An autoimmune disease risk variant: A trans master regulatory effect mediated by IRF1 under immune stimulation?

Margot Brandt,Sarah Kim-Hellmuth,Johannes Schumacher,Zharko Daniloski,Tuuli Lappalainen,Yocelyn Recinos,Veit Hornung,Nora Lam,Aaron Wolman,Alper Gokden,Marcello Ziosi,John A Morris,Xin He

doi:10.1371/journal.pgen.1009684

Abstract

Functional mechanisms remain unknown for most genetic loci associated to complex human traits and diseases. In this study, we first mapped trans-eQTLs in a data set of primary monocytes stimulated with LPS, and discovered that a risk variant for autoimmune disease, rs17622517 in an intron of C5ORF56, affects the expression of the transcription factor IRF1 20 kb away. The cis-regulatory effect specific to IRF1 is active under early immune stimulus, with a large number of trans-eQTL effects across the genome under late LPS response. Using CRISPRi silencing, we showed that perturbation of the SNP locus downregulates IRF1 and causes widespread transcriptional effects. Genome editing by CRISPR had suggestive recapitulation of the LPS-specific trans-eQTL signal and lent support for the rs17622517 site being functional. Our results suggest that this common genetic variant affects inter-individual response to immune stimuli via regulation of IRF1. For this autoimmune GWAS locus, our work provides evidence of the functional variant, demonstrates a condition-specific enhancer effect, identifies IRF1 as the likely causal gene in cis, and indicates that overactivation of the downstream immune-related pathway may be the cellular mechanism increasing disease risk. This work not only provides rare experimental validation of a master-regulatory trans-eQTL, but also demonstrates the power of eQTL mapping to build mechanistic hypotheses amenable for experimental follow-up using the CRISPR toolkit.

Highlights

The discovery of tens of thousands of genetic loci associated to complex diseases and traits has introduced the challenge of characterizing the biological mechanisms that mediate these associations
We identified that a genetic variant associated to autoimmune diseases affects the expression of the nearby transcription factor IRF1 gene in early immune response, followed by expression change of other genes in late immune response
We studied this effect in cell lines, using the CRISPR approach to silence the activity of the genomic element of this variant and cause mutations at that position

Summary

Introduction

The discovery of tens of thousands of genetic loci associated to complex diseases and traits has introduced the challenge of characterizing the biological mechanisms that mediate these associations. Most GWAS loci include a large number of associated variants in linkage disequilibrium (LD) and are located in noncoding regions with likely gene regulatory functions. It is typically unknown what is the causal variant, affected regulatory element, target gene in cis, and downstream molecular pathways that mediate genetic associations to complex disease phenotypes. Response cis-eQTL mapping for immune cells with in vitro stimuli have provided powerful evidence of genetic regulatory effects that are specific to tissues and to cell states, and disease associations that are driven by disrupted response to environmental stimuli [2,3,4,5]. While a large number of trans-eQTLs are mediated by a cis-eQTL, indicating potential biological mechanism, trans-eQTLs in humans rarely have strong master-regulatory effects on pathways of multiple genes [6,9,10,11]

Methods

Results

Discussion

Conclusion