Early-onset autoimmune vitiligo associated with an enhancer variant haplotype that upregulates class II HLA expression.

Vitiligo is an autoimmune disease in which melanocyte destruction causes skin depigmentation, with 49 loci known from previous GWAS. Aiming to define vitiligo subtypes, we discovered that age-of-onset is bimodal; one-third of cases have early onset (mean 10.3 years) and two-thirds later onset (mean 34.0 years). In the early-onset subgroup we found novel association with MHC class II region indel rs145954018, and independent association with the principal MHC class II locus from previous GWAS, represented by rs9271597; greatest association was with rs145954018del-rs9271597A haplotype (P = 2.40 × 10-86, OR = 8.10). Both rs145954018 and rs9271597 are located within lymphoid-specific enhancers, and the rs145954018del-rs9271597A haplotype is specifically associated with increased expression of HLA-DQB1 mRNA and HLA-DQ protein by monocytes and dendritic cells. Thus, for vitiligo, MHC regulatory variation confers extreme risk, more important than HLA coding variation. MHC regulatory variation may represent a significant component of genetic risk for other autoimmune diseases.

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

Vitiligo is an autoimmune disease in which depigmented skin results from the destruction of melanocytes, with epidemiological association with other autoimmune diseases. In previous linkage and genome-wide association studies (GWAS1 and GWAS2), we identified 27 vitiligo susceptibility loci in patients of European ancestry. We carried out a third GWAS (GWAS3) in European-ancestry subjects, with augmented GWAS1 and GWAS2 controls, genome-wide imputation, and meta-analysis of all three GWAS, followed by an independent replication. The combined analyses, with 4,680 cases and 39,586 controls, identified 23 new significantly associated loci and 7 suggestive loci. Most encode immune and apoptotic regulators, with some also associated with other autoimmune diseases, as well as several melanocyte regulators. Bioinformatic analyses indicate a predominance of causal regulatory variation, some of which corresponds to expression quantitative trait loci (eQTLs) at these loci. Together, the identified genes provide a framework for the genetic architecture and pathobiology of vitiligo, highlight relationships with other autoimmune diseases and melanoma, and offer potential targets for treatment.

Multiplex SNaPshot-a new simple and efficient CYP2D6 and ADRB1 genotyping method.

BACKGROUND: Reliable, inexpensive, high-throughput genotyping methods are required for clinical trials. Traditional assays require numerous enzyme digestions or are too expensive for large sample volumes. Our objective was to develop an inexpensive, efficient, and reliable assay for CYP2D6 and ADRB1 accounting for numerous polymorphisms including gene duplications. MATERIALS AND METHODS: We utilized the multiplex SNaPshot® custom genotype method to genotype CYP2D6 and ADRB1. We compared the method to reference standards genotyped using the Taqman Copy Number Variant Assay followed by pyrosequencing quantification and determined assigned genotype concordance. RESULTS: We genotyped 119 subjects. Seven (5.9 %) were found to be CYP2D6 poor metabolizers (PMs), 18 (15.1 %) intermediate metabolizers (IMs), 89 (74.8 %) extensive metabolizers (EMs), and 5 (4.2 %) ultra-rapid metabolizers (UMs). We genotyped two variants in the ß1-adrenoreceptor, rs1801253 (Gly389Arg) and rs1801252 (Ser49Gly). The Gly389Arg genotype is Gly/Gly 18 (15.1 %), Gly/Arg 58 (48.7 %), and Arg/Arg 43 (36.1 %). The Ser49Gly genotype is Ser/Ser 82 (68.9 %), Ser/Gly 32 (26.9), and Gly/Gly 5 (4.2 %). The multiplex SNaPshot method was concordant with genotypes in reference samples. CONCLUSIONS: The multiplex SNaPshot method allows for specific and accurate detection of CYP2D6 genotypes and ADRB1 genotypes and haplotypes. This platform is simple and efficient and suited for high throughput.

NLRP1 haplotypes associated with vitiligo and autoimmunity increase interleukin-1ß processing via the NLRP1 inflammasome.

