MHC class II super-enhancer increases surface expression of HLA-DR and HLA-DQ and affects cytokine production in autoimmune vitiligo

Abstract

Genetic risk for autoimmunity in HLA genes is most often attributed to structural specificity resulting in presentation of self-antigens. Autoimmune vitiligo is strongly associated with the MHC class II region. Here, we fine-map vitiligo MHC class II genetic risk to three SNPs only 47 bp apart, located within a predicted super-enhancer in an intergenic region between HLA-DRB1 and HLA-DQA1, localized by a genomewide association study of 2,853 Caucasian vitiligo patients. The superenhancer corresponds to an expression quantitative trait locus for expression of HLA-DR and HLA-DQ RNA; we observed elevated surface expression of HLA-DR (P = 0.008) and HLA-DQ (P = 0.02) on monocytes from healthy subjects homozygous for the high-risk SNP haplotype. Unexpectedly, pathogen-stimulated peripheral blood mononuclear cells from subjects homozygous for the high-risk super-enhancer haplotype exhibited greater increase in production of IFN-γ and IL-1β than cells from subjects homozygous for the low-risk haplotype. Specifically, production of IFN-γ on stimulation of dectin-1, mannose, and Toll-like receptors with Candida albicans and Staphylococcus epidermidis was 2.5-and 2.9-fold higher in high-risk subjects than in low-risk subjects, respectively (P = 0.007 and P = 0.01). Similarly, production of IL-1β was fivefold higher in high-risk subjects than in low-risk subjects (P = 0.02). Increased production of immunostimulatory cytokines in subjects carrying the high-risk haplotype may act as an "adjuvant" during the presentation of autoantigens, tying together genetic variation in the MHC with the development of autoimmunity. This study demonstrates that for risk of autoimmune vitiligo, expression level of HLA class II molecules is as or more important than antigen specificity.A utoimmune diseases are a group of over 80 disorders that together affect 3-5% of the United States population (1, 2). Many autoimmune diseases are associated with genetic variation in the HLA class I and class II gene regions of the major histocompatibility complex (MHC) on chromosome 6p21.3. HLA class I molecules present peptide antigens on the surface of almost all cells, whereas HLA class II molecules present antigens on the surface of antigen-presenting cells, such as dendritic cells, mononuclear phagocytes, and B cells. Contributions of HLA molecules to autoimmunity have almost exclusively focused on antigenic diversity and specificity. Although polymorphisms in intergenic regions of the MHC might additionally affect the complex transcriptional regulation of HLA genes, the potential role of these noncoding regions in the pathogenesis of autoimmune diseases has received much less attention.Vitiligo is an autoimmune disease in which white spots of skin and overlying hair result from progressive destruction of melanocytes by autoreactive T cells (3). In previous genome-wide association studies of autoimmune vitiligo in European-derived Caucasian (EUR) populations, we have identified association with 27 different loci (4-6), most strongly with MHC class II r...

Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci

“…Detailed analyses on large sample sizes will be needed to disentangle the regulatory effects from the strong amino acid effects. While amino acid changes causing differential antigen display may be the primary autoimmune mechanism at the HLA locus, our data underscores the possibility that expression levels of HLA class II may also play a crucial and unappreciated role (35,36). Over the past several decades, there has been literature suggesting variation in expression among different HLA alleles (26,(37)(38)(39) -but to date the idea that this regulation changes with cell-state has not been established.…”

Genetics of Vitiligo

“…The Spritz group has shown that for both MHC class I ( HLA-A ) [68,69] and MHC class II ( HLA-DRB1/-DQA1 ) [70,71], the vitiligo-associated causal SNPs are located in transcriptional enhancer elements that up-regulate expression of the corresponding MHC genes, resulting in gain of function. Interestingly, the MHC class II association signal also constitutes a quantitative trait locus (QTL) for vitiligo age-of-onset [72].…”

“…Of these associations in Chinese, only that in the RNASET2-FGFR1OP-CCR6 region corresponds to an association detected in Caucasian patients [63]. Indeed, while MHC class I and class II region associations were detected in Caucasians [62,65,68,69,71] and Chinese [76], the specific underlying associations appear to be somewhat different. This is surprising, as a GWAS of vitiligo in Japanese [79] detected an MHC class I association with HLA-A*02:01 that appears identical to that in European-derived whites, while an immunocentric GWAS of vitiligo in Asian Indian and Pakistani patients detected an MHC class II association that similar to that European-derived whites [80], though more detailed MHC analysis in Indians [81] found class II association that was the same as in Chinese [76].…”

Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants

“…For TYR 21 , GZMB 53 , and MC1R 7 , principal vitiligo risk derives from missense substitutions, whereas for OCA2 6 and the MHC class I 54 and class II 55 loci principal vitiligo risk is associated with causal variation in nearby transcriptional regulatory elements. To assess the fraction of vitiligo-associated loci for which causal variation is likely regulatory, we carried out conditional logistic regression analysis of all loci to define independent association signals, and for each signal we compiled all variants that could not be statistically distinguished.…”