Genome-wide Association Studies Followed By Independent Replication Identify IRF3 As A Novel Locus For Systemic Lupus Erythematosus

Object: Systemic lupus erythematosus?SLE?is a complex prototype autoimmune disease with diverse causes.All the disease-associated loci identified by genome-wide association studies?GWAS?can only explain a small part of heritability of SLE,indicating that there are still many other loci to be discovered.This study intends to further analyze the existing SLE GWAS data,aiming at identifying new SLE susceptibility genes/sites and further revealing the biological mechanism,providing targets for drug researches.Method: This project includes two stages: discovery stage and replication stage.Discovery stage was based on published SLE GWAS from Europe cohort comprising 4943 SLE cases and 8483 controls and Asian cohort including 2485 cases and 3947 controls.Then imputation was performed to infer the genotypes of those sites without being called directly by referring to 1000 Genome Project.Three SNPs were selected for further validation after quality control.On replication stage,these candidate SNPs were firstly genotyped in Hong Kong cohort with 1255 cases and 951 corresponding controls.Case-control association analysis was performed and those SNPs showing contradicted disease effects with discovery stage were removed,while the consistent SNP was kept.The remaining SNP was further replicated in Anhui cohort?1014 cases and 4122 controls?and Guangzhou cohort?GZ??1667 cases and 990 controls?,and meta-analysis was performed combining the date from discovery stage and replication stage to identify susceptibility variant.Then 654 SLE cases with complete clinical data and 951 controls in Hong Kong cohort were used for genotype-subphenotype analysis.Finally,functional annotation was applied to understand the biological function of the newly identified susceptibility locus.Result: On discovery stage,three SNPs with suggestive association signals were selected for replication from SLE GWAS data: rs7251?P=1.79E-05,OR=0.880?,rs3008?P=3.80E-04,OR=1.14?,rs4763630?P=4.36E-06,OR=0.845?.The result of TaqMan genotyping assay of these three SNPs performed in HK cohort on replication stage showed that the effects of rs3008?P=0.884,OR=0.989?and rs4763630?P=0.266,OR=1.09?on the disease contradicted that on the discovery stage,while rs7251?P=0.301,OR=0.922?was consistent.rs3008 and rs4763630 were removed and rs7251 was kept for further replication.After multiple replication and meta-analysis,we found that rs7251?P=5.74E-08,OR=0.885?was significantly associated with SLE.Genotype-subphenotype analysis showed that rs7251 may have association with lupus nephritis?LN??P=0.045,OR=0.767?.rs7251 is located in exon 10 near the 3' UTR of IRF3?NM₀01571.5?,whose variation may result in a threonine to serine substitution in amino acid position 427?T427S?.IRF3 is a key transcriptional regulator of type I interferon?IFN I?in immune response inducing the production of IFN I and other pro-inflammatory factors.Conclusion: This study identified a genetic variant in IRF3?rs7251?locus was significantly associated with SLE through GWAS and replication studies,in addition,genotype-subphenotype analysis suggested that IRF3 had association with LN.Functional annotation showed that abnormal regulation of IRF3 may contribute to the pathogenesis of the disease by the production of IFN I and inflammatory factors through Toll-like receptor pathway.