Genetic susceptibility for inflammatory bowel disease across ethnicities and diseases

The inflammatory bowel diseases (IBD), encompassing Crohn’s disease (CD) and ulcerative colitis (UC), have a broad disease spectrum and disease course and response to therapy are unpredictable. We need to understand the aetiology and the influence of genetic risk factors. This thesis contributes to this by identifying 38 new genetic risk factors. We show that the majority of genetic risk factors are shared between populations. A small proportion differs between populations, possibly environmental factors underlie this. Furthermore we replicated a few UC associated loci, which encode genes with functions in the intestinal barrier. We also developed a method to select genetic risk factors based on their relationship with gene expression, hypothesis that these represent biologically relevant signals. In this way we identified 2 new CD loci.In order to make a translation to biologically relevant processes we investigated the influence of genetic risk factors on gene expression in the Th17/IL23 pathway, a pathway that is important in IBD pathogenesis. We didn’t find a correlation and we expect this is due to the fact that gene expression is cell specific and we used a mix of cells. Lastly, we investigated the overlap in genetic risk factors between IBD and a group of diseases that occur often with IBD: the extra-intestinal manifestations and with a disease that occurs after allogeneic cell transplantation and resembles CD: gastro-intestinal graft-.vs.-host disease. We find substantial overlap, not only based on genetic factors, but also based on co-expression of genes and protein-protein interaction

Complex host genetics influence the microbiome in inflammatory bowel disease

Background: Human genetics and host-associated microbial communities have been associated independently with a wide range of chronic diseases. One of the strongest associations in each case is inflammatory bowel disease (IBD), but disease risk cannot be explained fully by either factor individually. Recent findings point to interactions between host genetics and microbial exposures as important contributors to disease risk in IBD. These include evidence of the partial heritability of the gut microbiota and the conferral of gut mucosal inflammation by microbiome transplant even when the dysbiosis was initially genetically derived. Although there have been several tests for association of individual genetic loci with bacterial taxa, there has been no direct comparison of complex genome-microbiome associations in large cohorts of patients with an immunity-related disease. Methods: We obtained 16S ribosomal RNA (rRNA) gene sequences from intestinal biopsies as well as host genotype via Immunochip in three independent cohorts totaling 474 individuals. We tested for correlation between relative abundance of bacterial taxa and number of minor alleles at known IBD risk loci, including fine mapping of multiple risk alleles in the Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) gene exon. We identified host polymorphisms whose associations with bacterial taxa were conserved across two or more cohorts, and we tested related genes for enrichment of host functional pathways. Results: We identified and confirmed in two cohorts a significant association between NOD2 risk allele count and increased relative abundance of Enterobacteriaceae, with directionality of the effect conserved in the third cohort. Forty-eight additional IBD-related SNPs have directionality of their associations with bacterial taxa significantly conserved across two or three cohorts, implicating genes enriched for regulation of innate immune response, the JAK-STAT cascade, and other immunity-related pathways. Conclusions: These results suggest complex interactions between genetically altered host functional pathways and the structure of the microbiome. Our findings demonstrate the ability to uncover novel associations from paired genome-microbiome data, and they suggest a complex link between host genetics and microbial dysbiosis in subjects with IBD across independent cohorts. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0107-1) contains supplementary material, which is available to authorized users

