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Romanos J.,University of Groningen | Romanos J.,Lebanese American University | Rosen A.,Umea University | Kumar V.,University of Groningen | And 23 more authors.
Gut | Year: 2014

Background The majority of coeliac disease (CD) patients are not being properly diagnosed and therefore remain untreated, leading to a greater risk of developing CD-associated complications. The major genetic risk heterodimer, HLA-DQ2 and DQ8, is already used clinically to help exclude disease. However, approximately 40% of the population carry these alleles and the majority never develop CD. Objective We explored whether CD risk prediction can be improved by adding non-HLA-susceptible variants to common HLA testing. Design We developed an average weighted genetic risk score with 10, 26 and 57 single nucleotide polymorphisms (SNP) in 2675 cases and 2815 controls and assessed the improvement in risk prediction provided by the non-HLA SNP. Moreover, we assessed the transferability of the genetic risk model with 26 non-HLA variants to a nested case-control population (n=1709) and a prospective cohort (n=1245) and then tested how well this model predicted CD outcome for 985 independent individuals. Results Adding 57 non-HLA variants to HLA testing showed a statistically significant improvement compared to scores from models based on HLA only, HLA plus 10 SNP and HLA plus 26 SNP. With 57 non-HLA variants, the area under the receiver operator characteristic curve reached 0.854 compared to 0.823 for HLA only, and 11.1% of individuals were reclassified to a more accurate risk group. We show that the risk model with HLA plus 26 SNP is useful in independent populations. Conclusions Predicting risk with 57 additional non-HLA variants improved the identification of potential CD patients. This demonstrates a possible role for combined HLA and non-HLA genetic testing in diagnostic work for CD.

Trynka G.,University of Groningen | Hunt K.A.,Queen Mary, University of London | Bockett N.A.,Queen Mary, University of London | Romanos J.,University of Groningen | And 62 more authors.
Nature Genetics | Year: 2011

Using variants from the 1000 Genomes Project pilot European CEU dataset and data from additional resequencing studies, we densely genotyped 183 non-HLA risk loci previously associated with immune-mediated diseases in 12,041 individuals with celiac disease (cases) and 12,228 controls. We identified 13 new celiac disease risk loci reaching genome-wide significance, bringing the number of known loci (including the HLA locus) to 40. We found multiple independent association signals at over one-third of these loci, a finding that is attributable to a combination of common, low-frequency and rare genetic variants. Compared to previously available data such as those from HapMap3, our dense genotyping in a large sample collection provided a higher resolution of the pattern of linkage disequilibrium and suggested localization of many signals to finer scale regions. In particular, 29 of the 54 fine-mapped signals seemed to be localized to single genes and, in some instances, to gene regulatory elements. Altogether, we define the complex genetic architecture of the risk regions of and refine the risk signals for celiac disease, providing the next step toward uncovering the causal mechanisms of the disease. © 2011 Nature America, Inc. All rights reserved.

Castellanos-Rubio A.,Immunogenetics Research Laboratory | Castellanos-Rubio A.,University of the Basque Country | Santin I.,Immunogenetics Research Laboratory | Irastorza I.,Pediatric Gastroenterology Unit | And 7 more authors.
Human Immunology | Year: 2010

An aberrant immune response triggered by dietary gluten is the main driving force underlying celiac disease (CD), but other biologic pathways that are dysregulated also participate in disease development. Genetic variation within these pathways might influence expression, contributing to susceptibility to CD. We have investigated the implication of ubiquitin D (UBD), a member of the ubiquitin-proteasome system that is strongly upregulated in the intestinal mucosa of active CD. Reverse transcriptase-polymerase chain reaction analysis of intestinal biopsy sample pairs (at diagnosis vs treated) from 30 CD patients confirmed overexpression of UBD in active disease tissue (fold change = 8.3; p = 0.0022). In silico prediction tools identified rs11724 as a putative regulatory single nucleotide polymorphism and association analysis of 468 CD patients and 459 controls revealed that the minor rs11724*C allele was more frequent among patients (minor allele frequency = 0.44 vs 0.39; odds ratio [OR] = 1.23; p = 0.028) and suggested a dominant allele effect (OR = 1.49; p = 0.0045). Correlation of the rs11724 genotype and UBD mRNA levels (OR = 0.76; p = 0.0021) further supports its implication in disease development. © 2010 American Society for Histocompatibility and Immunogenetics.

Castellanos-Rubio A.,Immunogenetics Research Laboratory | Caja S.,University of Tampere | Irastorza I.,University of the Basque Country | Fernandez-Jimenez N.,Immunogenetics Research Laboratory | And 5 more authors.
Autoimmunity | Year: 2012

Celiac Disease (CD) involves disturbance of the small-bowel mucosal vascular network, and transglutaminase autoantibodies (TGA) have been related to angiogenesis disturbance, a complex phenomenon probably also influenced by common genetic variants in angiogenesis-related genes. A set of genes with "angiogenesis" GO term identified in a previous expression microarray experiment (SCG2, STAB1, TGFA, ANG, ERBB2, GNA13, PML, CASP8, ECGF1, JAG1, HIF1A, TNFSF13 and TGM2) was selected for genetic and functional studies. SNPs that showed a trend for association with CD in the first GWAS were genotyped in 555 patients and 541 controls. Gene expression of all genes was quantified in 15 pairs of intestinal biopsies (diagnosis vs. GFD) and in three-dimensional HUVEC and T84 cell cultures incubated with TGA-positive and negative serum. A regulatory SNP in TNFSF13 (rs11552708) is associated with CD (p = 0.01, OR = 0.7). Expression changes in biopsies pointed to TGM2 and PML as up-regulated antiangiogenic genes and to GNA13, TGFA, ERBB2 and SCG2 as down-regulated proangiogenic factors in CD. TGA seem to enhance TGM2 expression in both cell models, but PML expression was induced only in T84 enterocytes while GNA13 and ERBB2 were repressed in HUVEC endothelial cells, with several genes showing discordant effects in each model, highlighting the complexity of gene interactions in the pathogenesis of CD. Finally, cell culture models are useful tools to help dissect complex responses observed in human explants. © Informa UK, Ltd.

Fernandez-Jimenez N.,Immunogenetics Research Laboratory | Fernandez-Jimenez N.,University of the Basque Country | Santin I.,Immunogenetics Research Laboratory | Irastorza I.,Pediatric Gastroenterology Unit | And 7 more authors.
Human Immunology | Year: 2011

Killer cell immunoglobulin-like receptors (KIRs) modulate natural killer (NK) and T-cell function by human leukocyte antigen class I interaction and have been implicated in celiac disease (CD). Qualitative expression of 16 KIR genes was determined in biopsies from 22 CD patients at diagnosis and after >2 years on a gluten-free diet (GFD). Quantitative expression analysis of KIR2DL4, KIR3DL1, KIR3DL3, and KLRC2 (a marker of an NK-reprogrammed T-cell subpopulation augmented in CD) was performed in 35 additional CD biopsy pairs and 14 non-CD control biopsies. No specific KIR expression profile was observed in CD. KIR3DL1 was more frequently expressed in active CD compared with GFD (p = 0.0312) and controls (p = 0.0008), with slightly increased levels in active disease. KLRC2 was overexpressed in active (p = 0.0037) and GFD (p = 0.0469) patients compared with non-CD controls and coexpressed with KIR3DL1. Results suggest the participation of KIR3DL1 overexpression in the overall immune activation seen in CD mucosa, which could be partly explained by the NK-like T-cell subpopulation increase. © 2011 American Society for Histocompatibility and Immunogenetics.

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