Expression quantitative trait loci analysis identifies associations between genotype and gene expression in human intestine.

paper Cited Public

Authors: Kabakchiev, Boyko; Silverberg, Mark S
Year: 2013
Journal: Gastroenterology
PMID: 23474282
DOI: 10.1053/j.gastro.2013.03.001
PMCID: PMC3775712

BACKGROUND & AIMS: Genome-wide association studies have greatly increased our understanding of intestinal disease. However, little is known about how genetic variations result in phenotypic changes. Some polymorphisms have been shown to modulate quantifiable phenotypic traits; these are called quantitative trait loci. Quantitative trait loci that affect levels of gene expression are called expression quantitative trait loci (eQTL), which can provide insight into the biological relevance of data from genome-wide association studies. We performed a comprehensive eQTL scan of intestinal tissue. METHODS: Total RNA was extracted from ileal biopsy specimens and genomic DNA was obtained from whole-blood samples from the same cohort of individuals. Cis- and trans-eQTL analyses were performed using a custom software pipeline for samples from 173 subjects. The analyses determined the expression levels of 19,047 unique autosomal genes listed in the US National Center for Biotechnology Information database and more than 580,000 variants from the Single Nucleotide Polymorphism database. RESULTS: The presence of more than 15,000 cis- and trans-eQTL was detected with statistical significance. eQTL associated with the same expression trait were in high linkage disequilibrium. Comparative analysis with previous eQTL studies showed that 30% to 40% of genes identified as eQTL in monocytes, liver tissue, lymphoblastoid cell lines, T cells, and fibroblasts are also eQTL in ileal tissue. Conversely, most of the significant eQTL have not been previously identified and could be tissue specific. These are involved in many cell functions, including division and antigen processing and presentation. Our analysis confirmed that previously published cis-eQTL are single nucleotide polymorphisms associated with inflammatory bowel disease: rs2298428/UBE2L3, rs1050152/SLC22A4, and SLC22A5. We identified many new associations between inflammatory bowel disease susceptibility loci and gene expression. CONCLUSIONS: eQTL analysis of intestinal tissue supports findings that some eQTL remain stable across cell types, whereas others are specific to the sampled location. Our findings confirm and expand the number of known genotypes associated with expression and could help elucidate mechanisms of intestinal disease.

Figure 1

Twelve significant cis-eQTL. Box plot depiction of the 12 most significant, unique cis-eQTL using a 50-kb window. The x-axis of each plot corresponds to the 3 observed SNP genotypes in forward orientation, and the y-axis represents log2-normalized gene expression values. Listed P values are FDR corrected.

LLM interpretation

This figure consists of 12 individual box plots showing the relationship between specific SNP genotypes (x-axis) and $\log_2$-normalized gene expression values (y-axis) for 12 different genes. Each plot displays a trend where gene expression levels vary across the three observed genotypes, with FDR-corrected p-values ranging from $2.08 \times 10^{-24}$ to $9.22 \times 10^{-19}$. The visualizations demonstrate either a positive or negative correlation between the number of alternative alleles and the level of gene expression.

Figure 2

MAF distribution of eSNPs. Distribution of MAF among 13,907 significant eSNPs after cis-eQTL analysis with 50-kb windows and an α level of 5%.

LLM interpretation

This is a histogram showing the distribution of Minor Allele Frequency (MAF) for 13,907 significant eSNPs. The x-axis represents MAF (ranging from 0 to 0.5) and the y-axis represents the percentage of SNPs. The data shows a general upward trend, with a higher percentage of significant eSNPs occurring at higher MAF values.

Figure 3

Visualization of LD between SNPs surrounding the gene MMEL1. Visual representation of pairwise LD between markers about the MMEL1 gene. Color intensity and values in the triangular matrix indicate the corresponding r2 values. Bar plot heights represent the intensity of each –log10-transformed P value, and markers identified as an LD cluster by eQTLA are colored uniformly. White bars did not cluster with other markers. The horizontal red line corresponds to the Bonferroni cutoff for significance.

LLM interpretation

This figure consists of a bar plot aligned above a triangular linkage disequilibrium (LD) heatmap for SNPs surrounding the *MMEL1* gene. The bar plot displays $-\log_{10}(P)$ values, with a red horizontal line indicating the Bonferroni significance threshold and colored bars identifying eQTLA LD clusters. The heatmap uses a grayscale gradient and numerical $r^2$ values to represent the strength of pairwise LD between the 21 labeled markers.

Figure 4

Locus size distribution after LD correction with eQTLA. Distribution of locus sizes for 4196 significant clusters after cis-eQTL analysis with 50-kb windows, an α level of 5%, and subsequent LD correction.

LLM interpretation

This is a histogram showing the distribution of locus sizes for 4,196 significant clusters after LD correction. The x-axis represents "Locus size" and the y-axis represents "Percent." The data is heavily right-skewed, with the highest percentage of loci occurring at the smallest size (approximately 35%) and a rapid decline as locus size increases.

Figure 5

eQTL comparison of human ileum with other tissues. Percentage overlap between significant cis expression traits detected in other tissues (monocytes, lymphoblastoid cell lines, liver, T cells, and fibroblasts) and human small intestinal tissue. Results are presented with varying windows sizes and α levels for the analysis in intestinal tissue.

LLM interpretation

This grouped bar chart shows the percentage overlap of significant cis expression traits between the human ileum and five other tissues (Monocytes, LCL, Liver, T cells, and Fibroblasts). The data is categorized by two window sizes (50 kb and 1 mb) and two $\alpha$ levels (5% and 10%). Across all conditions, LCL consistently shows the highest percentage of overlap, while the highest overall overlap percentages are observed in the 50 kb window at the 10% $\alpha$ level.

#	Section	Preview
20	Results — eQTL and IBD	Finally, in a case study applying eQTL data to a specific disease, expression traits and eSNPs…
21	Discussion	This study in human small intestinal tissue strongly corroborates the hypothesis of overarching gene…
22	Discussion	However, interpretation of eQTL equivalence between tissues must be considered in the context of…
23	Discussion	Identification of SNPs in high apparent LD and statistical retesting with these newly defined…
24	Discussion	Trans-eQTL analysis was also very sensitive to statistical power. As other investigators have…
25	Discussion	To contrast these data, cis-eQTL analysis of IBD susceptibility loci identified the expression of a…
26	Conclusions	eQTL analysis of intestinal tissue substantiates reports in the literature that some eQTL remain…

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