Nuclear localization leucine-rich-repeat protein 1 (NLRP1) is a key regulator of the innate immune system, particularly in the skin where, in response to molecular triggers such as pathogen-associated or damage-associated molecular patterns, the NLRP1 inflammasome promotes caspase-1-dependent processing of bioactive interleukin-1ß (IL-1ß), resulting in IL-1ß secretion and downstream inflammatory responses. NLRP1 is genetically associated with risk of several autoimmune diseases including generalized vitiligo, Addison disease, type 1 diabetes, rheumatoid arthritis, and others. Here we identify a repertoire of variation in NLRP1 by deep DNA resequencing. Predicted functional variations in NLRP1 reside in several common high-risk haplotypes that differ from the reference by multiple nonsynonymous substitutions. The haplotypes that are high risk for disease share two substitutions, L155H and M1184V, and are inherited largely intact due to extensive linkage disequilibrium across the region. Functionally, we found that peripheral blood monocytes from healthy subjects homozygous for the predominant high-risk haplotype 2A processed significantly greater (P < 0.0001) amounts of the IL-1ß precursor to mature bioactive IL-1ß under basal (resting) conditions and in response to Toll-like receptor (TLR) agonists (TLR2 and TLR4) compared with monocytes from subjects homozygous for the reference haplotype 1. The increase in basal release was 1.8-fold greater in haplotype 2A monocytes, and these differences between the two haplotypes were consistently observed three times over a 3-mo period; no differences were observed for IL-1α or TNFα. NLRP1 RNA and protein levels were not altered by the predominant high-risk haplotype, indicating that altered function of the corresponding multivariant NLRP1 polypeptide predisposes to autoimmune diseases by activation of the NLRP1 inflammasome.

Genome-wide association analyses identify 13 new susceptibility loci for generalized vitiligo.

We previously reported a genome-wide association study (GWAS) identifying 14 susceptibility loci for generalized vitiligo. We report here a second GWAS (450 individuals with vitiligo (cases) and 3,182 controls), an independent replication study (1,440 cases and 1,316 controls) and a meta-analysis (3,187 cases and 6,723 controls) identifying 13 additional vitiligo-associated loci. These include OCA2-HERC2 (combined P = 3.80 × 10(-8)), MC1R (P = 1.82 × 10(-13)), a region near TYR (P = 1.57 × 10(-13)), IFIH1 (P = 4.91 × 10(-15)), CD80 (P = 3.78 × 10(-10)), CLNK (P = 1.56 × 10(-8)), BACH2 (P = 2.53 × 10(-8)), SLA (P = 1.58 × 10(-8)), CASP7 (P = 3.56 × 10(-8)), CD44 (P = 1.78 × 10(-9)), IKZF4 (P = 2.75 × 10(-14)), SH2B3 (P = 3.54 × 10(-18)) and TOB2 (P = 6.81 × 10(-10)). Most vitiligo susceptibility loci encode immunoregulatory proteins or melanocyte components that likely mediate immune targeting and the relationships among vitiligo, melanoma, and eye, skin and hair coloration.

Analysis of genomewide association signals for nonsyndromic cleft lip/palate in a Kenya African Cohort.

Nonsyndromic cleft lip with or without cleft palate is a common birth defect with a wide range of prevalence among different populations, apparently highest in Asians and Amerindians and lowest in Africans. Recent genomewide association studies of European-derived and Asian populations have identified six confirmed loci for this phenotype: 1p22.1, 1q32.2 (IRF6), 8q24, 10q25.3, 17q22, and 20q12. However, there have thus far been no studies of these loci in African patients with nonsyndromic cleft lip with or without cleft palate. We carried out association analysis of SNPs in these six candidate chromosomal regions in 128 nonsyndromic cleft lip with or without cleft palate cases and 105 controls from the Rift Valley of Kenya. We observed no apparent association of this phenotype with any of these SNPs, though there was strong statistical power only for 8q24. These results indicate that at least the 8q24 locus does not play a major role in the pathogenesis of nonsyndromic cleft lip with or without cleft palate in east Africa, supporting locus heterogeneity for susceptibility to this phenotype among different major populations of the world.

Slc7a11 gene controls production of pheomelanin pigment and proliferation of cultured cells.

