Fine Mapping Of Psoriasis-associated IL23R Locus In Chinese Han Population

Introduction: Psoriasis is a common chronic inflammatory skin disease characterized by sharply demarcated erythematous plaques with adherent silvery scales,mainly happens in young adults.It gets worse in winter and improves in spring.Psoriasis incidence varies in different parts of the world,and is related to race,geography and environmental factors.It affects 0.1-3% populations worldwide and chinese incidence is 0.123%..Mostly due to its hard to cure and easy to relapse,psoriasis brings endless hurt including economic burden and mental pressure for patients and their families which impacts severely the patients' quality of life.The etiology and pathogenesis of psoriasis are largely unknown and it is believed that psoriasis is the result of genetic and environmental interactions.Currently,some research found that T cell activation was a key point in psoriasis chronic inflammation mechanism and IL-23/Th17 signaling pathway played an important role in the pathogenesis of autoimmune diseases.In recent years,Genome Wide Association Study?GWAS?was found to be one of the most common methods for complex disease susceptibility genes.It brought revolutionary breakthrough for the study of IL-23/Th17 signaling pathway involved in chronic inflammatory process.However,it was not enough for depending on SNPs as the directly biological evidence and more and more studies identified that other variant which showed strong LD association with SNPs in GWAS was the real functional variant.It has become a key content for post GWAS era to perform fine mapping for GWAS susceptibility loci by imputation and target sequencing and identify the real functional variant eventually.In 2014,our group identified a low-frequency variant c.530 G > A,p.Gly149 Arg in IL23R by whole exome sequencing and targeted sequencing which provided evidence for IL23R gene involved in psoriasis pathogenesis and a clue for functional variant searching in this locus.We also developed psoriasis meta-analysis of genome-wide association studies with other seven groups from other countries and found that IL23R gene was shared in Chinese Han and Caucasian population with heterogeneity.These findings suggested that difference was existed for IL23R functional variant between Chinese Han and Caucasian population and there were specific functional variants in Chinese Han population.So it has important scientific value to perform functional variant research in IL23R locus which may clarify differences for the pathogenesis of psoriasis between different populations and benefit for specific therapeutic drugs.Objectives: To identify potential functional variants in psoriasis-associated IL23R locus by imputation and bioinformatics methods in Chinese Han poputation Methods: We implemented imputation to improve SNP coverage in IL23R locus.We implemented a two-stage fine mapping design in this study.In the discovery stage,we performed imputation with the 1000 Genomes Project data as references.In the validation stage we included data for IL23R locus from whole-exome array analysis in psoriasis.Considering the SNPs information was not enough,we also included part of 1000 Genomes Project data as references.Then we performed quality control,single-variant association,conditional analyses and haplotype analyses with the use of SNP test and chose the variant with significant association as potential functional variant.With the help of ENCODE database,we screened out the potential functional variant.Results: We conducted two stage of imputation.In the discovery stage,we found three significant SNPs?rs111637561,rs1004819 and rs147158164 respectively?and rs111637561?P = 5.89 x 10-10;OR = 1.76;95% CI: 1.44 2.15?reached the GWAS significance.Further step conditional analysis showed that the three SNPs were all independent signals.In the validation stage,we found a series SNPs with GWAS significance and step conditional analysis also identified another three independent signals?rs78377598,rs12755265 and rs11576518 respectively?with only rs78377598?P = 2 ×10-9;OR = 1.27;95%CI: 1.17-1.38?shown GWAS significance.In order to verify the above results,we combined the two phases of data and further analysis found that the most significant point was rs6693659?P = 3.03 x 10-11?which was the same signal with rs78377598.Our LD analyses showed that the six SNPs found in the two stages were in low or moderate LD which further proved that these SNPs were all independent signals.Besides,we also performed haplotype analyses including all the six SNPs and we found Hap₃ and Hap₄ which carries the protective alleles of rs111637561 and rs78377598 were strongly associated with protective.We selected some significant SNPs from the discovery and combined stage into further annotation by use of ENCODE database.We noticed that these SNPs are located within known functional elements and rs111637561 was annotated as enhancer in Th17 cells and rs6693659 annotated as promoter in T helper naive cells and enhancer in keratinocyte.Conclusion: We performed fine mapping of psoriasis-associated IL23R locus in Chinese Han Population and identified six independent signals and potential functional variants.We provided research direction for the next functional experiment and give certain enlightenment for illuminating the differences between different population and specific target drugs in future.