How risk SNPs affect response to regular antidiabetic drugs

1. Pharmacogenomic implications
of risk SNPs in type 2 diabetes mellitus
Dr Muhammad Huzaimi Haron
Trainee Lecturer in Pharmacology
Pharmacology CME
28 March 2011

2. Outline
Introduction
T2DM revisit
What are SNPs?
Individual SNPs conferring T2DM risk
SNPs and Pharmacogenomics
What lies ahead
Take home message

3. Introduction
Genetic component to diabetes
High concordance rate between monozygotic twins
Different prevalence between populations
Different effect of traditional risk factors
Single nucleotide polymorphisms (SNPs)
Common
Functional
Heritable?

4. Revisit:
T2DM pathogenesis

5. Revisit:
T2DM pathogenesis
Incretins
K+ channel
Incretins

6. T2DM: Global Epidemic!
120
100
Prevalence (millions)
80
60
40
20
0
2000
WHO Regions

7. T2DM: Global Epidemic!
120
100
Prevalence (millions)
80
60
40
20
0
WHO Regions
2000
2030

8. T2DM: Back home…
Increasing prevalence
6.3% in 1986 (NHMS I) 11.0% in 2006 (MyNCDS-1)
NHMS II (1996): 8.3% (>30 yrs old)
NHMS III (2008): 11.6% (>18)
14.9% (>30)
39% did not know they were diabetic!
83% of 18-30yr old diabetic newly diagnosed!
Ethnic discrepancy (NHMS III)
Indian highest (19.9%)
Malay (11.9%) and Chinese (11.4%)

9. Worrying signs in NHMS III
High prevalence of undiagnosed DM in younger age
group (18 – 30 years old)
Increasing prevalence despite:
1. Health awareness campaigns
2. Increasing education and information levels
Need for a better screening program?

10. Single Nucleotide Polymorphism
A
T
C
G
G
T
C
A
C
T
T
G
C
G
A
A
A
T

11. Implication of
SNPs
DNA seq
change
Coding region
Non-coding
region
mRNA
mRNA seq
change
Intronic
transcription
alteration
Exonic
mRNA
processing
altered
AA seq change
Changes in
protein

12. How SNPs confer risk?
Variations in how body handles glucose
Absorption
Rate of emptying of stomach
Distribution
Action of insulin
Metabolism
Alteration in metabolic pathways
Disposition
Excretion of excess

13. SNPs conferring risk to T2DM
Year
Gene
Description
Peroxisome proliferator-activated receptor
gamma
Potassium inwardly-rectifying channel, subfamily
J, member 11
Phenotype
Chromosome
Major /
minor
allele
rs13081389
3
A/G
rs5215
11
C/T
Reduced
SNP
Beta cell
function
2000
PPARG
2003
KCNJ11
2006
TCF7L2
Transcription factor 7-like 2
rs7903146
10
C/T
Reduced
2007
CDKAL1
CDK5 regulatory subunit associated protein1-like 1
rs10440833
6
A/T
Reduced
2007
HHEX/IDE
Haematopoietically expressed homeobox /
insulin-degrading enzyme
rs5015480
10
C/T
Reduced
2007
SLC30A8
Solute carrier family 30 (zinc transporter),
member 8
rs3802177
8
C/T
Reduced
2007
CDKN2A/B Cyclin-dependent kinase inhibitor 2A/B
rs10965250
9
A/G
Reduced
2007
IGF2BP2
Insulin-like growth factor 2 mRNA binding protein
2
rs1470579
3
A/C
Reduced
2007
FTO
Fat mass and obesity associated
rs11642841
16
A/C
2008
KCNQ1
Potassium voltage-gated channel, KQT-like
subfamily, member 1
rs231362,
rs163184
11
A/C, G/T
Insulin
action
Reduced
Reduced
Reduced

