Noble, Colin Lamont

2018-05-14T10:15:08Z

2018-05-14T10:15:08Z

2010

The aims of this thesis were firstly to investigate gene expression profiles in human colonic and terminal ileal biopsies using microarray technology in a well phenotyped cohort of patients with Crohn's disease, ulcerative colitis and a control cohort. The role in disease pathogenesis of differentially expressed genes was investigated along with the expression of candidate genes identified by genome wide association study and cell lineage analysis. Parallel studies attempted to replicate the Nature Genetics publications of Peltekova and Stoll and colleagues who investigated the role the IBD5 locus and the DLG5 gene respectively in patients with inflammatory bowel disease.

In the healthy adult colon cluster analysis showed differences in gene expression between the right and left colon. (x²=25.1, p<0.0001). Developmental genes HOXA13, (p=2.3x10⁻¹⁶, HOXB13 (p <1xl0⁻⁴⁵), GL11 (p=4.0xl0⁻²⁴), and GLI3 (p=2.1x10⁻²⁸) primarily drove this separation.

Upregulated genes in the Crohn's disease biopsies compared to the controls included SAA1 (Fold change (FC) +7.5, p=1.47xl0⁻⁴¹) and REGL (FC +7.3, p=2.3xl0⁻¹⁶). Cellular detoxification genes including-SLC14A2 (FC -2.49, p= 0.00002) were downregulated. In the Crohn's disease terminal ileal biopsies diubiquitin (FC+11.3, p<1x10⁻⁴⁵), MMP3 (FC +7.4, p=1.3x10⁻¹¹) and IRTA1 (FC -11.4, p= 4.7xl0⁻¹²) were differentially expressed compared to controls. In the colon SAA1 (FC +6.3, p= 5.3xl0⁻⁸) was upregulated and TSLP (FC -2.3, p= 2.7xl0⁻⁶) was downregulated comparing non-inflamed Crohn's disease and control biopsies.

Of the Crohn's disease susceptibility genes identified by genome wide association scan IL-23A, JAK2 and STAT3 were upregulated in Crohn's disease confirming dysregulation of Thl7 signalling. Modest differential expression was also observed in a number of the autophagy genes, notably ATG16L1. When clustering analysis was undertaken, terminal ileal Crohn's disease and terminal ileal control biopsies separated from colonic Crohn's disease and colonic control biopsies. Further clustering analysis of the terminal ileal biopsies showed separation between the terminal ileal Crohn's disease and control biopsies.

When the ulcerative colitis biopsies and control biopsies were compared, differentially upregulated genes in ulcerative colitis included SAA1 (p<10⁻⁴⁵) the alpha defensins, DEFA5&6 (p=0.00003 and p=6.95xl0⁻⁷ respectively), MMP3 (p=5.6x10⁻¹⁰) and MMP7 (p=2.3x10⁻⁷). Increased DEFA5&6 expression was further characterized to Paneth cell metaplasia by immunohistochemistry and in-situ hybridization.

Variants in all the examined IBD5 SNPs were associated with Crohn's disease (p<0.003). The IBD5 locus was also associated more severe Crohn's disease behaviour. In the absence of the IBD5 risk haplotype, no association of OCTN1/2 variants with Crohn's disease was detected. The analysis of the DLG5 variant 113A showed there were no associations with inflammatory bowel disease, Crohn's disease or ulcerative colitis.

Overall these data emphasise the key role of a number of inflammatory molecules and pathways in pathogenesis of Crohn's disease and ulcerative colitis, and their potential for translation to therapeutic targets. The results also add considerably to the recent genome wide association studies in providing complimentary human colonic and ileal expression data along with detailed analysis of the IL-23 and autophagy pathways.

http://hdl.handle.net/1842/29921

The University of Edinburgh

Annexe Thesis Digitisation Project 2018 Block 18

Already catalogued

Investigation into the molecular genetics of the inflammatory bowel diseases

Thesis or Dissertation

Doctoral

MD Doctor of Medicine