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A Functional Candidate Screen for Coeliac Disease Genes

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A Functional Candidate Screen for Coeliac Disease Genes European Journal of Human Genetics (2006)14, 1215–1222 & 2006 Nature Publishing Group All rights reserved 1018-4813/06 $30.00 www.nature.com/ejhg ARTICLE A functional candidate screen for coeliac disease genes Christine R Curley1,4, Alienke J Monsuur2,4, Martin C Wapenaar2, John D Rioux1,3 and Cisca Wijmenga*,2 1The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; 2Complex Genetics Section, DBG-Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands; 3Universite´ de Montreal and the Montreal Heart Institute/Institut de Cardiologie de Montreal, Montreal, Quebec, Canada It is increasingly evident that different inflammatory disorders show some overlap in their pathological features, concurrence in families and individuals, and shared genetic factors. This might also be true for coeliac disease, a chronic inflammatory disorder of the gastrointestinal system, which shares two linkage regions with inflammatory bowel disease: on chromosome 5q31 (CELIAC2 and IBD5) and 19p13 (CELIAC4 and IBD6). We hypothesised that these regions contain genes that contribute to susceptibility to both disorders. The overlapping 5q31 region contains only five positional candidate genes, whereas the overlapping 19p13 region has 141 genes. As the common disease gene probably plays a role in inflammation, we selected five functional candidate genes from the 19p13 region. We studied these 10 positional and functional candidate genes in our Dutch coeliac disease cohort using 44 haplotype tagging single-nucleotide polymorphisms. Two genes from 19p13 showed a small effect on familial clustering: the cytochrome P450 F3 gene CYP4F3 (Pnominal 0.0375, odds ratio (OR) 1.77) and CYP4F2 (Pnominal 0.013, OR 1.33). CYP4F3 and CYP4F2 catalyse the inactivation of leukotriene B4 (LTB4), a potent mediator of inflammation responsible for recruitment and activation of neutrophils. The genetic association of LTB4- regulating gene variants connects the innate immune response of neutrophil mobilisation with that of the established Th1 adaptive immunity present in coeliac disease patients. The findings in coeliac disease need to be replicated. Expanding genetic association studies of these cytochrome genes to other inflammatory conditions should reveal whether their causative influence extends beyond coeliac disease. European Journal of Human Genetics (2006) 14, 1215–1222. doi:10.1038/sj.ejhg.5201687; published online 12 July 2006 Keywords: coeliac disease; inflammatory bowel disease; MYO9B; inflammation; candidate gene study; IBD5 Introduction impaired intestinal epithelial barrier.1 It is a complex genetic Coeliac disease is a chronic disease characterised by an disorder, involving multiple genetic variants. Genetic inflammatory response in the gastrointestinal tract and an studies on coeliac disease patients indicate that multiple chromosomal regions predispose to disease susceptibility, confirming the suggestion that common genes contribute *Correspondence: Professor C Wijmenga, Complex Genetics Section, Stratenum 2.117, DBG-Department of Biomedical Genetics, University to this disorder. Two of the coeliac disease loci, CELIAC2 on 2,3 Medical Centre Utrecht, PO Box 85060, 3508 AB Utrecht, The Nether- chromosome 5q23–q33 and CELIAC4 on 19p13.1, coin- lands. Tel: þ 31 30 253 8427; Fax: þ 31 30 253 8479; cide with linkage regions for inflammatory bowel disease E-mail: [email protected] (IBD),4,5 giving rise to the hypothesis of common disease 4These authors have contributed equally to this work. Received 14 December 2005; revised 18 May 2006; accepted 30 May susceptibility. The IBD5 and IBD6 loci on 5q31 and 19p13.1, 2006; published online 12 July 2006 respectively, are among the most significant and consistently Screen for coeliac disease genes CR Curley et al 1216 replicated IBD loci.6,7 There is ample evidence that influencing inflammation in the gut. The CELIAC2 locus (auto)immune-related disorders share some of their genetic on 5q23–q33 overlaps with a 250 kb haplotype on 5q31 susceptibility factors, the best examples being variations in associated with Crohn’s disease (IBD5).16 The implicated the CTLA-4 gene8 and PTPN22,9–11 both of which help haplotype contains five genes (P4HA2, IRF1, SLC22A5/ regulate T-cell responsiveness. OCTN2, SLC22A4/OCTN1, PDLIM3) (see Table 1), all of IBD, clinically classified as Crohn’s disease and ulcerative which are positional candidate genes for coeliac disease colitis, also shows a chronic inflammation of the gastro- pathogenesis. The CELIAC4 locus ranging from 15.38 to intestinal tract.6 Coeliac disease and IBD co-occur in 21.08 Mb (99% confidence interval (CI), Ensembl version families and patients, with an approximately five-fold 35) lies completely within the IBD6 locus, which spans a increased prevalence of IBD in coeliac disease patients,12 – 15 large part of chromosome 19p. Of the 141 genes in the further suggesting common pathophysiological mechan- overlapping region, five are known to be involved