A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the VSTM1 gene locus

• DOI: 10.1186/s13073-017-0404-6
• Publication Date: 2017-02-20T17:01:51Z
• Authors: Dilip Kumar; Kia Joo Puan; Anand Kumar Andia...; Bernett Lee; Geertje H. A. Wes...; Doreen Haase; Rossella Melchiotti; Zhuang Li; Nurhashikin Yusof; Josephine Lum; Geraldine Koh; Shihui Foo; Joe Yeong; Alexessander Cout...; Juha Pekkanen; Liang Dan Sun; Astrid Irwanto; Benjamin P. Fairfax; Vivek Naranbhai; John E. A. Common; Mark Tang; Chin Keh Chuang; Marjo-Riitta Jarv...; Julian C. Knight; Xuejun Zhang; Fook Tim Chew; Shyam Prabhakar; Liu Jianjun; De Yun Wang; Francesca Zolezzi; Michael Poidinger; E. Birgitte Lane; Linde Meyaard; Olaf Rötzschke
• Keywords: Male; 0301 basic medicine; genetic association; sequence analysis; VSTM1; Neutrophils; genotype; QH426-470; Monocytes; molecular pathology; single nucleotide polymorphism; binding affinity; HUMAN GENOME; GWAS; genetics; Genetics(clinical); TRANSCRIPTION; Receptors, Immunologic; Promoter Regions, Genetic; DNA METHYLATION; Genetics & Heredity; transcription factor YY1; DNA methylation; atopic dermatitis; adult; immunoglobulin receptor; R; SIGNAL INHIBITORY RECEPTOR; gene expression regulation; protein function; cohort analysis; Signal inhibitory receptor on leukocytes-1 (SIRL-1); unclassified drug; female; regulator protein; transcription factor PU 1; monocyte; Medicine; Molecular Medicine; Female; Life Sciences & Biomedicine; EXPRESSION; 610; chromatin immunoprecipitation; gene frequency; protein DNA binding; gel mobility shift assay; Polymorphism, Single Nucleotide; Article; Dermatitis, Atopic; Expression quantitative trait loci (eQTL); Young Adult; 03 medical and health sciences; promoter region; male; Asian People; signal inhibitory receptor on leukocyte 1; Journal Article; Genetics; bisulfite; Humans; controlled study; LEUKOCYTES-1; human; gene; protein expression; Molecular Biology; SIRL1 protein; gene identification; Atopic dermatitis; 0604 Genetics; Science & Technology; binding site; flow cytometry; human cell; Research; disease association; PU.1; Reactive oxygen species (ROS); VSTM1 gene; 1103 Clinical Sciences; molecular docking; DNA Methylation; gene function; Gene Expression Regulation; CPG ISLANDS; CpG island; gene expression; disease activity; protein determination; upregulation; Asian continental ancestry group; HUMAN PHAGOCYTES

Expression quantitative trait loci (eQTL) databases represent a valuable resource to link disease-associated SNPs to specific candidate genes whose gene expression is significantly modulated by the SNP under investigation. We previously identified signal inhibitory receptor on leukocytes-1 (SIRL-1) as a powerful regulator of human innate immune cell function. While it is constitutively high expressed on neutrophils, on monocytes the SIRL-1 surface expression varies strongly between individuals. The underlying mechanism of regulation, its genetic control as well as potential clinical implications had not been explored yet.Whole blood eQTL data of a Chinese cohort was used to identify SNPs regulating the expression of VSTM1, the gene encoding SIRL-1. The genotype effect was validated by flow cytometry (cell surface expression), correlated with electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP) and bisulfite sequencing (C-methylation) and its functional impact studied the inhibition of reactive oxygen species (ROS).We found a significant association of a single CpG-SNP, rs612529T/C, located in the promoter of VSTM1. Through flow cytometry analysis we confirmed that primarily in the monocytes the protein level of SIRL-1 is strongly associated with genotype of this SNP. In monocytes, the T allele of this SNP facilitates binding of the transcription factors YY1 and PU.1, of which the latter has been recently shown to act as docking site for modifiers of DNA methylation. In line with this notion rs612529T associates with a complete demethylation of the VSTM1 promoter correlating with the allele-specific upregulation of SIRL-1 expression. In monocytes, this upregulation strongly impacts the IgA-induced production of ROS by these cells. Through targeted association analysis we found a significant Meta P value of 1.14 × 10-6 for rs612529 for association to atopic dermatitis (AD).Low expression of SIRL-1 on monocytes is associated with an increased risk for the manifestation of an inflammatory skin disease. It thus underlines the role of both the cell subset and this inhibitory immune receptor in maintaining immune homeostasis in the skin. Notably, the genetic regulation is achieved by a single CpG-SNP, which controls the overall methylation state of the promoter gene segment.