In mammals, >100 genes regulate pigmentation by means of a wide variety of developmental, cellular, and enzymatic mechanisms. Nevertheless, genes that directly regulate pheomelanin production have not been described. Here, we demonstrate that the subtle gray (sut) mouse pigmentation mutant arose by means of a mutation in the Slc7a11 gene, encoding the plasma membrane cystine/glutamate exchanger xCT [Kanai, Y. & Endou, H. (2001) Curr. Drug Metab. 2, 339-354]. A resulting low rate of extracellular cystine transport into sut melanocytes reduces pheomelanin production. We show that Slc7a11 is a major genetic regulator of pheomelanin pigment in hair and melanocytes, with minimal or no effects on eumelanin. Furthermore, transport of cystine by xCT is critical for normal proliferation, glutathione production, and protection from oxidative stress in cultured cells. Thus, we have found that the Slc7a11 gene controls the production of pheomelanin pigment directly. Cells from sut mice provide a model for oxidative stress-related diseases and their therapies.

Genome-wide scan of Graves' disease: evidence for linkage on chromosome 5q31 in Chinese Han pedigrees.

Graves' disease (GD), which is a common organ-specific autoimmune disorder, is multifactorial and develops in genetically susceptible individuals. Despite many studies of candidate genes, only associations with human leukocyte antigen and cytotoxic T lymphocyte antigen 4 have been generally detected, and the number of susceptibility genes remains unknown. To identify chromosomal regions contributing to GD, we conducted a genome-wide scan on 322 individuals from 54 Chinese Han multiplex GD pedigrees. Parametric linkage analysis revealed the strongest evidence for linkage at D5S436 on chromosome 5q31, with a maximum two-point LOD score of 2.8 and a maximum multipoint LOD score of 2.3. To further assess the significance of this suggestive finding, we typed four additional markers around D5S436 in this chromosome region, and a maximum two-point LOD score of 4.31 and a maximum multipoint LOD score of 4.12 were obtained for marker D5S2090 (with heterogeneity, = 0.38). Nonparametric multipoint analysis also showed significant excess allele sharing, with a P value as low as 0.001, at the same locus. Our findings provide evidence for a susceptibility locus for GD on chromosome 5q31 and support the existence of genetic heterogeneity in GD.

[The human major histocompatibility complex region is not a major susceptibility locus for Graves disease among the Hans in north of China].

OBJECTIVE: To determine if the human major histocompatibility complex (MHC) region located on chromosome 6 p21 is a major susceptibility locus for Graves' disease (GD) among the Hans in North of China. METHODS: Four highly polymorphic microsatellite markers spanning the entire region of chromosome 6 p21 were employed to screen the DNA from blood samples of 54 Han multiplex families with GD (322 individuals) in Liaoning Province, northeast China. Tow-point and multi-point Lod scores were calculated under different levels of penetrance, assuming both dominant and recessive models. Multipoint nonparametric linkage (NPL) scores were also calculated. RESULTS: The two-point Lod scores (theta = 0) and multipoint Lod scores for the 4 microsatellites were all less than -2 for all the markers tested, at all levels of penetrance, and in both the dominant and recessive modes of inheritance. No family showed a two-point Lod score or a multipoint Lod score of 1.0 or even larger under the assumed inheritance models. The maximum multipoint Lod score was 0.55 under the assumption of genetic heterogeneity, with the proportion of linked families of 29%. P values of greater than 0.05 were observed for all the multipoint NPL scores obtained. CONCLUSION: No locus linked with GD among the Hans in North of China exists on chromosome 6 p21. Human MHC region is not a major susceptibility locus for northern Chinese Han Graves' disease.

[A linkage study of cytotoxic T lymphocyte-associated antigen 4 gene and Graves' disease in northern Chinese Han ethnic].

OBJECTIVE: To determine if the cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) gene, which is located on chromosome 2q31-q33, is the major susceptibility gene for Graves' disease (GD) of northern Chinese Han nationality. METHODS: Five highly polymorphic microsatellite markers spanning the entire region of chromosome 2q31-q33 were employed to screen 54 families with multiple incidences of GD (322 individuals) of northern Chinese Han nationality. Tow-point and multi-point Lod scores were calculated under different levels of penetrance, assuming both dominant and recessive models. Multipoint nonparametric linkage (NPL) scores were also calculated. RESULTS: Two-point Lod scores (theta = 0) and multipoint Lod scores of less than -2 were observed for all the markers tested, at all levels of penetrance, in both the dominant and recessive models of inheritance. P values of greater than 0.05 were observed for all the multipoint NPL scores obtained. CONCLUSION: We obtained evidence against the linkage of GD with chromosome 2q31-q33, thus we are of the opinion that CTLA-4 gene is not the major susceptibility locus for Graves' disease of northern Chinese Han nationality.