Genetic characterisation of the CARD9-locus and Inflammatory Bowel Disease

INTRODUCTION: Inflammatory Bowel Disease (IBD) are common, chronic gastrointestinal inflammatory disorders. The major forms are Crohn’s disease (CD) and ulcerative colitis (UC). The pathogenesis consists of an aberrant immune response in reaction to normal gastrointestinal flora in a genetically susceptible host. The genetic factors are increasingly uncovered. Recently, locus 9q34.3 was found to be associated with IBD. There is strong linkage disequilibrium (LD) in this ~120 kb spanning locus, which complicates the identification of the candidate gene and the causal mutation. CARD9 is a likely candidate gene, because its encoded protein is involved in the differentiation of T cells in type 17 helper T cells, which are associated with immune related diseases. In this study several steps were taken to identify a common causal mutation which explains the association with IBD. MATERIAL AND METHODS: The correlation between the risk alleles of the associated SNPs and gene expression (eQTL-effect) was investigated. The region was finemapped by testing four additional single nucleotide polymorphisms (SNPs) in 534 IBD cases and 600 controls. Exon sequencing of CARD9 was performed on 300 IBD cases and 350 controls. The found mutation in CARD9 was genotyped in 826 Dutch IBD cases and 1264 controls. Several deletion polymorphisms are described in this region; Trityper was used to identify deletion polymorphisms in this region. RESULTS: The risk alleles of the associated SNPs are correlated with higher expression of CARD9. With finemapping we were able to narrow down the region. The region with strongest LD with the associated SNPs is the region ~16 kb upstream of CARD9. The highest association signal was found in CARD9. Sequencing results identified a rare splice site mutation, which protects against UC. This mutation was replicated in the Dutch cohort. No difference was seen in expression level of CARD9 between different genotypes for the splice site mutation. Several deletion polymorphisms were identified with Trityper. These deletions have the same eQTL-effect as the associated SNPs, but were not associated with IBD. DISCUSSION: This study indicates that CARD9 is the candidate gene for association with IBD, because a mutation which protects against UC was found. However, the splice site mutation turned out not to be the causal mutation. The identified deletion polymorphisms are also not plausible as causal mutation. Extensive finemapping of the region is necessary to further narrow down the region in order to find a causal mutation.

Extraintestinal Manifestations and Complications in Inflammatory Bowel Disease: From Shared Genetics to Shared Biological Pathways

Background: The clinical presentation of the inflammatory bowel diseases (IBD) is extremely heterogenous and is characterized by various extraintestinal manifestations and complications (EIM). Increasing genetic insight for IBD and EIM shows multiple shared susceptibility loci. We hypothesize that, next to these overlapping genetic risk loci, distinct disease pathways are shared between IBD and EIM. Methods: The overlapping genetic risk loci for IBD and its EIM were searched in literature. We assessed shared disease pathways by performing an extensive pathway analysis by protein-protein interaction and cotranscriptional analysis, using both publicly available and newly developed databases. Results: Reliable genetic data were available for primary sclerosing cholangitis, ankylosing spondylitis, decreased bone mineral density, colorectal carcinoma, gallstones, kidney stones, and deep venous thrombosis. We found an extensive overlap in genetic risk loci, especially for IBD and primary sclerosing cholangitis and ankylosing spondylitis. We identified 370 protein-protein interactions, of which 108 are statistically specific. We identified 446 statistically specific cotranscribed gene pairs. The interactions are shown to cluster in specific biological pathways. Conclusions: We show that the pathogenetic overlap between IBD and its EIM extends beyond shared risk genes to distinctive shared biological pathways. We define genetic background as a risk factor for IBD-EIM alongside known mechanisms such as malabsorption and medication. Clustering patients based on distinctive pathways may enable stratification of patients to predict development of EIM

Correlation of Genetic Risk and Messenger RNA Expression in a Th17/IL23 Pathway Analysis in Inflammatory Bowel Disease

Background: The Th17/IL23 pathway has both genetically and biologically been implicated in the pathogenesis of the inflammatory bowel diseases (IBD), Crohn's disease, and ulcerative colitis. So far, it is unknown whether and how associated risk variants affect expression of the genes encoding for Th17/IL23 pathway proteins. Methods: Ten IBD-associated SNPs residing near Th17/IL23 genes were used to construct a genetic risk model in 753 Dutch IBD cases and 1045 controls. In an independent cohort of 40 Crohn's disease, 40 ulcerative colitis, and 40 controls, the genetic risk load and presence of IBD were correlated to quantitative PCR-generated messenger RNA (mRNA) expression of 9 representative Th17/IL23 genes in both unstimulated and PMA/CaLo stimulated peripheral blood mononuclear cells. In 1240 individuals with various immunological diseases with whole genome genotype and mRNA-expression data, we also assessed correlation between genetic risk load and differential mRNA expression and sought for SNPs affecting expression of all currently known Th17/IL23 pathway genes (cis-expression quantitative trait locus). Results: The presence of IBD, but not the genetic risk load, was correlated to differential mRNA expression for IL6 in unstimulated peripheral blood mononuclear cells and to IL23A and RORC in response to stimulation. The cis-expression quantitative trait locus analysis showed little evidence for correlation between genetic risk load and mRNA expression of Th17/IL23 genes, because we identified for only 2 of 22 Th17/IL23 genes a cis-expression quantitative trait locus single nucleotide polymorphism that is also associated to IBD (STAT3 and CCR6). Conclusions: Our results suggest that only the presence of IBD and not the genetic risk load alters mRNA expression levels of IBD-associated Th17/IL23 genes