in isms for both diseases. inflammation and were considered as functional candidate The sharing of the linkage regions, the concurrence in genes: CYP4F3, CYP4F2, HSH2D, IL12RB1 and IFI30 (see patients and the pathological commonalities between Table 1). A complementary approach to identifying the coeliac disease and IBD led us to hypothesise that genes susceptibility gene for coeliac disease in the chromosome on chromosomes 5q31 and 19p13.1 might be associated 19 region involves fine-mapping of the region. We with susceptibility for both disorders, most probably by simultaneously undertook such a strategy, which led to Table 1 Overview of the 10 positional and functional candidate genes studied in relation to the overlapping regions in coeliac disease and IBD Gene No. of tag name Chromosome Location (bps) Function References SNPsa P4HA2 5 131 556 202–131 590 458 Prolyl 4-hydroxylase a-2 subunit precursor. Catalyses the 25 F post-translational formation of 4-hydroxyproline in –Xaa– Pro–Gly– sequences in collagens and other proteins PDLIM4 5 131 621 285–131 637 046 PDZ and LIM domain 4. Interacts with the LIM domain with 16 F the second and fourth PDZ domains of PTPN13 SLC22A4 5 131 658 043–131 707 796 Organic cation/carnitine transporter 1 (solute carrier family 16 5 22, member 4). Sodium-ion-dependent, low-affinity carnitine transporter. Defects in SLC22A4 may be a cause of susceptibility to Crohn’s disease and rheumatoid arthritis SLC22A5 5 131 733 343–131 759 202 Organic cation/carnitine transporter 2 (solute carrier family 16 2 22). Sodium-ion-dependent, high-affinity carnitine transporter. Involved in the active cellular uptake of carnitine. Transports one sodium ion with one molecule of carnitine Defects are the cause of systemic primary carnitine deficiency and may be a cause of susceptibility to Crohn’s disease IRF1 5 131 846 678–131 854 333 Interferon regulatory factor 1. Specifically binds to the 16 F upstream regulatory region of type I IFN and IFN-inducible MHC class I genes (the interferon consensus sequence) and activates those genes. Deletion or rearrangement of IRF1 are a cause of preleukaemic myelodysplastic syndrome and of acute myelogenous leukaemia CYP4F3 19 15 613 226–15 631 234 Member of P450 family of cytochromes. Catalyses the 26 – 28 8 inactivation of leukotriene B4 (LTB4), a potent mediator of inflammation CYP4F2 19 15 849 834–15 869 885 Member of P450 family of cytochromes. Catalyses the 24,29 8 inactivation of LTB4, a potent mediator of inflammation HSH2D 19 16 115 501–16 130 375 Target of the two most important signalling pathways of T- 30,31 5 cell activation; T-cell receptor antigen signalling and costimulation of the naive T cell IL12RB1 19 18 030 806–18 104 521 IL-12 receptor b chain 1, which is involved in inducing cell- 32 – 34 3 mediated immunity to intracellular pathogens via the Th1 pathway and interferon production. Deficiency leads to impaired mycobacterial immunity. Large amounts of IL-12 are secreted in mice with an NOD2 mutation in response to TLR2, which facilitates a Th1 response IFI30 19 18 145 579–18 149 927 Induced by interferon-g 35 2 aSeven of the 16 haploblock tagging SNPs on chromosome 5 are located in the genes, and the others are located outside the genes. European Journal of Human Genetics Screen for coeliac disease genes CR Curley et al 1217 the identification of the myosin IXB gene (MYO9B)asa Genotyping susceptibility gene for coeliac disease.17 The odds ratio Genomic DNA extracted from whole-blood samples was (OR) for this gene is lower than the expected OR for the used. Genotyping assays were designed using the Seque- CELIAC4 locus, leaving room for another susceptibility nom Assay Design program and genotypes were obtained gene in this locus. In this study, we report our association using the Sequenom Mass Array system at the Broad findings of the five positional candidate genes comprising Institute of MIT and Harvard as described by Gabriel the 250 kb haplotype on 5q31 and the five functional et al.18 Genotyping data was analysed for Hardy–Weinberg candidate genes from 19p13.1; all were tested using a equilibrium and allele frequency. The quality control haplotype block tag approach for association with coeliac criteria used to determine if genotyping results were disease in a cohort of Dutch patients. successful were: a minimum of 75% genotyping success for each SNP, Hardy–Weinberg equilibrium values 40.01 and observed heterozygosity 40.5%. Of 44 SNPs tested in the region, 42 SNPs passed the above criteria (one was Materials and methods monomorphic and the other failed owing to Hardy– Samples Weinberg errors). A case–control cohort consisting of 309 independent coeliac disease patients and 358 independent controls, all Statistical analysis of Dutch Caucasian origin, was used for the genetic Allele and haplotype counts in cases versus controls were association study. Patients were diagnosed according to analysed for association. A single-marker and multimarker the ESPGHAN criteria and approximately 93% of the association study for each gene in the case–control cohort 2 patients were HLA-DQ2 positive.
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