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Genome-Wide Association Study in Alopecia Areata Implicates Both Innate and Adaptive Immunity

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Genome-Wide Association Study in Alopecia Areata Implicates Both Innate and Adaptive Immunity Vol 466 | 1 July 2010 | doi:10.1038/nature09114 LETTERS Genome-wide association study in alopecia areata implicates both innate and adaptive immunity Lynn Petukhova1, Madeleine Duvic2, Maria Hordinsky3, David Norris4, Vera Price5, Yutaka Shimomura1, Hyunmi Kim1, Pallavi Singh1, Annette Lee6, Wei V. Chen7, Katja C. Meyer8, Ralf Paus8,9, Colin A. B. Jahoda10, Christopher I. Amos7, Peter K. Gregersen6 & Angela M. Christiano1,11 Alopecia areata (AA) is among the most highly prevalent human multiple lines of evidence4. AA hair follicles are surrounded by an autoimmune diseases, leading to disfiguring hair loss due to the immune infiltrate with activated T-helper cells (TH cells), cytotoxic T collapse of immune privilege of the hair follicle and subsequent cells (TC cells) and natural killer (NK) cells, characterized as a TH1- autoimmune attack1,2. The genetic basis of AA is largely unknown. type inflammatory response5,6. The notion of a collapse of immune We undertook a genome-wide association study (GWAS) in a privilege is thought to be a key event in triggering AA4,7. sample of 1,054 cases and 3,278 controls and identified 139 single Evidence supporting a genetic basis for AA stems from multiple nucleotide polymorphisms that are significantly associated with AA lines of research, including the observed heritability in first-degree (P # 5 3 1027). Here we show an association with genomic regions relatives8,9, twin studies10 and, most recently, from our family-based containing several genes controlling the activation and prolifera- linkage studies11. Although a number of candidate-gene association tion of regulatory T cells (Treg cells), cytotoxic T lymphocyte- studies were performed over the past two decades, the informative- associated antigen 4 (CTLA4), interleukin (IL)-2/IL-21,IL-2 ness of these studies was inherently limited by small sample sizes and receptor A (IL-2RA; CD25)andEos (also known as Ikaros family preselection of candidate genes. zinc finger 4; IKZF4), as well as the human leukocyte antigen (HLA) To determine the genetic architecture of AA, we genotyped or used region. We also find association evidence for regions containing publicly available data for up to 1,054 AA cases and 3,278 controls with genes expressed in the hair follicle itself (PRDX5 and STX17). A a combination of Illumina 610K and 550K arrays. We performed region of strong association resides within the ULBP (cytomegalo- association tests adjusted for residual population stratification virus UL16-binding protein) gene cluster on chromosome 6q25.1, (l 5 1.051) and found 139 single nucleotide polymorphisms (SNPs) encoding activating ligands of the natural killer cell receptor significant at 5 3 1027 (Fig. 1 and Supplementary Table 1). NKG2D that have not previously been implicated in an auto- Our analysis identified several susceptibility loci for AA, most of immune disease. By probing the role of ULBP3 in disease patho- which clustered into eight genomic regions and fell within discrete genesis, we also show that its expression in lesional scalp from linkage disequilibrium (LD) blocks (Fig. 2 and Table 1). These patients with AA is markedly upregulated in the hair follicle dermal include loci on chromosome 2q33.2 containing CTLA4, chro- sheath during active disease. This study provides evidence for the mosome 4q27 containing IL-2/IL-21, chromosome 6p21.32 contain- involvement of both innate and acquired immunity in the patho- ing the HLA, chromosome 6q25.1 harbouring the ULBP genes, genesis of AA. We have defined the genetic underpinnings of AA, chromosome 10p15.1 containing IL-2RA (CD25), and chromosome placing it within the context of shared pathways among auto- 12q13 containing Eos (IKZF4) and ERBB3. One SNP resides on chro- immune diseases, and implicating a novel disease mechanism, the mosome 9q31.1 within syntaxin 17 (STX17), and one resides on upregulation of ULBP ligands, in triggering autoimmunity. AA affects about 5.3 million people in the United States alone, 40 including males and females across all ethnic groups, with a lifetime 30 risk of 1.7% (refs 1, 2). Autoimmunity develops against the hair P follicle, resulting in non-scarring hair loss that may begin as patches 20 –log that can coalesce and progress to cover the entire scalp (alopecia 10 totalis) or eventually the entire body (alopecia universalis) (Sup- 0 plementary Fig. 1). The phenomenon of ‘sudden whitening of the 1 2 3 4 5 6 7 8 91011121315171921 14 16 18 20 22 hair’ is ascribed to the acute onset of AA at times of profound grief, Position in genome stress or fear3, in which the pigmented hair is selectively shed while Figure 1 | Manhattan plot of the joint analysis of the discovery GWAS and the white hair persists. AA spares the stem cell compartment and the replication GWAS. Results are plotted as negative log-transformed P attacks only the base of the hair follicle, which is surrounded by values from a genotypic association test controlled for residual population infiltrating lymphocytes. Despite these marked perturbations in the stratification as a function of the position in the genome. Odd chromosomes hair follicle, there is no permanent organ destruction, and regrowth are in green and even chromosomes in blue. Eight genomic regions contain of the hair remains possible. The concept of an autoimmune mech- SNPs that exceed the genome-wide significance threshold of 5 3 1027 (red anism as the basis for AA emerged during the twentieth century from line). 