Project description:Little is known about the contribution of the epigenome to the pathophysiology of type 2 diabetes (T2D). Here we have used genome-wide DNA methylation profiling to obtain the first comprehensive DNA methylation data set for human T2D pancreatic islets. Therefore, we analyzed the methylation profile of 27,578 CpG sites affiliated to more than 14,000 genes in 16 samples of pancreatic islets, 11 normal and 5 type 2-diabetic. Keywords: DNA methylation Keywords: Methylation profiling by array We measured the methylation status of the 27,578 CpG sites (Human Methylation27 DNA BeadChip array) in genomic DNA obtained from pnacreatic islets of 11 non-diabetic and 5 type-2-diabetic male human donors to identify genes that are differentially methylated in T2D.
Project description:Little is known about the contribution of the epigenome to the pathophysiology of type 2 diabetes (T2D). Here we have used genome-wide DNA methylation profiling to obtain the first comprehensive DNA methylation data set for human T2D pancreatic islets. Therefore, we analyzed the methylation profile of 27,578 CpG sites affiliated to more than 14,000 genes in 16 samples of pancreatic islets, 11 normal and 5 type 2-diabetic. Keywords: DNA methylation Keywords: Methylation profiling by array
Project description:Circulating cell-free unmethylated DNA fragments arising from the human INS gene have been proposed as biomarkers of β-cell death for the presymptomatic detection of diabetes. However, given the variability of CpG methylation in the INS gene in different cell types, this gene alone may not yield sufficiently specific information to unambiguously report β-cell damage. We employed an unbiased approach using data from a human DNA methylation gene array to identify the CHTOP gene as a candidate biomarker whose CpGs show a greater frequency of unmethylation in human islets. When tested across an array of non-islet human tissues by digital PCR, both INS and CHTOP contain unmethylated CpG sites in several of these tissues, but in a non-overlapping pattern: INS showed a slightly higher frequency of unmethylation in adipose tissue, whereas CHTOP appeared to be unmethylated in pancreas, brain, and skeletal muscle. Notably, INS and CHTOP genes are both unmethylated in human β and α cells, suggesting that each species at best would represent markers of islet cell death in general, and together might distinguish death arising from islets vs. other tissues. To validate unmethylated CHTOP as a biomarker for islet cell damage, we used digital PCR to measure cell-free circulating DNA in human populations. Compared to healthy controls, we observed that levels of differentially methylated CHTOP and INS were higher in youth with new onset type 1 diabetes and in healthy youth who have first-degree relatives with T1D. When tested in youth across a spectrum of metabolic dysfunction, increased levels of unmethylated INS and CHTOP were observed in obese individuals compared to lean controls. Together, these data suggest that simultaneous measurement of both circulating differentially methylated INS and CHTOP is likely to detect islet death in T1D, and raise new questions about β-cell health in populations at risk for both T1D and T2D. Importantly, our data support the use of multiple parameters to increase the accuracy of biomarkers of β-cell health in youth with diabetes.
Project description:Epigenetic factors regulate tissue-specific expression and X-chromosome inactivation. Previous studies have identified epigenetic differences between sexes in some human tissues. However, it is unclear whether epigenetic modifications contribute to sex-specific differences in insulin secretion and metabolism. In this study, we investigated the impact of sex on the genome-wide DNA methylation pattern in human pancreatic islets from 53 males and 34 females, and related the methylome to changes in expression and insulin secretion. 53 male and 34 female human pancreatic islet samples. Normally methylated, non-methylated and fully methylated human DNA samples were included as controls
Project description:Epigenetic factors regulate tissue-specific expression and X-chromosome inactivation. Previous studies have identified epigenetic differences between sexes in some human tissues. However, it is unclear whether epigenetic modifications contribute to sex-specific differences in insulin secretion and metabolism. In this study, we investigated the impact of sex on the genome-wide DNA methylation pattern in human pancreatic islets from 53 males and 34 females, and related the methylome to changes in expression and insulin secretion.
