This study aims to investigate the functional relationship between the rs1111875 single nucleotide polymorphism (SNP) and type 2 diabetes susceptibility by determining the effect of the SNP on the expression of the HHEX and IDE genes. The study will generate isogenic beta cell lines that differ only in their rs1111875 genotype using CRISPR/Cas9 genome editing. Gene expression analysis will then be performed on the cell lines using TaqMan assays to measure relative expression of HHEX and IDE and determine if the risk allele of rs1111875 alters their expression levels, which could provide insight into how this SNP contributes to type 2 diabetes risk.

1. The functional relationship between rs1111875 and type 2 diabetes susceptibility
B T Macintyre, T Zheng, T Wahed
Introduction
Figure 1: Loci associated with T2D in the human genome. HHEX and IDE genes (located on chromosome 10) have been shown
to be significantly associated with T2D in humans.4 (Image taken from Frazer et al., 2009)8
Materials and Methods
Step 1: Genotype human foetal blood to
identify two homozygous rs1111875 alleles;
the C/C allele and the T/T allele. This will to
allow relative expression to be quantified.
Step 2: Generate a stable and functional
human β cell line according to the method
established by Ravassard et al. 16
Step 3: Design rs1111875 specific CRISPR
guide RNA (gRNA) sequence using the
protocol developed by Ran et al. 15
Step 4: Produce three isogenic β cell lines
using: (a) β cells without transfection; (b) β
cells transfected with all CRISPR reagents
except genetic material; (c) mutant cell line
with alternative homozygous genotype,
produced using CRISPR.
Step 5: Use ARMS PCR25 to confirm the
genotypes of each cell line (e.g. T/T(a),
T/T(b), and C/C(c))
Step 6: Perform TaqMan expression assays
on each of the cell lines to measure relative
HHEX and IDE expression.
Prospective Results
Discussion and Conclusion
References
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 Type 2 diabetes (T2D) is the most common form of diabetes in the human population (90% of people
with diabetes around the world), affecting over 300 million people.24
 The significantly increased morbidity and mortality in people with T2D, and the rising prevalence over
recent years, makes elaborating the genetic basis of the disease very important.
 GWAS meta-analysis showed that the C allele of rs1111875, a SNP within an enhancer region, is strongly
associated to T2D in the LD block on chromosome 10q23.33, which contains the genes IDE, KIF1117, and
HHEX.5,12,13,19
 Knock-out rat in which IDE has been deleted exhibit T2D7, while deletion of HHEX is embryo lethal2,3;
HHEX is a transcription factor that is essential for normal pancreatic development2,3,10,21,27, therefore
dysregulation of HHEX expression may contribute to T2D via aberrant downstream interactions.
 The aim of this study is to investigate the significance of rs1111875 to the expression of IDE and HHEX;
we anticipate that rs1111875 modulates the enhancer’s activity on one or both of these genes, which
would provide a functional basis for its association with T2D.
Potential outcomes:
1. Increased expression of HHEX and/or IDE
Upregulation of HHEX suggests that the mutant
enhancer contribute to T2D in a complex manner.
However, upregulation of IDE is unlikely to indicate
a functional relevance in T2D.
2. Decreased expression of HHEX and/or IDE
Downregulated IDE suggests that the enhancer
contribute to T2D by increasing insulin resistance
and impairing secretion of insulin.23
Downregulated HHEX suggests that the enhancer
contribute to T2D by reducing epistasis, given that
it is a transcription factor.
3. No change in expression
This would confirm the null hypothesis that
rs1111875 does not contribute to T2D at this locus
suggesting other SNPs in proxy to this SNP maybe
linked to the expression of these genes.
1. Beta cell culture
Human foetal pancreatic β cells (hfpβ cells) must be used because the proliferative potential of adult β
cells is extremely low, and procedures for generating functional β cells from human embryonic stem cells
have not been fully developed.
Although hfpβ cells are anticipated to be crucial to T2D research (given the significance of the differences
between humans and animal models), differences between in vivo and in vitro β cells may distort
experimental results.
