DNA methylation profiles of the brain-derived neurotrophic factor (BDNF) gene as a potent diagnostic biomarker in major depression

Abstract

Major depression, because of its recurring and life-threatening nature, is one of the top 10 diseases for global disease burden. Major depression is still diagnosed on the basis of clinical symptoms in patients. The search for specific biological markers is of great importance to advance the method of diagnosis for depression. We examined the methylation profile of 2 CpG islands (I and IV) at the promoters of the brain-derived neurotrophic factor (BDNF) gene, which is well known to be involved in the pathophysiology of depression. We analyzed genomic DNA from peripheral blood of 20 Japanese patients with major depression and 18 healthy controls to identify an appropriate epigenetic biomarker to aid in the establishment of an objective system for the diagnosis of depression. Methylation rates at each CpG unit was measured using a MassArray® system (SEQUENOM), and 2-dimensional hierarchical clustering analyses were undertaken to determine the validity of these methylation profiles as a diagnostic biomarker. Analyses of the dendrogram from methylation profiles of CpG I, but not IV, demonstrated that classification of healthy controls and patients at the first branch completely matched the clinical diagnosis. Despite the small number of subjects, our results indicate that classification based on the DNA methylation profiles of CpG I of the BDNF gene may be a valuable diagnostic biomarker for major depression.

Figure 1. The schema of CpGs and primers used for DNA methylation analyses.

The target region used for methylation analysis consists of 1092 bp including 81 CpGs upstream of exon I, and 1137 bp including 28 CpGs upstream of exon IV.

Figure 2. Hierarchic cluster analysis of subjects and their methylation profiles at CpG I of the BDNF gene.

Two-way hierarchic cluster analysis of 38 samples (rows) and DNA methylation of CpG units at CpG I of the BDNF gene (columns). DNA methylation values are depicted by a pseudocolor scale as indicated (methylation increases from red [nonmethylated] to white [methylated]). Samples with overall poor data quality were removed before clustering. Gray denotes data of poor quality. Samples are color-coded according to the diagnoses of samples (legend depicted lower left). The stars(★) ahead of several CpG units indicate CpG units which have statistically significant p-values in subsequent analyses by t-test.

Figure 3. Hierarchic cluster analysis of subjects and their methylation profiles at CpG IV of the BDNF gene.

Two-way hierarchic cluster analysis of 38 samples (rows) and DNA methylation of CpG units at CpG IV of the BDNF gene (columns). DNA methylation values are depicted by a pseudocolor scale as indicated (methylation increases from red [nonmethylated] to white [methylated]). Samples with overall poor data quality were removed before clustering. Gray denotes data of poor quality. Samples are color-coded according to the diagnoses of samples (legend depicted lower left).