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Study Describes Epigenetic Shifts Linking Obesity, Diabetes

Cell Metabolism study highlights epigenetic differences found in fat tissue from obese and lean mammals.

NEW YORK (GenomeWeb) – A new Cell Metabolism study is highlighting epigenetic differences found in fat tissue from obese and lean mammals, revealing conserved methylation changes in some of the same parts of the genome implicated in type 2 diabetes risk through past genome-wide association studies.

In an effort to understand potential epigenetic ties between obesity and type 2 diabetes, researchers from the US, Sweden, and the UK did array-based cytosine methylation profiling on adipose and other tissues from lean and obese mice and humans, as well as adipose samples from humans who had undergone Roux-en-Y gastric bypass surgery.

The analyses revealed widespread methylation differences in mice that had been nudged toward obesity based on their diet. And as it turned out, samples from obese and lean humans showed many of the same differentially methylated regions (DMRs) — obesity-related methylation shifts that appeared to be largely reversible after gastric bypass surgery.

By folding in gene expression data and information on sites in the genome associated with type 2 diabetes in the past, the team found evidence for overlap between type 2 diabetes-associated regions of the genome and a subset of sites that are differentially methylated in obese individuals.

"Mice and humans are separated by 50 million years of evolution, so it's interesting that obesity causes similar epigenetic changes to similar genes in both species," senior author Andrew Feinberg, a medicine and epigenetics researcher at Johns Hopkins University, said in a statement.

"It's likely that when food supplies are highly variable, these epigenetic changes help our bodies adapt to temporary surges in calories," Feinberg said. "But if the high-calorie diet continues over the long term, the same epigenetic pattern raises the risk for disease."

Type 2 diabetes has been attributed to a combination of inherited and environmental factors, including obesity, the study's authors explained. But while some genetic variants have been linked to the disease via GWAS and other studies, there is more to be learned about the full suite of factors that determine diabetes susceptibility and development.

"It's well known that most common diseases like diabetes result from a combination of genetic and environmental risk factors," Feinberg noted. "What we haven't been able to do is figure out how, exactly, the two are connected."

With that goal in mind, he and his colleagues started by comparing cytosine methylation patterns in a dozen adipose tissue samples taken from obese and lean mice fed a high- or low-fat diet, respectively.

Fat samples from the lean and obese animals — assessed using an approach known as comprehensive high-throughput array-based relative methylation (CHARM) — showed diet/obesity-related methylation differences in 625 sites in the mouse genome.

The researchers subsequently confirmed and expanded these results by using CHARM or bisulfite sequencing to test fat, pancreatic islet cell, and/or liver samples from these and other mice.

Based on existing mouse gene expression data and results from targeted quantitative PCR testing, meanwhile, they saw signs that decreased methylation typically coincided with a jump in nearby gene expression and vice versa.

The team detected a similar set of DMRs when comparing CHARM-based methylation profiles in fat tissue samples from seven lean and 14 obese humans. Nearly 500 DMRs from mice were conserved and could be measured in humans, with more than half of those sites displaying distinct methylation profiles in the obese or lean humans.

Consistent with their role in regulating processes related to obesity, many of the DMRs reverted to a lean-like pattern in samples taken from eight formerly obese individuals who'd lost weight as a result of Roux-en-Y gastric bypass surgery, researchers reported.

When the team took a closer look at the genes found in and around sites with higher- or lower-than-usual methylation levels in the obese mice, it saw unusually strong representation by genes involved in immunity, inflammation, and lipid metabolism — some of the same pathways that tend to get upregulated in individuals with type 2 diabetes. 

Finally, when they looked at the obesity-related DMRs in relation to variants identified through type 2 diabetes GWAS and meta-analyses, the researchers identified overlap between 30 obesity-related DMRs and 27 diabetes-associated SNPs, including variants found in and around at least four genes with reported roles in insulin resistance.

Together, the study's authors argued, such findings "show that DNA methylation changes in metabolic disease are conserved across species and that this conservation overlaps genomic regions where genetic polymorphisms have been associated with [type 2 diabetes]."