RESUMO
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 (r² > 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.
Assuntos
Ilhas de CpG , Metilação de DNA , Diabetes Mellitus Tipo 2/genética , Epigênese Genética , Ilhotas Pancreáticas/metabolismo , Polimorfismo de Nucleotídeo Único , Idoso , Processamento Alternativo , Estudos de Coortes , Diabetes Mellitus Tipo 2/metabolismo , Feminino , Regulação da Expressão Gênica , Estudos de Associação Genética , Humanos , Insulina/metabolismo , Secreção de Insulina , Desequilíbrio de Ligação , Masculino , Pessoa de Meia-Idade , RNA Mensageiro/metabolismo , Países Escandinavos e Nórdicos , Técnicas de Cultura de Tecidos , Doadores de TecidosRESUMO
A model-based interpretation of laboratory-scale experimental data is presented. Hydrolysis experiments carried out using thin glass tanks filled with glass beads to construct a hypothetical and inert, homogeneous porous medium were analysed using a 2D numerical model. A new empirical formula, based upon results for non-reactive (tracer) experiments is used to calculate transversal dispersivity values for a range of grain sizes and any flow velocities. Combined with effective diffusion coefficients calculated from Stokes-Einstein type equations, plume lengths arising from mixing between two solutes can be predicted accurately using numerical modelling techniques. Moreover, pH and ion concentration profiles lateral to the direction of flow of the mixing species can be determined at any given point downstream, without the need for result fitting. In our case, this approach does not lead to overpredictions of lateral mixing, as previously reported when using parameters derived from non-reactive tracer experiments to describe reactive solute transport. The theory is based on the assumption of medium homogeneity.