2. In vitro experiment6
Advantages:
Ease of manipulation
Cell homogeneity
Extended replicative capacity in generating specific cell of interest
Disadvantages:
Transcription profiles between in vivo human beta cells and in vitro beta cells.16
Limited access to tissue samples.
3. CRISPR9
Advantages - Less labour intensive, higher targeting specificity, high transfection efficiency.11
Why use CRISPR instead of ZFN and TALENs?
ZFNs induce off-target cleavage and assembly of multiple ZFNs lead to reduced specificity to target DNA.
TALENs enable highly specific targeting of genes, but the length of DNA it can recognise is limited.
5. TaqMan
Advantages:
Differentially labelled fluorophore probes allow amplification of two distinct sequences in one reaction.
The use of probe and primers to the region of interest makes this technique highly specific.
Post-PCR processing is eliminated, which reduces assay labour and material costs.
Disadvantage:
Poor primer design can lead to nonspecific binding and amplification of inappropriate genes.
Synthesis of different probes is required for different sequences.
The Future:
If the rs1111875 risk allele (C) significantly alters HHEX and/or IDE gene expression in hfpβ cells, this
suggest a potential mechanism by which this can contribute to T2D, providing a possible method for
modifying HHEX and/or IDE gene expression in human beta cells.
If no difference in expression is observed, other significant SNPs can be investigated within the LD block
using the same methods.12,21,22,26
Additional loci associated with T2D could potentially be investigated using a similar method.14,22
Figure 4: SNP genotyping assay using ARMS PCR
The foetal blood sample genotyped in step 1 of Materials and
Methods must either be homozygous for the C allele (pink) or
the T allele (dark blue). The mutant cell line produced using
CRISPR will be engineered to be homozygous for the other
allele. (Figure adapted from You et al., 2008)25
Figure 5: TaqMan expression assay results: If the risk allele (C) increases expression of HHEX or IDE, results
resembling the blue lines will indicate this by showing a higher RFU score than the alternative allele (T, which would
be represented by the green lines).1
Figure 2: Pairwise linkage disequilibrium diagram for IDE-KIF11-HHEX. The bar graph represents the negative logarithm of the
P-value for each SNP; this study demonstrates the significance of the association between rs111185 (indicated in the black box)
and T2D (-log10[P] = >4). The asterisk indicates that this SNP was chosen for confirmatory studies. (Figure adapted from Sladek
et al., 2007)20
Figure 3: Comparing CRISPR used by prokaryotes and artificially
designed CRISPR.
A) CRISPR system in prokaryotes incorporate foreign DNA into
CRISPR arrays, producing crRNA with a protospacer region
complementary to the foreign DNA. crRNA and tracrRNA are
associated with the cas9 protein complex, which recognise and
cleave foreign DNAs bearing the protospacer sequences. B)
Artificially designed gRNA complex uses a fused crRNA and tracrRNA
sequence. A single RNA complexes with cas9 to mediate cleavage of
target DNA sites that are complementary to the gRNA that lie next to
the PAM sequence. C) Illustrate example of crRNA-tracrRNA hybrid
and a gRNA.18 (Diagram adapted from Sander and Joung, 2013)
rs1111875 is a SNP that has been shown to be strongly associated with Type 2 Diabetes (T2D) in GWA
studies. It lies within a linkage disequilibrium (LD) block on chromosome 10q23.33 containing three genes:
Insulin degrading enzyme (IDE), kinesin family member 11 (KIF11) and hematopoietically-expressed
homeobox protein (HHEX, a transcription factor). Animal studies have shown that IDE and HHEX are
associated with type 2 diabetes 2,3,7,10. Given that rs1111875 lies within an enhancer region5, it is likely that
by modulating the expression of one or both of these genes, this SNP may contribute to the development
of T2D. In this study we investigate the functional relevance of rs1111875 to the expression of these genes
by introducing the risk allele into human pancreatic beta cells and assessing gene expression.
Abstract