Genome-wide DNA methylation analysis of human brain tissue from schizophrenia patients

Abstract

Recent studies suggest that genetic and environmental factors do not account for all the schizophrenia risk, and epigenetics also has a role in disease susceptibility. DNA methylation is a heritable epigenetic modification that can regulate gene expression. Genome-wide DNA methylation analysis was performed on post-mortem human brain tissue from 24 patients with schizophrenia and 24 unaffected controls. DNA methylation was assessed at over 485,000 CpG sites using the Illumina Infinium HumanMethylation450 Bead Chip. After adjusting for age and post-mortem interval, 4641 probes corresponding to 2929 unique genes were found to be differentially methylated. Of those genes, 1291 were located in a CpG island and 817 were in a promoter region. These include NOS1, AKT1, DTNBP1, DNMT1, PPP3CC and SOX10, which have previously been associated with schizophrenia. More than 100 of these genes overlap with a previous DNA methylation study of peripheral blood from schizophrenia patients in which 27,000 CpG sites were analysed. Unsupervised clustering analysis of the top 3000 most variable probes revealed two distinct groups with significantly more people with schizophrenia in cluster one compared with controls (P=1.74 × 10(-4)). The first cluster composed of 88% of patients with schizophrenia and only 12% controls, whereas the second cluster composed of 27% of patients with schizophrenia and 73% controls. These results strongly suggest that differential DNA methylation is important in schizophrenia etiology and add support for the use of DNA methylation profiles as a future prognostic indicator of schizophrenia.

Figure 1

Multidimensional scaling (MDS) plot of the adjusted M-values with recursively partitioned mixture model (RPMM) cluster of adjusted β-values denoted by black (cluster 1) or grey (cluster 2) (a). MDS plot of the adjusted β-values with RPMM cluster of adjusted β-values denoted by black (cluster 1) or grey (cluster 2) (b).

Figure 2

Probe relation to CpG island and probes regulatory feature group. Number of probes found in regions of gene associated, non-gene associated, promoter associated and unclassified, both (a) unadjusted and (b) adjusted for age and post-mortem interval (PMI) (excluding those with no regulatory feature group information n=13214 and n=3002, respectively). Number of probes found in CpG islands, shelves (north and south) and shores (north and south), including those with no CpG island information (unknown), both (c) unadjusted and (d) adjusted for age and PMI.

Figure 3

Box plots of β-values for the control and schizophrenia groups for probes associated with genes of interest. The median β-value is denoted by the solid middle line (a) ‘cg27026005' is promoter associated (PA) and located on a CpG island, it is associated with AKT1. (b) ‘cg01749142' is also PA and located on a shore, it is associated with AKT1. (c) ‘cg21273407' is located on a CpG island, it is associated with NOS1. (d) ‘cg23401624' is located on a CpG island and is PA, it is associated to DNMT1. (e) ‘cg06128182' is located on a CpG island and is PA, it is associated to DNMT1. (f) ‘cg06614002' is located on a shore and is associated with SOX10.