI, body mass index; HAMD-17, 17-Item Hamilton Rating Scale for Depression; SD, standard deviation.
aChi-square test; bindependent samples t test; cMann–Whitney test.
Figure 6Gene set enrichment analysis (GSEA) for gene sets related to ATP5G1 expression. The gene sets of “NITROGEN_METABOLISM,” “LYSINE_DEGRADATION,” “PYRIMIDINE_METABOLISM,” and “RNA_POLYMERASE” were enriched in MDD samples in which ATP5G1 was highly expressed.