Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression

Abstract

Unrecognized depression during adolescence can result in adult suicidal behaviour. The aim of this study was to identify, replicate and characterize DNA methylation (DNAm) shifts in depression aetiology, using a longitudinal, multi-tissue (blood and brain) and multi-layered (genetics, epigenetics, transcriptomics) approach. We measured genome-wide blood DNAm data at baseline and one-year follow-up, and imputed genetic variants, in 59 healthy adolescents comprising the discovery cohort. Depression and suicidal symptoms were determined using the Development and Well-Being Assessment (DAWBA) depression band, Montgomery-Åsberg Depression Rating Scale-Self (MADRS-S) and SUicide Assessment Scale (SUAS). DNAm levels at follow-up were regressed against depression scores, adjusting for sex, age and the DNAm residuals at baseline. Higher methylation levels of 5% and 13% at cg24627299 within the MET gene were associated with higher depression scores (p_raw<1e-4) and susceptibility for suicidal symptoms (p_adj.<0.005). The nearby rs39748 was discovered to be a methylation and expression quantitative trait locus in blood cells. mRNA levels of hepatocyte growth factor (HGF) expression, known to strongly interact with MET, were inversely associated with methylation levels at cg24627299, in an independent cohort of 1180 CD14+ samples. In an open-access dataset of brain tissue, lower methylation at cg24627299 was found in 45 adults diagnosed with major depressive disorder compared with matched controls (p_adj.<0.05). Furthermore, lower MET expression was identified in the hippocampus of depressed individuals compared with controls in a fourth, independent cohort. Our findings reveal methylation changes at MET in the pathology of depression, possibly involved in downregulation of HGF/c-MET signalling the hippocampal region.

Keywords: Adolescent depression; DNA methylation; HGF/c-MET signalling; epigenetics; epigenome-wide analysis.

Figure 1.

Study design for methylation and expression association with depression using four cohorts. Blood associations between DNA methylation and depression risk, genotype and mRNA expression were investigated using two independent cohorts, i.e. the discovery cohort and methylation-expression cohort. In brain, methylation and mRNA levels were separately analysed in relation to MDD in two independent cohorts. * Individuals with depression DAWBA band risk scores below 15% and MADRS-S scores <9 were defined as ‘Controls’, while individuals with depression DAWBA level bands 3 (≈ 15%), 4 (≈ 50%) or 5 (>70%) and MADRS-S scores ≥9 were assigned to the ‘Cases’ category. SNPs: single nucleotide polymorphisms; MDD: major depression disease.

Figure 2.

Manhattan plot of the longitudinal epigenome-wide association of depressive-transformed variable in whole-blood samples of 59 adolescents. The depressive-transformed variable was calculated based on depression DAWBA band risk scores and MADRS-S scores. The blue line represents the significance level at p = 10⁻⁴.

Figure 3.

Blood DNAm levels (β-values) at cg24627299 within the MET gene for adolescents defined as ‘controls’ and ‘cases’. Individuals with depression DAWBA band risk scores below 15% and MADRS-S scores <9 were defined as ‘Controls’, while individuals with depression DAWBA level bands 3 (≈ 15%), 4 (≈ 50%) or 5 (>70%) and MADRS-S scores ≥9 were assigned to the ‘Cases’ category.

Figure 4.

Methylation levels at cg24627299 (MET) in brain samples of MDD-diagnosed individuals and controls.

Figure 5.

LD matrix of the 39 investigated genetic variants within the ±100 kbp of the differentially methylated CpG site (cg24627299, MET gene).

Figure 6.

a) MET and HGF expression levels among different brain regions and whole blood. b) Genomic context of the most significant CpG site associated with the depressive phenotype in the longitudinal analyses. Genomic positions of RefSeq genes are displayed in the bottom part and indicated by arrows. The position of the significant CpG site is highlighted by black lines. Since analyses were performed based on data obtained in blood, chromatin marks overlapping in brain and blood cells were investigated. Chromatin states of eight tissues downloaded from the 37/hg19 WashU Epigenome Browser are illustrated. Each functional role of a segment is indicated by a particular colour. BrainAC: brain anterior caudate; BrainCG: brain cingulate gyrus; BrainHIPPO: brain hippocampus; BrainITL: brain inferior temporal lobe; BrainDPC: brain dorsolateral prefrontal cortex; BrainSN: brain substantia nigra; BrainAG: brain angular gyrus; PBMC: peripheral blood mononuclear primary cells.

Figure 7.

Connections in the hippocampal formation. In the hippocampus, sensory information arrives from the cerebral association neocortex via the entorhinal cortex, parahippocampal gyrus and/or perirhinal cortex. The hippocampal subfield CA1 sends axons to both subcortical areas and the deep layers of the entorhinal cortex, either directly or through the subiculum. Processed information is sent back from the hippocampal CA1 area to the cerebral association cortex through the same pathway. Higher methylation levels at the promoter of MET may alter the autocrine mechanism of HGF/c-MET signalling necessary for promoting axonal growth at the excitatory synapses of the CA1 hippocampal pyramidal neurons. The response to the environmental stimuli may therefore be altered, leading to depressive symptoms.