Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder

Abstract

Studies of the major psychoses, schizophrenia (SZ) and bipolar disorder (BD), have traditionally focused on genetic and environmental risk factors, although more recent work has highlighted an additional role for epigenetic processes in mediating susceptibility. Since monozygotic (MZ) twins share a common DNA sequence, their study represents an ideal design for investigating the contribution of epigenetic factors to disease etiology. We performed a genome-wide analysis of DNA methylation on peripheral blood DNA samples obtained from a unique sample of MZ twin pairs discordant for major psychosis. Numerous loci demonstrated disease-associated DNA methylation differences between twins discordant for SZ and BD individually, and together as a combined major psychosis group. Pathway analysis of our top loci highlighted a significant enrichment of epigenetic changes in biological networks and pathways directly relevant to psychiatric disorder and neurodevelopment. The top psychosis-associated, differentially methylated region, significantly hypomethylated in affected twins, was located in the promoter of ST6GALNAC1 overlapping a previously reported rare genomic duplication observed in SZ. The mean DNA methylation difference at this locus was 6%, but there was considerable heterogeneity between families, with some twin pairs showing a 20% difference in methylation. We subsequently assessed this region in an independent sample of postmortem brain tissue from affected individuals and controls, finding marked hypomethylation (>25%) in a subset of psychosis patients. Overall, our data provide further evidence to support a role for DNA methylation differences in mediating phenotypic differences between MZ twins and in the etiology of both SZ and BD.

Figure 1.

Idiogram illustrating the mean DNA methylation difference (Δβ-value) (well-twin minus ill-twin) for each CpG site included in our analysis across all 22 pairs of psychosis-discordant MZ twins. The red-colored dots correspond to the 100 top-ranked CpG sites (Supplementary Material, Table S3). Similar idiograms for SZ- and BD-discordant twins-pairs are shown in Supplementary Material, Figure S4.

Figure 2.

DNA methylation differences (Δβ-value) (well-twin minus ill-twin) for the top-ranked probes from (A) the combined psychosis-discordant analysis group: ST6GALNAC1 (cg13015534), (B) SZ-discordant analysis group: PUS3 (cg02659232) and (C) the BD-discordant analysis group: GPR24 (cg21342728). Psychosis = twin pairs 1–22, SZ = twin pairs 1–11, BD = twin pairs 12–22.

Figure 3.

DNA methylation differences (Δβ-value) (well-twin minus ill-twin) for a CpG site located at ZNF659 (cg18267381), which shows disease-associated hypermethylation in SZ (twin pairs 1–11, blue bars) but disease-associated hypomethylation in BD (twin pairs 12–22, red bars).

Figure 4.

DNA methylation across multiple CpG sites in the promoter of ST6GALNAC1 in postmortem brain tissue from psychosis patients and controls. Postmortem brain tissue from affected individuals showed no overall significant hypomethylation, but 4 out of the 30 (13.3%) psychosis cases tested showed marked (up to 27%) hypomethylation at the same CpG site nominated from the array analysis, with hypomethylation extending across several adjacent CpG sites. No such hypomethylation was observed in any unaffected control samples which all demonstrated very similar methylation values (shown is mean control sample methylation; error bars denote standard deviation).