Project details

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Functional characterization of genetic susceptibility variants of Celiac disease

Keywords:
transcription factor celiac disease autoimmune disease EMSA ChIP assay

Researchers:
V. Kumar
dr. S. Withoff
prof. dr. C. Wijmenga

Type of project:
Stage Wetenschap / Research project

Nature of the research:
Functional genomics. Interested students will be involved in ongoing research to reveal mechanistic links between genetic susceptibility variants and celiac disease pathogenesis.

Fields of study:
cell biology molecular biology genetics

Background / introduction
Single nucleotide polymorphisms (SNP) based genome wide association studies (GWAS) have been very successful in identifying genetic susceptibility factors to several complex autoimmune diseases, such as type 1 diabetes (T1D), rheumatoid arthritis (RA), celiac disease (CeD), and multiple sclerosis (MS).Our lab focuses on CeD. CeD is an autoimmune-mediated chronic inflammation of the small intestines that results from a T-cell mediated immune response to ingested gluten (Gluten is a protein present in Wheat, Barley, rye etc). Characteristic features of CeD include gluten-dependent damage of the mucosa of the small bowel (villous atrophy, crypt hyperplasia, symptoms of malabsorption). The genetic make-up of an individual contributes to disease susceptibility. It has been shown that siblings of CeD patients (who share 50% of their genome) have a 30 fold higher risk of developing CeD and that besides specific HLA alleles (DQ2 and DQ8) several other genetic factors are involved in the pathogenesis of this complex disorder. In a recent GWAS, aimed at identification of susceptibility genes for CeD, we have identified 57 independent (non-HLA) SNPs to be strongly associated with CeD.

One of the biggest surprises coming from GWAS studies was the observation that majority of the disease susceptibility variants are located within non-protein coding regions (intronic, UTR’s, promoters, enhancers etc). Currently, we are employing several bioinformatic tools and gene expression datasets to annotate functions of these SNPs. Interestingly, preliminary analysis indicates that several strong candidate SNPs affect gene expression by altering the binding sites for transcription factors. Presently we are validating these predictions by performing Electrophoretic Mobility Shift Assay (EMSA) and several other techniques like Chromatin Immuno-Precipitation (ChIP), Luciferase reporter assay etc.
Research question / problem definition
We intend to prove that the SNPs in question alter gene expression by changing transcription factor binding sites. This will be followed up by pathway analysis to predict which pathways are involved in CeD.
Workplan
We will summarize all CeD susceptibility SNPs identified thus far that alter binding sites of transcription factors. The candidate binding sites will be validated by performing EMSA, ChIP and other relevant techniques. A detailed working programme will be discussed with students.
References
Pervasive sharing of genetic effects in autoimmune disease.
Cotsapas C, et al. PLoS Genet. 2011 Aug;7(8):e1002254.

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
Anderson CA et al. Nat Genet. 2011 Mar;43(3):246-52. Epub 2011 Feb 6.

A genetic perspective on coeliac disease.
Trynka G, Wijmenga C, van Heel DA.
Trends Mol Med. 2010 Nov;16(11):537-50.

Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
Stahl EA, et al. Nat Genet. 2010 Jun;42(6):508-14.

Multiple common variants for celiac disease influencing immune gene expression.
Dubois PC, et al. Nat Genet. 2010 Apr;42(4):295-302.

Complex nature of SNP genotype effects on gene expression in primary human leucocytes. Heap GA, et al. BMC Med Genomics. 2009 Jan 7;2:1
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