Characterising the role of TLE1 in Crohn’s disease
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Sharma2016.docx (13.93Mb)
Date
02/07/2016Author
Sharma, Nidhi
Metadata
Abstract
The inflammatory bowel diseases (IBD) are chronic, relapsing and remitting diseases
of the gastrointestinal tract. There are two main types of IBD: Crohn’s disease (CD)
and ulcerative colitis (UC). The prevalence of IBD is highest in the western world,
approximately 100-200 people per 100,000 are affected. In recent years there has
been a marked increase in the incidence of CD and UC, in both adults and children
(Henderson et al., 2012; Molodecky et al., 2012). This is particularly relevant in
Scotland where recent research shows that there has been a 79% increase in the
number of cases of paediatric IBD since the 1990’s (Henderson et al., 2012).
A yeast 2 hybrid screen identified TLE1as an interacting partner of the known CD
susceptibility gene; Nucleotide- binding oligomerisation protein 2 (Nod2). An initial
genome wide association study (GWAS) also found an association between the
rs6559629 SNP, located in Tle1 and ileal CD (p =3.1 x 10-5) and showed that
carriage of the Tle1 risk allele increases the effects of Nod2 mutations in CD. TLE1
functions as a transcriptional co repressor in a variety of different cellular and
developmental pathways
The work presented in this thesis investigates the potential role of TLE1 in CD. This
has been approached using four different strategies: sequencing TLE1 in CD patients
and controls, analysing the effects of knocking down TLE1 on genome wide
expression, investigating whether the known IBD susceptibility protein XBP1 binds
to a predicted binding site in TLE1 and investigating TLE1 levels and localisation in
human intestinal samples from CD patients and controls
Sequencing TLE1 exons and introns 15/16 and 16/17 in a Scottish cohort of 24 CD
patients and healthy controls identified a number of potentially pathogenic exonic
and intronic SNPs. Two exonic SNPs and thirteen intronic SNPs were identified and
these were further investigated in larger Scottish (203 CD cases, 190 HC) and
European cohorts (6,333 CD cases and 15,056 HC) but were not present at
statistically significantly different frequencies. Secondly, the effects of TLE1 knock down on genome wide expression were
analysed using an Illumina HT12 expression chip. The results showed that TLE1
knock down significantly altered expression of 19 loci (Bonferroni) and 526 loci
(FDR). Four of the 19 Bonferroni significant loci are potentially involved in CD:
RIOK1 (p=4.3×10-3), SGPL1 (p=4.3×10-3), TUSC3 (p=1.8×10-2) and CCND1
(p=2.7×10-3). Furthermore, expression of SGPL1 and RIOK1 were shown to be
differentially expressed at the mRNA level between inflamed patients and controls.
The third approach investigates a predicted binding site for the known IBD
susceptibility gene, XBP1 in TLE1 which was identified using the Haploreg program.
This work shows, using chromatin immunoprecipitation, that exogenous XBP1 does
not appear to bind to this predicted binding site.
Finally, TLE1 expression was analysed in human intestinal resection samples from
patients of known NOD2 status. This work shows that TLE1 and NOD2 are
expressed in Paneth cells, however TLE1 expression is not altered in patients
carrying CD associated NOD2 variants.
In this work TLE1 sequence, expression and potential interacting proteins have been
analysed. The results presented suggests multiple mechanisms by which TLE1 may
be influencing susceptibility to CD including: the unfolded protein response
(TUSC3), S1P signalling and ribosome biogenesis. They also implicate TLE1 in
Paneth cell function alongside NOD2. The exact means by which TLE1 may play a
role in IBD pathogenesis has yet to be fully elucidated.
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