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ANKRD55 and DHCR7 Are Novel Multiple Sclerosis Risk Loci

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ANKRD55 and DHCR7 Are Novel Multiple Sclerosis Risk Loci Genes and Immunity (2012) 13, 253 --257 & 2012 Macmillan Publishers Limited All rights reserved 1466-4879/12 www.nature.com/gene ORIGINAL ARTICLE ANKRD55 and DHCR7 are novel multiple sclerosis risk loci I Alloza1,14, D Otaegui2,14, A Lopez de Lapuente1, A Antigu¨ edad3, J Varade´ 4,CNu´n˜ez4, R Arroyo5, E Urcelay4, O Fernandez6, L Leyva6, M Fedetz7, G Izquierdo8, M Lucas9, B Oliver-Martos6, A Alcina7, A Saiz10, Y Blanco10, M Comabella11, X Montalban11, J Olascoaga12, F Matesanz7,8,14 and K Vandenbroeck1,13,14 Multiple sclerosis (MS) shares some risk genes with other disorders hallmarked by an autoimmune pathogenesis, most notably IL2RA and CLEC16A. We analyzed 10 single-nucleotide polymorphisms (SNPs) in nine risk genes, which recently emerged from a series of non-MS genome-wide association studies (GWAS), in a Spanish cohort comprising 2895 MS patients and 2942 controls. We identified two SNPs associated with MS. The first SNP, rs6859219, located in ANKRD55 (Chr5), was recently discovered in a meta-analysis of GWAS on rheumatoid arthritis (RA), and emerged from this study with genome-wide significance (odds ratio (OR) ¼ 1.35; P ¼ 2.3 Â 10À9). The second SNP, rs12785878, is located near DHCR7 (Chr11), a genetic determinant of vitamin D insufficiency, and showed a size effect in MS similar to that recently observed in Type 1 diabetes (T1D; OR ¼ 1.10; P ¼ 0.009). ANKRD55 is a gene of unknown function, and is flanked proximally by the IL6ST-- IL31RA gene cluster. However, rs6859219 did not show correlation with a series of haplotype-tagging SNPs covering IL6ST--IL31RA, analyzed in a subset of our dataset (D0o 0.31; r2o 0.011). Our results expand the number of risk genes shared between MS, RA and T1D. Genes and Immunity (2012) 13, 253--257; doi:10.1038/gene.2011.81; published online 1 December 2011 Keywords: multiple sclerosis; polymorphism; susceptibility; ANKRD55; DHCR7; vitamin D INTRODUCTION that is, AFF3, ANKRD55, CCR6, CYP2R1, DHCR7, IL2RA, IL10, Multiple sclerosis (MS) is a heterogeneous chronic inflammatory PRDM1 and PXK, all of which emerged recently from GWAS on a disease of the central nervous system driven by a complex number of diseases and conditions different from MS (Table 1). pathogenesis characterized by demyelination and neurodegen- The screen was performed in a Spanish Caucasian cohort eration. Extensive epidemiological data on familial aggregation of comprising 2895 MS patients and 2942 controls, composed of the disease, in conjunction with twin and adoptee studies, argue four geographically separate collections; North of Spain (Basque for a polygenic, multifactorial mechanism.1 Since the advent of Country; 786 MS patients and 718 controls), South of Spain genome-wide association studies (GWAS), swift progress has been (Andalucı´a; 1104 MS patients and 1225 controls), East of Spain made in identification of risk loci for MS. Most allelic risk variants (Catalunya; 466 MS patients and 464 controls) and Central identified to date exhibit low penetrance and high frequency of Spain (Madrid; 539 cases and 535 controls). This cohort was the risk allele in unaffected subjects, bringing about modest odds recently used to successfully identify allelic risk variants in the ratios (ORs) that rarely exceed 1.2---exception