1Department of Dermatology, Columbia University, New York, New York 10032, USA. 2Department of Dermatology, M. D. Anderson Cancer Center, Houston, Texas 77030, USA. 3Department of Dermatology, University of Minnesota, Minneapolis, Minnesota 55455, USA. 4Department of Dermatology, University of Colorado, Denver, Colorado 80010, USA. 5Department of Dermatology, UCSF, San Francisco, California 94115, USA. 6The Feinstein Institute for Medical Research, North Shore LIJHS, Manhasset, New York 11030, USA. 7Department of Epidemiology, M. D. Anderson Cancer Center, Houston, Texas 77030, USA. 8Department of Dermatology, University of Lu¨beck, 23538 Lu¨beck, Germany. 9School of Translational Medicine, University of Manchester, Manchester M13 9PT, UK. 10Department of Biological Sciences, University of Durham, Durham DH1 3LE, UK. 11Department of Genetics and Development, Columbia University, New York, New York 10032, USA. 113 ©2010 Macmillan Publishers Limited. All rights reserved LETTERS NATURE | Vol 466 | 1 July 2010 Table 1 | Genes with significant association to AA Region Gene Function Strongest association (P value) Maximum odds ratio Involved in other autoimmune disease 2q33.2 CTLA4 Co-stimulatory family 3.55 3 10213 1.44 T1D, RA, CeD, MS, SLE, GD ICOS Co-stimulatory family 4.33 3 1028 1.32 4q27 IL-21/IL-2 T-, B- and NK-cell proliferation 4.27 3 1028 1.34 T1D, RA, CeD, PS 6q25.1 ULBP6 NKG2D activating ligand 4.49 3 10219 1.65 None ULBP3 NKG2D activating ligand 4.43 3 10217 1.52 None 9q31.1 STX17 Premature hair greying 3.60 3 1027 1.33 None 10p15.1 IL-2RA T-cell proliferation 1.74 3 10212 1.41 T1D, MS, GD, GV 11q13 PRDX5 Antioxidant enzyme 4.14 3 1027 1.33 MS 28 12q13 Eos (IKZF4)Treg transcription factor 3.21 3 10 1.34 T1D, SLE ERBB3 Epidermal growth factor receptor 1.27 3 1027 1.34 T1D, SLE 6p21.32 MICA NKG2D activating ligand 1.19 3 1027 1.44 T1D, RA, CeD, UC, PS, SLE (HLA) NOTCH4 Haematopoietic differentiation 1.03 3 1028 1.61 T1D, RA, MS C6orf10 Unknown 1.45 3 10216 2.36 T1D, RA, PS, GV BTNL2 Co-stimulatory family 2.11 3 10226 2.70 T1D, RA, UC, CD, SLE, MS, GV HLA-DRA Antigen presentation 2.93 3 10231 2.62 T1D, RA, CeD, MS, GV HLA-DQA1 Antigen presentation 3.60 3 10217 2.15 T1D, RA, CeD, MS, SLE, PS, CD, UC, GD HLA-DQA2 Antigen presentation 1.38 3 10235 5.43 T1D, RA HLA-DQB2 Antigen presentation 1.73 3 10213 1.60 RA Each of the eight regions implicated in our study contains multiple significant SNPs, which are detailed in Supplementary Tables 1 and 2. Here we display candidate genes within the implicated regions, and include the P value of the most significant SNP, and the odds ratio for the SNP with the largest effect estimate. Diseases are listed for which a GWAS or previous candidate gene study identified the same region (http://www.genome.gov/gwastudies, http://www.cdc.gov/genomics/hugenet): Crohn’s disease (CD), celiac disease (CeD), Graves disease (GD), generalized vitiligo (GV), multiple sclerosis (MS), psoriasis (PS), rheumatoid arthritis (RA), system lupus erythematosus (SLE), type I diabetes (T1D), and ulcerative colitis (UC). chromosome 11q13, upstream from peroxiredoxin 5 (PRDX5). control individuals or those with other inflammatory scalp disorders Several of these LD blocks coincide with regions of linkage that we (data not shown). Quantitative immunohistochemistry corroborated reported previously on chromosomes 6p (HLA), 6q (ULBPs), 10p a significantly increased number of ULBP31 cells in 16 additional AA (IL-2RA)and18p(PTPN2)11. We also identified an additional 163 samples (Fig. 3p). We also noted a massive inflammatory cell infiltrate SNPs that were nominally significant (1024 , P , 5 3 1027), which characterized by CD81CD31 T cells (Fig. 3g–l), but only rare NK cells include 12 regions containing genes involved in the immune response, (data not shown). Double immunostaining with an anti-CD8 and an notably IL-13, IL-6, IL-26, IFNG, SOCS1 and PTPN2 (Supplementary anti-NKG2D antibody revealed that most NKG2D1 cells were CD81 Tables 2 and 3). Finally, imputation analysis from HapMap release 2.2 T cells (Fig. 3m–o). These results suggest that the autoimmune identified additional statistically significant SNPs within each of the destruction in AA may be mediated in part by CD81NKG2D1 cyto- eight regions and one additional SNP in PTPN2 that raised it above toxic T cells, whose activation may be induced by upregulation of statistical significance (Supplementary Tables 3 and 4).
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