Genome-wide association scan in north Indians reveals three novel HLA-independent risk loci for ulcerative colitis

Objective Over 100 ulcerative colitis (UC) loci have been identified by genome-wide association studies (GWASs) primarily in Caucasians (CEUs). Many of them have weak effects on disease susceptibility, and the bulk of the heritability cannot be ascribed to these loci. Very little is known about the genetic background of UC in non-CEU groups. Here we report the first GWAS on UC in a genetically distinct north Indian (NI) population

Complex host genetics influence the microbiome in inflammatory bowel disease

Abstract Background Human genetics and host-associated microbial communities have been associated independently with a wide range of chronic diseases. One of the strongest associations in each case is inflammatory bowel disease (IBD), but disease risk cannot be explained fully by either factor individually. Recent findings point to interactions between host genetics and microbial exposures as important contributors to disease risk in IBD. These include evidence of the partial heritability of the gut microbiota and the conferral of gut mucosal inflammation by microbiome transplant even when the dysbiosis was initially genetically derived. Although there have been several tests for association of individual genetic loci with bacterial taxa, there has been no direct comparison of complex genome-microbiome associations in large cohorts of patients with an immunity-related disease. Methods We obtained 16S ribosomal RNA (rRNA) gene sequences from intestinal biopsies as well as host genotype via Immunochip in three independent cohorts totaling 474 individuals. We tested for correlation between relative abundance of bacterial taxa and number of minor alleles at known IBD risk loci, including fine mapping of multiple risk alleles in the Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) gene exon. We identified host polymorphisms whose associations with bacterial taxa were conserved across two or more cohorts, and we tested related genes for enrichment of host functional pathways. Results We identified and confirmed in two cohorts a significant association between NOD2 risk allele count and increased relative abundance of Enterobacteriaceae, with directionality of the effect conserved in the third cohort. Forty-eight additional IBD-related SNPs have directionality of their associations with bacterial taxa significantly conserved across two or three cohorts, implicating genes enriched for regulation of innate immune response, the JAK-STAT cascade, and other immunity-related pathways. Conclusions These results suggest complex interactions between genetically altered host functional pathways and the structure of the microbiome. Our findings demonstrate the ability to uncover novel associations from paired genome-microbiome data, and they suggest a complex link between host genetics and microbial dysbiosis in subjects with IBD across independent cohorts

Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans

<p>Candida albicans is the most common human fungal pathogen causing mucosal and systemic infections. However, human antifungal immunity remains poorly defined. Here by integrating transcriptional analysis and functional genomics, we identified Candida-specific host defence mechanisms in humans. Candida induced significant expression of genes from the type I interferon pathway in human peripheral blood mononuclear cells. This unexpectedly prominent role of type I interferon pathway in anti-Candida host defence was supported by additional evidence. Polymorphisms in type I interferon genes modulated Candida-induced cytokine production and were correlated with susceptibility to systemic candidiasis. In in vitro experiments, type I interferons skewed Candida-induced inflammation from a Th17 response towards a Th1 response. Patients with chronic mucocutaneous candidiasis displayed defective expression of genes in the type I interferon pathway. These findings indicate that the type I interferon pathway is a main signature of Candida-induced inflammation and has a crucial role in anti-Candida host defence in humans.</p>