made for the HLA KIF5A, CD226 and SH2B3 loci, originally discovered in RA and T1D, class II DR*15 haplotype that is identifiable with ORs of 2--3.4.2 as MS risk factors.3 Comparison of data from GWAS on various autoimmune/chronic We provide here a brief overview of the studies that have inflammatory disorders has been shown to be instrumental in enabled the discovery of the nine autoimmune risk genes referred uncovering both disease-specific and shared genetic risk factors. to above. AFF3 emerged originally from a GWAS on T1D, though The latter of these are indicative for intersection of common its association was short of genome-wide significance; rs11676922 pathogenic pathways across a spectrum of diverse conditions, and (or its genetic proxy rs1160542 (D0 ¼ 1, r2 ¼ 1)) located 48 kb 50 are therefore arguably of greater translational interest. The from the AFF3 transcription initiation site was subsequently archetypal, shared autoimmune risk gene is IL2RA that demon- identified and robustly validated as risk locus for RA and juvenile strates susceptibility effects in MS, Type 1 diabetes (T1D), Graves’ idiopathic arthritis.4--7 rs6859219 located in the ANKRD55 gene disease and rheumatoid arthritis (RA), albeit with divergent allelic was identified in a meta-analysis of RA GWAS, and successfully association patterns.1 replicated in the same study.6 An intronic SNP, rs2301436 in In an attempt to identify additional pan-autoimmune loci of FGFR10P, which flanks the CCR6 gene locus was first identified in relevance to MS, we performed a screen of 10 risk single- Crohn’s disease (CD).8 More recently, rs3093023 in the promoter nucleotide polymorphisms (SNPs) located in or nearby nine genes, area of CCR6 at 1.9 kb from the transcription initiation site 1Neurogenomiks Laboratory, Department of Neuroscience, University of the Basque Country UPV/EHU, Leioa, Spain; 2A´ rea de Neurociencias, Inst. Investigacio´n Sanitaria Biodonostia, San Sebastia´n, Spain; 3Servicio de Neurologı´a, Hospital de Basurto, Bilbao, Spain; 4Immunology Department Hospital Clinico San Carlos, Instituto de Investigacio´n Sanitaria San Carlos, Madrid, Spain; 5Multiple Sclerosis Unit, Neurology Department H. Clı´nico S. Carlos, Instituto de Investigacio´ n Sanitaria San Carlos, Madrid, Spain; 6Servicio de Neurologı´a y Laboratorio de Investigacio´n, Instituto de Neurociencias Clı´nicas del Hospital Regional Universitario Carlos Haya de Ma´laga, Ma´laga, Spain; 7Instituto de Parasitologı´a y Biomedicina ‘Lo´ pezNeyra’, CSIC, Granada, Spain; 8Unidad de Esclerosis Mu´ltiple, Hospital Virgen Macarena, Sevilla, Spain; 9Servicio de Biologı´a Molecular, Hospital Virgen Macarena, Sevilla, Spain; 10Neurology Service, Hospital Clinic and Institut d’Investigacio´ Biome`dica Pi i Sunyer, Barcelona, Spain; 11Centre d’Esclerosi Mu´ltiple de Catalunya, CEM- Cat, Unitat de Neuroimmunologia Clı´nica, Hospital Universitari Vall d’Hebron, Barcelona, Spain; 12Servicio de Neurologı´a, Unidad de Esclerosis Mu´ltiple, Hospital Donostia, San Sebastia´n, Spain and 13IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; 14These authors contributed equally to this work. Correspondence: Dr K Vandenbroeck, Neurogenomiks Laboratory, Department of Neuroscience, Universidad del Paı´s Vasco (UPV/EHU), Edificio 205, Planta --1, Parque Tecnolo´ gico de Bizkaia, Zamudio 48170, Spain. E-mail: [email protected] Received 23 June 2011; revised 3 October 2011; accepted 31 October 2011; published online 1 December 