14. TCF7L2 and T2DM
Protein: transcription factor 7-like-2
Gene on long arm of chromosome 10
Nuclear
Wnt pathway
Controls expression of downstream genes
Proglucagon (Ni et al, 2003) – promote expression in intestinal
L-cells
mRNA silencing of TCF7L2: apoptosis of beta-cells
(Shu et al, 2008)
proliferation, GSIS
Reduced levels lead to defective insulin granule exocytosis
(da Silva Xavier et al, 2009)

15. TCF7L2 SNPs
Multiple SNPs in multiple population
rs7903146
rs12255372
rs4506565
rs11196205
rs7901695
rs290487
Intronic

16. TCF7L2 SNPs and T2DM
Effect of SNPs on:
Expression of TCF7L2 gene
Increased in pancreatic beta-cells (Lyssenko et al, 2007)
Expression of other genes
Proglucagon – reduced in pancreatic L-cells (Yi et al, 2008)
Impaired GLP-1 synthesis
Its protein levels: unknown
Glucose handling
Blunting of incretin effect (Lyssenko et al, 2007; Schafer et al, 2007)
Reduction in pro-insulin conversion (Stancakova et al, 2009)
Increased hepatic gluconeogenesis (Pilgaard, 2009)

17. Impact on T2DM risk
Icelandic carriers of SNPs at increased risk of T2DM
(Grant et al, 2006)
Dose-dependent
Heterozygous carrier of T allele of rs7903146: OR 1.5
Homozygous carrier: OR 2.1
Replicated in various Caucasian and Asian populations
However with differing impact due to different allele
frequencies

18. Impact on T2DM risk
Malaysian population
No large scale data
Known data collected from UMMC 2009-2010 from
Malay, Chinese and Indian patients and non-diabetic
volunteers
Case-control study of 800 people

19. Type 2 DM Risk Analysis
TCF7L2
SNP
Subject
rs7903146
rs12255372
rs11196205
rs4506565
rs7901695
Minor allele
frequency
p-value
Diabetic
Non-diabetic
0.16
0.10
0.0061
Diabetic
Non-diabetic
0.13
0.06
0.0010
Diabetic
Non-diabetic
0.81
0.88
0.0047
Diabetic
Non-diabetic
0.16
0.08
0.0013
Diabetic
Non-diabetic
0.85
0.92
0.0025
OR [95% CI] *
of wildtype vs mutant allele
1.73
[1.17-2.58]
2.14
[1.35-3.40]
0.61
[0.43-0.86]
2.11
[1.33-3.36]
0.49
[0.31-0.79]
* Statistical test used: chi-square test

20. Type 2 DM Risk Analysis
TCF7L2
SNP
Subject
Genotype frequency (%)
OR [95% CI]*
WT
Ht
Mt
WT vs HZ genotype
Diabetic
Non-diabetic
72
83
25
15
3
2
1.66
rs12255372 Diabetic
Non-diabetic
77
90
20
8
3
2
rs11196205 Diabetic
Non-diabetic
7
4
24
17
69
79
0.95
[0.80-1.12]
rs4506565
Diabetic
Non-diabetic
73
86
23
11
4
3
2.16
Diabetic
Non-diabetic
4
3
23
11
73
86
rs7903146
rs7901695
[1.13-2.44]
2.37
[1.43-3.93]
[1.31-3.56]
1.06
[0.84-1.34]
* Statistical test used: chi-square test

21. Summary from Malaysian data
1. TCF7L2 SNPs increase the risk of T2DM in a
Malaysian population
2. The minor allele frequencies observed are:
much lower than in Caucasian and Indian population
(Grant et al, 2006; Chandak et al, 2007)
higher than in Japanese population (Miyake et al, 2008)
Impact?

