Mapping of gene expression reveals CYP27A1 as a susceptibility gene for sporadic ALS.

paper Cited Public

Amyotrophic lateral sclerosis (ALS) is a progressive, neurodegenerative disease characterized by loss of upper and lower motor neurons. ALS is considered to be a complex trait and genome-wide association studies (GWAS) have implicated a few susceptibility loci. However, many more causal loci remain to be discovered. Since it has been shown that genetic variants associated with complex traits are more likely to be eQTLs than frequency-matched variants from GWAS platforms, we conducted a two-stage genome-wide screening for eQTLs associated with ALS. In addition, we applied an eQTL analysis to finemap association loci. Expression profiles using peripheral blood of 323 sporadic ALS patients and 413 controls were mapped to genome-wide genotyping data. Subsequently, data from a two-stage GWAS (3,568 patients and 10,163 controls) were used to prioritize eQTLs identified in the first stage (162 ALS, 207 controls). These prioritized eQTLs were carried forward to the second sample with both gene-expression and genotyping data (161 ALS, 206 controls). Replicated eQTL SNPs were then tested for association in the second-stage GWAS data to find SNPs associated with disease, that survived correction for multiple testing. We thus identified twelve cis eQTLs with nominally significant associations in the second-stage GWAS data. Eight SNP-transcript pairs of highest significance (lowest p = 1.27 × 10(-51)) withstood multiple-testing correction in the second stage and modulated CYP27A1 gene expression. Additionally, we show that C9orf72 appears to be the only gene in the 9p21.2 locus that is regulated in cis, showing the potential of this approach in identifying causative genes in association loci in ALS. This study has identified candidate genes for sporadic ALS, most notably CYP27A1. Mutations in CYP27A1 are causal to cerebrotendinous xanthomatosis which can present as a clinical mimic of ALS with progressive upper motor neuron loss, making it a plausible susceptibility gene for ALS.

Figure 1

Study design.For each step, the number of resulting SNP-transcript pairs in cis is shown.

LLM interpretation

This figure is a study design flowchart illustrating a filtering process to identify significant SNP-transcript pairs. It shows a sequential reduction in the number of pairs from eQTL discovery (16,901) through eQTL selection (1,108) and replication (951), resulting in 8 final eQTL results. The process incorporates GWAS discovery (14,167 SNPs with $P_{GWAS} < 0.05$) and GWAS replication (SNPs with $P_{GWAS} < 0.05$ after Bonferroni correction) as integrating steps.

Figure 2

Regional linkage disequilibrium (LD) near the CYP27A1 locus on chromosome 2.Top: the position of GWAS SNPs and RefSeq genes located within the regional LD block are drawn. On the X-axis, genomic position in kb, aligned to NCBI genome build 36 coordinates. On the left Y-axis, −log10(p values) for the strongest cis eQTL association for a gene in the replication data, the vertical position of genes (drawn as arrows) are aligned to this axis and thus represent statistical significance. For one gene (RQCD1), no SNP-transcript pair and, therefore, no eQTL p value was available in our data. This gene is shown as a dashed arrow. On the right Y-axis, −log10(p values) from the replication GWAS analysis for SNPs within the region (black line), SNPs modulating CYP27A1 expression are shown as black dots, other SNPs are grey. Bottom: pairwise linkage disequilibrium for HapMap phase III release 2 SNPs (CEU+TSI populations). The LD plot was created in Haploview v4.2 [50], using the standard D'/LOD color scheme.

LLM interpretation

This figure consists of a genomic plot (top) and a linkage disequilibrium (LD) heat map (bottom) centered on the *CYP27A1* locus on chromosome 2. The top panel displays genomic positions (kb) on the x-axis, with the left y-axis showing $-\log_{10}(p\text{-values})$ for cis-eQTL associations for several genes (represented by arrows) and the right y-axis showing $-\log_{10}(p\text{-values})$ for GWAS SNPs (black line and dots). The bottom panel is a Haploview LD plot using a red-scale D'/LOD color scheme to show pairwise LD between HapMap SNPs across the region.

#	Section	Preview
20	Results — GWAS Discovery	In the GWAS discovery set, 2,261 ALS cases and 8,328 patients remained after quality control…
21	Results — GWAS Discovery	From the eQTL discovery results, we selected the 1,108 SNP-transcript pairs (755 eQTL SNPs) in cis…
22	Results — eQTL Replication	The eQTL replication set comprised 161 ALS patients and 206 control samples (Table S1). 951 out of…
23	Results — GWAS Replication	After quality control, there were 1,307 ALS cases and 1,835 controls in the GWAS replication set…
24	Results — Fine-mapping of Loci UNC13A and Chromosome 9p21.2	In addition to our genome-wide screen for eQTLs associated with sporadic ALS, we specifically…
25	Results — Fine-mapping of Loci UNC13A and Chromosome 9p21.2	SNP-transcript pairs was applied using a 5% FDR. Two SNP-transcript pairs reached the threshold for…
26	Discussion	The present study reports the results of a large and comprehensive genome-wide screening of the…
27	Discussion	cis eQTL, modulating CYP27A1 gene expression levels, which replicated in the second eQTL dataset and…
28	Discussion	As shown in Table S3, the SNPs modulating transcript levels had small effect sizes in our joint GWAS…
29	Discussion	We searched MEDLINE, Gene Ontology and OMIM databases to identify links to known pathways in ALS…
30	Discussion	The strengths of our study are the meticulous pruning of expression probes as present on the…
31	Discussion	A drawback of the present study lies in the use of whole blood instead of neuronal tissue for the…
32	Discussion	between two studies on brain tissue, which may partly be due to low statistical power [26], [46]. In…
33	Discussion	The focused analysis of variants in the chromosome 9p21.2 locus, which was previously associated…
34	Discussion	on a common haplotype in 9p21.2 linked families with ALS and FTD [15], [16], [47] thus illustrates…
35	Discussion	In summary, our genome-wide study of the genetics of gene expression has identified one cis eQTL for…

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