Identification of CpG-SNPs associated with type 2 diabetes and differential DNA methylation in human pancreatic islets

• Published in: Diabetologia Vol. 56; no. 5; pp. 1036 - 1046
• Main Authors: Dayeh, T. A., Olsson, A. H., Volkov, P., Almgren, P., Rönn, T., Ling, C.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01-05-2013; Springer; Springer Nature B.V
• Subjects: Aged; Alternative Splicing; Biological and medical sciences; Clinical Medicine; Cohort Studies; CpG Islands; Diabetes; Diabetes Mellitus, Type 2 - genetics; Diabetes Mellitus, Type 2 - metabolism; Diabetes. Impaired glucose tolerance; DNA Methylation; Endocrine pancreas. Apud cells (diseases); Endocrinology and Diabetes; Endocrinopathies; Endokrinologi och diabetes; Epigenesis, Genetic; Epigenetics; Etiopathogenesis. Screening. Investigations. Target tissue resistance; Female; Gene expression; Gene Expression Regulation; Genetic Association Studies; Genomes; Human Physiology; Humans; Insulin; Insulin - metabolism; Insulin Secretion; Internal Medicine; Islets of Langerhans - metabolism; Klinisk medicin; Linkage Disequilibrium; Male; Medical and Health Sciences; Medical sciences; Medicin och hälsovetenskap; Medicine; Medicine & Public Health; Metabolic Diseases; Middle Aged; Pathogenesis; Polymorphism, Single Nucleotide; RNA, Messenger - metabolism; Scandinavian and Nordic Countries; Tissue Culture Techniques; Tissue Donors; Scandinavian and Nordic Countries; Type 2 diabetes; Alternative splicing; Human pancreatic islets; Glucagon; SNP; DNA methylation; Epigenetics; Splice index; CpG-SNP; Insulin secretion; Endocrinopathy; Human; Pancreatic hormone; Secretion; Peptide hormone; Metabolic diseases; Insulin; DNA; Methylation; Pancreas
• ISSN: 0012-186X; 1432-0428; 1432-0428
• DOI: 10.1007/s00125-012-2815-7

Aims/hypothesis
To date, the molecular function of most of the reported type 2 diabetes-associated loci remains unknown. The introduction or removal of cytosine–phosphate–guanine (CpG) dinucleotides, which are possible sites of DNA methylation, has been suggested as a potential mechanism through which single-nucleotide polymorphisms (SNPs) can affect gene function via epigenetics. The aim of this study was to examine if any of 40 SNPs previously associated with type 2 diabetes introduce or remove a CpG site and if these CpG-SNPs are associated with differential DNA methylation in pancreatic islets of 84 human donors.
Methods
DNA methylation was analysed using pyrosequencing.
Results
We found that 19 of 40 (48%) type 2 diabetes-associated SNPs introduce or remove a CpG site. Successful DNA methylation data were generated for 16 of these 19 CpG-SNP loci, representing the candidate genes
TCF7L2
,
KCNQ1
,
PPARG
,
HHEX
,
CDKN2A
,
SLC30A8
,
DUSP9
,
CDKAL1
,
ADCY5
,
SRR
,
WFS1
,
IRS1
,
DUSP8
,
HMGA2
,
TSPAN8
and
CHCHD9
. All analysed CpG-SNPs were associated with differential DNA methylation of the CpG-SNP site in human islets. Moreover, six CpG-SNPs, representing
TCF7L2
,
KCNQ1
,
CDKN2A
,
ADCY5
,
WFS1
and
HMGA2
, were also associated with DNA methylation of surrounding CpG sites. Some of the type 2 diabetes CpG-SNP sites that exhibit differential DNA methylation were further associated with gene expression, alternative splicing events determined by splice index, and hormone secretion in the human islets. The 19 type 2 diabetes-associated CpG-SNPs are in strong linkage disequilibrium (
r
2
 > 0.8) with a total of 295 SNPs, including 91 CpG-SNPs.
Conclusions/interpretation
Our results suggest that the introduction or removal of a CpG site may be a molecular mechanism through which some of the type 2 diabetes SNPs affect gene function via differential DNA methylation and consequently contributes to the phenotype of the disease.