22. Other SNPs
KCNJ11
Codes for component of ATP-sensitive K+ channels on
beta-cells (Kir6.2 subunit)
Mutations caused monogenic forms of DM
SNP (rs5215) cause defect to subunit
K+ channels fail to open in response to rising ATP:ADP ratio
Failed exocytosis of insulin granules (reviewed by Florez, 2008)

23. Other SNPs
KCNQ1
Encodes for a voltage-gated K+ channels
needed for repolarisation phase of cardiac
action potential
This channel also found on intestinal L-cells
SNPs (rs231362, rs163184) cause impaired
incretin effect
Reduction in GLP-1 secretion by L-cells (Tan et al, 2009)

24. Other SNPs
PPAR 2
Codes for nuclear receptor
Involved in lipid and glucose
homeostasis, differentiation of lipocytes, FA storage
SNP confers protection against T2DM
Increased insulin sensitivity
Lower BMI
Higher HDL
Lower BP
Reduced MI risk

25. Pharmacogenomics
Different DNA sequence, different response!
Drug-metabolizing enzymes
Cytochrome-p450 family, eg CYP2C9 and sulfonylureas
Statement 1:
SNPs conferring risk affect glucose handling
Statement 2:
Glucose handling modified by drugs
Can risk SNPs alter drug response?

26. TCF7L2 SNPs and Sulfonylurea
GoDARTs study (Pearson et al, 2007)
900 patients on a sulfonylurea
Treatment failure: HbA1c >7% after 3 – 12 months of
initiation
Adequate control of confounder
SNP carrier 2 times more likely to encounter treatment
failure – even after adjusting for baseline HbA1c

27. Genotypic comparison of
HbA1c levels (Metformin+Sulfonylurea, n=113)
HbA1c (%)
*
10
9
8
7
6
5
4
3
2
1
0
*
*
**
*
WT
HZ
Mt
rs7903146
rs12255372 rs11196205
TCF7L2 SNPs
* P<0.05, ** P<0.01
rs4506565
rs7901695

28. Genotypic Comparisons of
Achievement of HbA1c target
Metformin + Sulfonylurea (n=29/113)
WT
HZ
Mt
P-value
rs7903146
rs12255372
83
86
10
14
7
0
<0.001
rs4506565
rs7901695
rs11196205
86
7
10
7
7
4
7
86
86
WT: Wildtype, HZ: Heterozygous, Mt: Mutant
( 2)
<0.001

29. KCNJ11 SNPs and Sulfonylurea
Sesti et al, 2006
525 patients treated with sulfonylurea, either alone or
combination with metformin
Secondary failure: those requiring insulin therapy
despite combination therapy
Adequate control of confounders
SNP carrier more likely to get secondary failure with
sulfonylurea therapy
Sulfonylurea-stimulated insulin secretion lower in
pancreatic islets carrying the SNP

30. KCNJ11 SNP and Repaglinide
He et al, 2008
100 newly diagnosed Chinese patients, treated with
repaglinide over 24 weeks
SNP carriers had greater reduction in FPG and HbA1c
levels
SNP carriers had better improvements of HOMA-B

31. PPAR 2 SNP and
Kang et al (2005)
Improved response to rosiglitazone in heterozygous
SNP carriers
Greater drops in FPG and HbA1c

32. The future
is still uncertain
Identification of risk SNPs
Need cohort studies, long term follow-up
Involvement of epigenetics, CNVs
Pharmacogenomics
Better-designed clinical trials, controlling for confounder
Promise of personalised medicine in DM?

33. Take home message
Importance of genetic factors/variations in conferring
risk to T2DM is evident
Response to antidiabetic medications is heavily
influenced by genetic variations as well!
However, the specifics are still missing/unclear
– lots of “research holes” yet to be filled…

34. THANK YOU
for your kind attention

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36. Incretins and GSIS
Glu
Glu
Glu
GSIS and Incretins:
An Overview
Small intestine
Pancreatic
β-cells
• GSIS: glucose stimulated insulin secretion
lumen
• Accounts for majority of postprandial insulin release
GLP
• Earliest defect leading up to T2DM
-1
Ins
• Incretins
• Intestinal peptide hormones
• Released upon detection of glucose in GIT
GIP
• Glucagon-like peptide-1 (GLP-1)
• Glucose-dependent insulinotropic polypeptide (GIP)
Cell
Glu
Glu
Vasculature
Done

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