2011 ANKRD55 and DHCR7 are MS risk loci I Alloza et al 254 Table 1. Confirmed autoimmune loci and risk SNPs tested in the present study for association with MS Gene SNP Chromosome; Major/ Risk OR (95% CI); P-value Cases/controls Disease or conditionRef chromosome minor allele position allele a AFF3 rs11676922 Chr2; 100173372 T/A T 1.15 (1.10--1.20); 1.0 Â 10À14 12307/28975 RA6 a ANKRD55 rs6859219 Chr5; 55474337 C/A C 1.18 (1.07--1.28); 9.6 Â 10À12 12307/28975 RA6 a CCR6 rs3093023 Chr6; 167454280 G/A A 1.11 (1.06--1.16); 1.5 Â 10À11 12307/28975 RA6 CYP2R1 rs10741657 Chr11; 14871454 G/A G NA (NA); 3.27 Â 10À20 33996 Vitamin D insufficiency12 b G 1.04 (1.00--1.09); 3.0 Â 10À3 8517/10438 T1D14 (+ 1933 families) DHCR7 rs12785878 Chr11; 70845097 T/G G NA (NA); 2.12 Â 10À27 33996 Vitamin D insufficiency12 b G 1.07 (1.02--1.13); 1.2 Â 10À3 8517/10438 (+1933 T1D14 families) a IL2RA rs706778 Chr10; 6138955 C/T T 1.11 (1.06--1.17); 1.4 Â 10À11 12307/28975 RA6 IL10 rs3024505 Chr1; 205006527 C/T T 1.46 (1.31--1.62); 1.35 Â 10À12 1855/3091 UC19 T 1.26 (1.09--1.45); 1.9 Â 10À3 777/6197 UC20 T 1.24 (1.12--1.37); 2.1 Â 10À5 1689/6197 CD20 T 1.12 (1.07--1.17); 1.6 Â 10À14 22027/29082 CD21 T 1.19 (1.11--1.28); 4.0 Â 10À8 3273/12188 SLE22 C NA (NA); 1.9 Â 10À9 11781/13715 (+4342 T1D23 trios) C 1.32 (1.14--1.51); 1.5 Â 10À4 989/6197 T1D20 PRDM1 rs548234 Chr6; 106674727 T/C C 1.11 (NA); 2.1 Â 10À8 11350/24420 RA24 PRDM1 rs7746082 Chr6; 106541962 G/C C 1.17 (NA); 2.44 Â 10À10 5555/6638 CD8 a PXK rs13315591 Chr3; 58531881 T/C C 1.13 (1.04--1.23); 4.6 Â 10À8 12307/28975 RA6 Abbreviations: CD, Crohn’s disease; CI, confidence interval; MS, multiple sclerosis; NA, data not available; OR, odds ratio; RA, rheumatoid arthritis; SLE, systemic lupus erythematosus; SNP, single-nucleotide polymorphism; T1D, type 1 diabetes; UC, ulcerative colitis. aP-values refer to the full combined GWAS (genome- wide association studies) + replication dataset of cases and controls, while ORs (95% CI) are based on the replication dataset only (6768 cases, 8806 controls).6 bP-values refer to the combined dataset, while ORs (95 % CI) are based on the case/control set only (excluding families).14 emerged as risk factor for RA in populations of European ancestry, rs6911490, respectively, are in partial LD (D0 ¼ 0.76, r2 ¼ 0.265), while rs3093024, also located in the CCR6 promoter at 1.5 kb separated by a stretch of 87 kb and are located 50 from PRDM1.8,25 upstream from rs3093023 and in perfect linkage disequilibrium Similarly, the PRDM1 SNPs emerging from the RA and SLE studies, (LD) with it (D0 ¼ 1, r2 ¼ 1) in the European population, was rs548234 and rs6568431, respectively, are 21 kb apart, occur in LD identified as RA risk factor in the Japanese population.6,9 Further (D0 ¼ 0.92, r2 ¼ 0.69), and both are located 30 from PRDM1.22,24 evidence for the generalized involvement of the CCR6 gene region Neither of the UC/CD PRDM1 SNPs occurs in LD with any of the in autoimmune disease risk comes from two independent GWAS RA/SLE SNPs (D0p0.54, r2p0.09), an observation that may be on vitiligo each of which identified strongly associated SNPs indicative for the existence of independent susceptibility effects located 30--175 kb upstream from CCR6.10,11 The CYP2R1 and conferred either by allelic variants at the PRDM1 locus, or at any DHCR7 loci reached genome-wide significance in two GWAS on neighboring locus within reach of these discrete LD patterns.
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