Project description:Intrauterine growth restriction (IUGR) increases susceptibility to age-related diseases including type 2 diabetes (T2DM), and is associated with permanent and progressive changes in gene expression and epigenetic regulation. We studied cytosine methylation throughout the genome in pancreatic islets from a rat model of uteroplacental insufficiency, providing a novel and detailed assessment of the genomic distribution and locus-specific patterns of DNA methylation in normal islets as well as the changes that occur as a consequence of IUGR. Utilizing a high throughput approach to study DNA methylation at almost 1 million unique sites throughout the genome, we found ~1,400 changes in methylation (IUGR compared to control) with an estimated false discovery rate of 4.2%. These epigenetic differences were observed in IUGR male rats at 7 weeks of age, preceding the development of diabetes in this model. Therefore, these epigenetic differences represent candidates for mediating the pathogenesis of metabolic disease that occurs later in life in these animals. Moreover, many of the changes we identify are located near genes that regulate processes known to be abnormal in IUGR islets, such as vascularization, β-cell proliferation, insulin secretion, and cell death. Consistent changes in mRNA expression were identified at some of the epigenetically-dysregulated genes including Fgfr1, Gch1, Pcsk5, and Vgf. Globally, epigenetic dysregulation occurred preferentially at conserved intergenic sequences, which are candidate cis-regulatory elements driving differential expression of nearby genes. These results provide insights into the complex developmental consequences of IUGR, and suggest that changes in DNA methylation could mediate a constellation of changes in both gene expression and pancreatic islet development and function, with relevance to T2DM. Direct comparison of DNA methylation in 8 samples consisting of isolated, pooled pancreatic islets from 7-week-old male offspring belonging to 4 IUGR and 4 control litters (Sprague-Dawley rats). Each microarray consists of a two-color comparison of a methylation-sensitive representation of the genome (HpaII) with an internal methylation-insensitive control/reference (MspI).
Project description:Early postnatal overnutrition causes persistent dysregulation of endocrine pancreas function. We used genome-scale DNA methylation profiling in the suckling-period small litter (SL) mouse model to test whether this occurs via persistent epigenetic changes in pancreatic islets. Although SL islets showed DNA methylation changes directly after weaning and in adulthood, few of these were present at both ages, contrary to our hypothesis. Most interestingly, we discovered that genomic regions that are hypermethylated in exocrine relative to endocrine pancreas tend to gain methylation in islets during aging. Focusing on a subset of genes relevant to β cell function, we showed that these methylation differences are strongly correlated with expression. Together, our results provide the novel insight that DNA methylation changes that occur as islets age indicate an overall epigenetic drift toward the exocrine pancreas epigenome. These concerted shifts in the islet methylome could contribute to the age-associated decline in endocrine pancreas function. Pancreatic islets were isolated from P21/P180 SL or C mice. To ensure purity of islets, 3 rounds of manual picking were performed in each samples. Whole pancreas samples, ~98% of which is exocrine pancreas, were used as exocrine pancreas. There are 5 mice per group.
Project description:We have studied the impact of T2D on open chromatin in human pancreatic islets. We used assay for transposase-accessible chromatin using sequencing (ATAC-seq) to profile open chromatin in islets from T2D and non-diabetic donors. We identified ATAC-seq peaks representing open chromatin regions in islets of non-diabetic and diabetic donors. The majority of ATAC-seq peaks mapped near transcription start sites. Additionally, peaks were enriched in enhancer regions and in regions where islet-specific TFs bind. Islet ATAC-seq peaks overlap with SNPs associated with T2D and with additional SNPs in LD with known T2D SNPs. There was enrichment of open chromatin regions near highly expressed genes in human islets.
Project description:In this study, we achieved integrated transcriptomic and proteomic profiles of GK islets in a time-course fashion at different stages of T2D. Subsequent bioinformatics analysis revealed the chronological order of T2D-related molecular events during the deterioration of pancreatic islets. Our large quantitative dataset provide a valuable resource to obtain a comprehensive picture of the mechanisms responsible for islet dysfunction and to identify potential interventions to prevent beta-cell failure in human T2D.