Effects of palmitate on genome-wide mRNA expression and DNA methylation patterns in human pancreatic islets

Abstract

BackgroundCirculating free fatty acids are often elevated in patients with type 2 diabetes (T2D) and obese individuals. Chronic exposure to high levels of saturated fatty acids has detrimental effects on islet function and insulin secretion. Altered gene expression and epigenetics may contribute to T2D and obesity. However, there is limited information on whether fatty acids alter the genome-wide transcriptome profile in conjunction with DNA methylation patterns in human pancreatic islets. To dissect the molecular mechanisms linking lipotoxicity to impaired insulin secretion, we investigated the effects of a 48 h palmitate treatment in vitro on genome-wide mRNA expression and DNA methylation patterns in human pancreatic islets.MethodsGenome-wide mRNA expression was analyzed using Affymetrix GeneChip® Human Gene 1.0 ST whole transcript-based array (n = 13) and genome-wide DNA methylation was analyzed using Infinium HumanMethylation450K BeadChip (n = 13) in human pancreatic islets exposed to palmitate or control media for 48 h. A non-parametric paired Wilcoxon statistical test was used to analyze mRNA expression. Apoptosis was measured using Apo-ONE® Homogeneous Caspase-3/7 Assay (n = 4).ResultsWhile glucose-stimulated insulin secretion was decreased, there was no significant effect on apoptosis in human islets exposed to palmitate. We identified 1,860 differentially expressed genes in palmitate-treated human islets. These include candidate genes for T2D, such as TCF7L2, GLIS3, HNF1B and SLC30A8. Additionally, genes in glycolysis/gluconeogenesis, pyruvate metabolism, fatty acid metabolism, glutathione metabolism and one carbon pool by folate were differentially expressed in palmitate-treated human islets. Palmitate treatment altered the global DNA methylation level and DNA methylation levels of CpG island shelves and shores, 5′UTR, 3′UTR and gene body regions in human islets. Moreover, 290 genes with differential expression had a corresponding change in DNA methylation, for example, TCF7L2 and GLIS3. Importantly, out of the genes differentially expressed due to palmitate treatment in human islets, 67 were also associated with BMI and 37 were differentially expressed in islets from T2D patients.ConclusionOur study demonstrates that palmitate treatment of human pancreatic islets gives rise to epigenetic modifications that together with altered gene expression may contribute to impaired insulin secretion and T2D.

Human liver epigenetic alterations in non-alcoholic steatohepatitis are related to insulin action

“…One can hypothesize that due to insulin resistance, increased release into the circulation of freefatty acids from the adipose tissue is delivered to the liver, 1 which could potentially mediate the effect of insulin resistance on DNA methylation levels. [49][50][51][52] Due to the cross-sectional nature of this study, it is not possible to determine causality in our study. However, it is unethical to have serial liver biopsies including both histological analysis and epigenetics, in individuals with clearly defined liver phenotypes.…”

Epigenetic regulation of macrophage polarization and inflammation by DNA methylation in obesity

“…Most importantly, SFAs and TNF-α also significantly increased DNA methylation levels at the PPARγ1 promoter, leading to suppressed PPARγ1 expression in macrophages. Dietary SFAs have been shown to differentially regulate DNA methylation patterns in human blood leukocytes compared with those of mono-or polyunsaturated fatty acids (50), whereas dietary palmitate also dynamically alters DNA methylation patterns in human islets (51), further supporting an epigenetic regulation of gene expression by dietary SFAs. Therefore, our findings provide a mechanistic basis for how obesity results in a macrophage phenotypic switch to a more proinflammatory M1 phenotype, leading to increased inflammation and eventually the development of obesity-associated metabolic diseases, including insulin resistance.…”

DNA Methylation as a Diagnostic and Therapeutic Target in the Battle Against Type 2 Diabetes

“…We have also studied the genome-wide DNA methylation pattern in human pancreatic islets in response to palmitate treatment, to mimic the situation of elevated circulating free fatty acids often seen in Type 2 diabetes patients [15]. Global DNA methylation, in other words, the average of all 483,844 CpG sites analyzed, was significantly higher in islets exposed to palmitate for 48 h compared with control islets.…”