Fine-mapping Study Of The MHC Region For Vitiligo In Han Chinese Population

Background: Vitiligo is an idiopathic immune-related skin disorder,which is the most common depigmentation disease.It mainly affects the skin,hair and mucosa,and is characterized by milk-white patches with clear border.It is caused by selective destruction or dysfunction of the melanocytes in skin.Vitiligo often occurs in young adults before the age of 30 with no discomfort.Its prevalence rate ranges from 0.5% to 2% in the worldwide population,and about 0.56% in the Chinese population.Vitiligo is a tough skin disease and could not be completely cured.Due to its disfiguring appearance,patients have disturbances in mental health and experience low quality of life,which also increases the economic burden of the family and the society.Vitiligo is an acquired pigmentary disease,and researchers have found that severe sunburn,trauma,pregnancy,mental disorders and harmful chemicals may induce this disorder.In addition,the incidences of other autoimmune diseases in vitiligo patients are also higher than that in normal people.The pathogenesis of vitiligo has not yet been fully understood,and researchers have put forward several hypotheses,such as the autoimmune theory,the genetic theory,the neural theory,the oxidative stress theory,but these hypotheses could not be applied to all the conditions.Recently,much evidence has indicated the autoimmune theory and genetic theory,and some researchers have suggested vitiligo is caused by interplay between genetic and environmental risk factors that launches the autoimmune attack on melanocytes in the skin.The human leukocyte antigen(HLA)system plays a major role in human immune response.Therefore,it has been widely studied in immune-related diseases.The association studies between HLA and vitiligo started in the late 20 th century.In the early case-control studies for vitiligo,researchers used serological typing and PCR-based DNA typing experiments to detect HLA antigens or genes.Since 2010,researchers began to study the vitiligo susceptibility loci in the major histocompatibility complex(MHC)region using high-density DNA microarray in large scale samples,which is known as genome-wide association study.Although these methods have brought some achievements,there are some limitations,including high cost for the typing experiments and the technical shortcomings in directly detecting the HLA alleles and their corresponding amino acids that located in the MHC region.In 2013,Jia et al.developed the computational strategy SNP2 HLA,which enables researchers to study the relationship between HLA alleles and their corresponding amino acids and the immune-related diseases based on high-density DNA microarray data.This strategy brought some fruitful insights into the pathogenesis of autoimmune diseases,including psoriasis,systemic lupus erythematosus,Graves’ disease and so on,which accelerates our understanding of the genetic role of MHC variants in immune disorders.Object: Based on the population-specific MHC reference panel of Han Chinese,we performed fine-mapping analysis on vitiligo patients and controls using HLA imputation method to explore the role of genetic variants within the MHC region in the pathogenesis of vitiligo.Methods: Genome-wide single-nucleotide polymorphism(SNP)genotyping was performed on 1,149 vitiligo patients and 1,740 healthy controls in Han Chinese population using Illumina Human610-Quad Bead Chips.After quality control,SNP genotyping data of extended MHC region were extracted from the whole data.We then performed HLA imputation using SNP2 HLA based on the large-scale MHC reference panel of Han Chinese to investigate the associations between SNPs,classical HLA alleles and their corresponding amino acids and vitiligo.And then we performedstepwise conditional analysis to identify independent susceptibility loci for vitiligo.We also conducted linkage analysis,haplotype analysis,e QTL analysis,heritability analysis,gene-gene interaction analysis,genetic risk score calculation and genotype-phenotype analysis.Results: After post-imputation quality control,994 SNPs,13 classical HLA alleles and 40 HLA amino acid positions were found to be significantly associated with vitiligo(P < 2.32 × 10-6).Among them,there are seven four-digit HLA alleles,including three new alleles(HLA-DQB1*02:02、HLA-DQA1*02:01 and HLA-DPB1*17:01)and four previously reported alleles(HLA-B*13:02 、 HLA-C*06:02 、 HLA-A*30:01 and HLA-DRB1*07:01).Further stepwise conditional analysis identified four independent vitiligo-associated loci in the whole MHC region,including HLA-DQβ1 amino acid position 135,HLA-B amino acid positions 45-46,rs892666 and rs9268832.And by in-depth analysis,we also identified a super HLA haplotype HLA-A*30:01-C*06:02-B*13:02-DRB1*07:01-DQA1*02:01-DQB1*02:02-DPB1*17:01 that associated with vitiligo susceptibility.The e QTL analysis implied that HLA-G and HLA-DRA may be susceptible genes for vitiligo.The heritability analysis revealed that the variants in the MHC region could account for 6.2% of the phenotypic variance for vitiligo.The gene-gene interaction analysis suggested that rs9268832 may respectively interact with rs2051582 or rs11593576 in the development of vitiligo.The calculation of the genetic risk score showed that the overall risk scores of vitiligo patients were higher than that of the controls.Genotype-phenotype analysis suggested that amino acid position 135 of HLA-DQβ1 might be associated with the early-onset vitiligo.Conclusions: This is the first MHC fine-mapping study of vitiligo in Han Chinese population based on a population-specific large-scale MHC reference panel.And weidentified four independent vitiligo susceptibility loci in the whole MHC region.Our findings not only display the complex genetic architecture of MHC region for vitiligo in Han Chinese population,but also show the similarities and differences of vitiligo susceptibility HLA genes between different populations,which may lay the foundation for elucidating the role of MHC variants in the etiology of vitiligo in Han Chinese population.