Dyslexia risk variant rs600753 is linked with dyslexia-specific differential allelic expression of DYX1C1

<div><p>Abstract An increasing number of genetic variants involved in dyslexia development were discovered during the last years, yet little is known about the molecular functional mechanisms of these SNPs. In this study we investigated whether dyslexia candidate SNPs have a direct, disease-specific effect on local expression levels of the assumed target gene by using a differential allelic expression assay. In total, 12 SNPs previously associated with dyslexia and related phenotypes were suitable for analysis. Transcripts corresponding to four SNPs were sufficiently expressed in 28 cell lines originating from controls and a family affected by dyslexia. We observed a significant effect of rs600753 on expression levels of DYX1C1 in forward and reverse sequencing approaches. The expression level of the rs600753 risk allele was increased in the respective seven cell lines from members of the dyslexia family which might be due to a disturbed transcription factor binding sites. When considering our results in the context of neuroanatomical dyslexia-specific findings, we speculate that this mechanism may be part of the pathomechanisms underlying the dyslexia-specific brain phenotype. Our results suggest that allele-specific DYX1C1 expression levels depend on genetic variants of rs600753 and contribute to dyslexia. However, these results are preliminary and need replication.</p></div

eQTL map of mQTL loci.

<p>We analysed the top-SNPs of our mQTL analysis regarding association with gene-expression levels. A total of 54 top-SNPs were correlated with 28,295 probe expressions. Expression probes of auto- and gonosomes were analysed, while SNPs were restricted to autosomes. X-axis represents physical position of SNPs. Y-axis represents the physical position of the start of the regulated transcript. Points located on the diagonal line relate to cis-effects, while other points relate to trans-effects. Associations with FDR = 5% are highlighted. Trans-eQTLs with p-values ≤ 0.001 are also shown. Size of points represents the strength of association. Colors of points and gray shadings indicate distinct chromosomes. An interactive html version of this map allowing exploration of the results is provided as supplemental <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005510#pgen.1005510.s007" target="_blank">S7 Fig</a>.</p

GWAS results for amino acids (a) and acylcarnitines (b) in whole blood.

<p>Manhattan plots of the genome-wide association analysis for metabolic phenotypes in 2,107 individuals of the LIFE-Heart cohort. Results are presented separately for 36 acylcarnitines (including free and total carnitine) and 26 amino acids. Results for metabolite ratios are omitted. The horizontal line represents a p-value = 1.0x10^-7, which was the cutoff used for inclusion of identified associations in the replication state.</p

Network of discovered loci, eQTLs and metabolites.

<p>Significant relationships between genetic loci (top SNPs), gene-expression in PBMCs and metabolite levels in whole blood are displayed. Line thickness corresponds to amount of explained variance (Lightblue = genetic loci without triangles, darkblue = genetic loci with triangles, lightgreen = cis-regulated genes, darkgreen = trans-regulated genes, light orange = raw metabolites, darkorange = metabolite ratios). An interactive html-document document of the network can be found in the supplement material.</p

Results of SNP-metabolite association analyses.

<p>Table includes all validated loci of our analysis. Validation is based on either successful replications in the Sorbs or by additional published evidence. The latter applies for two loci (#4 and #14) where association of lead-SNPs did not replicate in the Sorbs cohort. For each locus, nearby genes, independently associated SNPs, associated metabolites and statistics for the strongest association between them are shown (Beta estimators, corresponding standard errors and p-values). We also present the results of replication analysis and published evidence. Six loci with no corresponding published genetic variants were considered as “novel”.</p><p>¹SNP with strongest association in the discovery cohort is presented in bold;</p><p>²Distance of SNPs to genes in kB in parentheses;</p><p>³Metabolite with strongest association in the discovery cohort is presented in bold. p-value Sorbs: best p-value of SNPs in Sorbs corresponding to the lead-SNP and metabolite of discovery cohort,</p><p>⁴Replication was successful for ratio Q14:Arg/Orn, only, hence, we report here on association with Q14:Arg/Orn</p><p>Results of SNP-metabolite association analyses.</p

Results of eQTL analysis of validated loci.

<p>¹SNP with strongest metabolite association is presented in <b>bold</b> while SNP with strongest eQTL was marked with an asterisk<b>*</b></p><p>²Gene with strongest association is presented in <b>bold</b></p><p>³A q-value<5% was considered as significant, i.e. FDR is controlled at 5%.</p><p>⁴These genes are located on the same chromosome as the lead-SNPs at distances larger than 1Mb</p><p>Results of eQTL analysis of validated loci.</p

Results of replication analysis.

<p>GWAS top-hits of the LIFE Leipzig Heart study were compared with corresponding results in the Sorbs study. Top-hits were selected applying a p-value cut-off of p<1.0x10^-7, which leads to the gap of z-scores at the x-axis. Associations below and above the dotted lines are considered as replicated controlling the false discovery rate at 5%. Colors and symbols correspond to physiologically related metabolites.</p

Results of associations between gene-expressions and metabolites.

<p>Table displays significant associations of eQTL genes and metabolites for validated loci. Genes and metabolites are ordered according to strength of association. Statistics of strongest associations are also presented.</p><p>¹Gene with strongest association is presented in <b>bold</b></p><p>²Metabolite with strongest association is presented in <b>bold</b></p><p>³A q-value<5% was considered as significant, i.e. FDR is controlled at 5%.</p><p>Results of associations between gene-expressions and metabolites.</p

Quantile-quantile plot for MCIC association results.

<p>The empirical and theoretical distributions are shown as dots and line, respectively.</p

Genome-wide association results for SNPs associated with hippocampal volume in the MCIC sample.

<p>SNP IDs with chromosome (CHR), basepair position (BP), minor (A1) and major allele (A2), minor allele frequency (MAF), regression coefficient (BETA), coefficient (STAT) and asymptotic p-value for t-statistic, and corresponding gene regions: <i>KIF26B</i> (kinesin family member 26B), <i>TRPM8</i> (transient receptor potential cation channel, subfamily M, member 8), <i>LOC283089</i> (uncharacterized), <i>NR2F6</i> (nuclear receptor subfamily 2, group F, member 6), <i>USHBP1</i> (Usher syndrome 1C binding protein 1), and <i>BABAM1</i> (BRISC and BRCA1 A complex member 1). For additional information see Table S3 in File S1.</p