An investigation of genetic and epigenetic factors in the regulation of gene expression in schizophrenia: insights into pathways involved in pathogenesis

Schizophrenia is a common psychiatric disorder with a complex aetiology that has a strong genetic component as well as a major contribution from non-genetic factors. Whilst GWAS studies have not yielded substantial evidence of DNA variants linked to schizophrenia, microarray expression studies, which reflect both genetic and environmental factors, have provided evidence of candidate genes whose expression changes significantly in schizophrenia. The present thesis is based on a prospective microarray study carried out on two brain regions implicated in schizophrenia: frontal cortex and superior temporal cortex (Maycox et al., 2009; Barnes et al., 2011). SNP variants in six of these genes were genotyped and allele, genotype and haplotype analysis carried out initially to investigate associations with levels of expression found in these microarray studies. Subsequently SNP associations with disease were investigated in an extended case-control cohort from the East UK region. The selected candidates genes, highlighted from microarray studies, reflected two main functional categories: synaptic plasticity and the Wnt signalling pathway. Initial ANOVA revealed a significant interaction of disease status with genotype/haplotype in ZnT3 with respect to levels of expression. Significant effects of specific genotypes and haplotypes in CACNA1E and FRZB on expression were also observed. Furthermore, ZnT3 was the gene for which the strongest evidence of association with schizophrenia was obtained in the East UK cohort, with four SNPs associated at the allelic and genotypic level. Significant associations of a number of haplotypes of ZnT3 with disease status were also identified. In addition, modest evidence of statistical epistasis between genes within both functional groups was identified. Finally, a method for analysis of CpG island methylation was developed based on bisulphite sequencing and methylation specific PCR (MSP) using previously validated primers for DKK3 (Yue et al., 2008). Although DKK3 showed a low density of methylation, the application of this method may prove useful for other candidate genes