Tissue-Specific Expression Quantitative Trait Loci (eQTL) in GI Symptomatic ASD Children

Background:  

Previously, we characterized, via whole transcriptome analysis of ileocolonic biopsy tissue, an IBD-like condition that occurs with high frequency in autism spectrum disorder (ASD) children. Using gene expression data from that study, together with whole genome single nucleotide polymorphism (SNP) data on DNA from the same individuals, we are exploring genome-wide expression quantitative trait loci (eQTL).

Objectives:  

The immediate goal of this study is to test the hypothesis that SNPs that influence gene expression (eQTL) in the colon and terminal ileum identified in our ASD population are associated with Crohn’s disease (CD), ulcerative colitis (UC) and inflammatory bowel disease (IBD).   

Methods:  Gene expression data (generated from Agilent whole genome microarrays) and SNP data (generated at 23&me on custom Illumina SNP chips) from 64 individuals were used for the eQTL analyses. Standard quality control was completed for association studies (e.g., SNP call rate, Hardy-Weinberg Equilibrium). Analyses were computed separately for colon and terminal illium samples and by ASD^IC (ASD with ileocolitis). For each transcript and tissue type, we computed a genome-wide association analysis using linear regression on single nucleotide polymorphism (SNP) cis (within 500kb) to the probe’s gene. In this eQTL analysis, we regressed the SNP’s genotype and the first principal components onto log₂ expression for the transcript. Given the modest sample size, only the dominant genetic model was computed. A fixed effect meta-analysis and the corresponding test for heterogeneity of effects were computed across disease groups. Significance of an eQTL effect was measured as p-value <1x10E-6 and expression fold change of at least 1.5. We cross referenced these eQTLs (or SNPs in linkage disequilibrium (LD: r-squared>0.7) with lists of SNPs associated with CD, UC and IBD obtained from the UCSC Genome Browser GWAS catalog.  

Results:  

The number of children analyzed varies by tissue. There were 18 ASD^IC+ with colon samples and 22 ASD^IC+ terminal ileum samples. In total, 189 eQTL SNPs had p<1x10E-6. Comparing these eQTL SNPs or their proxies (SNPs in high LD) to known published GWAS results failed to identify any known loci associated with CD, UC and IBD. Previously we reported eQTLs on chr 7q11.23 with known links to Williams Beuren Syndrome and ASD, RYR2 (colon: rs10802598, and 1q43, p=2.25x10^-8) and EPHB1 (colon: rs10512944, 3q22, p=1.88x10^-12) related to ASD and/or ASD-phenotypes through other studies and approaches. Examination of the region about rs10512944 on 3q22 region appears to show high trans-mammalian species conservation and is in proximity to a region of high taxonomic class (Mammal, Aves, Pisces) conservation. The cause of this high trans-species conservation is not known, however, as there are limited known regulatory (DNase I Hypersensitivity Clusters, transcription factors) elements in the region.

Conclusions:  

These data show no evidence that eQTL from the colon and terminal ileum, identified in our ASD population, are known CD, UC and IBD risk loci. However, eQTLs identified in this sample are associated with ASD and/or ASD-phenotype and are in areas of evolutionary high trans-species conservation.