A Haplotype Implicated in Schizophrenia Susceptibility Is Associated with Reduced COMT Expression in Human Brain

Abstract

The gene encoding catechol-O-methyltransferase (COMT) is a strong candidate for schizophrenia susceptibility, owing to the role of COMT in dopamine metabolism, and the location of the gene within the deleted region in velocardiofacial syndrome, a disorder associated with high rates of schizophrenia. Recently, a highly significant association was reported between schizophrenia and a COMT haplotype in a large case-control sample (Shifman et al. 2002). In addition to a functional valine-->methionine (Val/Met) polymorphism, this haplotype included two noncoding single-nucleotide polymorphisms (SNPs) at either end of the COMT gene. Given the role of COMT in dopamine catabolism and that deletion of 22q11 (containing COMT) is associated with schizophrenia, we postulated that the susceptibility COMT haplotype is associated with low COMT expression. To test this hypothesis, we have applied quantitative measures of allele-specific expression using mRNA from human brain. We demonstrate that COMT is subject to allelic differences in expression in human brain and that the COMT haplotype implicated in schizophrenia (Shifman et al. 2002) is associated with lower expression of COMT mRNA. We also show that the 3' flanking region SNP that gave greatest evidence for association with schizophrenia in that study is transcribed in human brain and exhibits significant differences in allelic expression, with lower relative expression of the associated allele. Our results indicate that COMT variants other than the Val/Met change are of functional importance in human brain and that the haplotype implicated in schizophrenia susceptibility is likely to exert its effect, directly or indirectly, by down-regulating COMT expression.

Genome‐wide significant schizophrenia risk variation on chromosome 10q24 is associated with altered cis‐regulation of BORCS7, AS3MT, and NT5C2 in the human brain

“…The strong linkage disequilibrium (D′) in the region meant that, in individuals who were heterozygous at a risk variant as well as an exonic variant, the risk allele would nearly always be carried on the same chromosome as a particular allele of the exonic SNP. An assessment of whether the risk alleles were associated with a general increase or decrease in the allelic expression of each candidate gene could, therefore, be made by comparing cDNA allele ratios in individuals who were heterozygous for the risk variant with allele ratios observed in genomic DNA (representing the true 1:1 ratio of the two alleles) [e.g., Bray et al, 2003a, 2005]. …”

“…Although comparisons between cDNA and gDNA allele ratios in heterozygous risk allele carriers under conditions of high‐linkage disequilibrium allow an assessment of whether the risk allele is associated with a general increase or decrease in allelic expression [Bray et al, 2003a, 2005; Hill and Bray, 2012], they do not specifically test whether genotype at the risk variant could directly account for altered cis ‐regulation of the gene. For this, it is necessary to compare cDNA allele ratios in heterozygotes for the risk variant (where any cis ‐regulatory effects of the two alleles will differ) with those in homozygotes for the risk variant (where any cis ‐regulatory effects of the variant will be equal) [Bray et al, 2003a, 2005; Williams et al, 2011; Hill and Bray, 2012].…”

“…For this, it is necessary to compare cDNA allele ratios in heterozygotes for the risk variant (where any cis ‐regulatory effects of the two alleles will differ) with those in homozygotes for the risk variant (where any cis ‐regulatory effects of the variant will be equal) [Bray et al, 2003a, 2005; Williams et al, 2011; Hill and Bray, 2012]. Small genotype groups precluded such an assessment of cis ‐regulatory effects of rs11191419, but genotype at ch10_104957618_I was associated with significant effects on the allelic expression of BORCS7 in fetal brain, adult DLPFC, adult hippocampus and adult caudate, AS3MT in the fetal brain and adult caudate, and NT5C2 in the fetal brain, adult DLPFC and adult hippocampus.…”

“…As an initial test of whether the risk alleles were associated with a relative increase or decrease in the allelic expression of each gene, we therefore compared cDNA allele ratios in samples that were heterozygous for each risk variant (where the risk alleles would usually be carried on the same chromosome as one of the expressed alleles and the non‐risk alleles would be usually carried on the same chromosome as the alternative expressed allele) with the allele ratios observed in genomic DNA (representing a true 1:1 ratio of the two alleles). As a more specific test of whether risk genotype could account for altered cis ‐regulation of each candidate gene, we also compared cDNA allele ratios between risk allele heterozygotes (where any cis ‐regulatory effects of that variant will differ) and homozygotes (where any cis ‐regulatory effects of the variant will be the same), as performed previously [Bray et al, 2003a, 2005; Hill and Bray, 2012]. Due to small numbers of homozygotes for rs11191419 in assayed exonic heterozygotes, these latter analyses were restricted to comparisons between ch10_104957618_I genotypes.…”

“…These variants do not appear to index variation influencing protein structure, and are therefore likely to confer risk for schizophrenia through effects on the expression of one or more genes in the region. Measures of allele‐specific expression provide a powerful means of assessing such cis ‐regulatory influences, because they allow the level of gene expression from chromosomes carrying the risk and non‐risk alleles of a given variant to be compared simultaneously within individual samples [Bray et al, 2003a]. This approach typically makes use of exonic (i.e., expressed) single nucleotide polymorphisms (SNPs) in genes of interest as allele‐specific tags, allowing the RNA transcribed from each parental chromosome to be distinguished and relatively quantified in individual heterozygotes [Yan et al, 2002].…”