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MRSA Susceptibility Study Uncovers Protective Variant in Methyltransferase

NEW YORK – A team led by researchers at Duke University has identified a variant in a DNA methyltransferase gene called DNMT3A that appears to increase an individual's ability to stave off infections involving methicillin-resistant Staphylococcus aureus (MRSA) bacteria.

"This study provides strong evidence of a genetic variant that appears to help people with MRSA to resolve their blood stream infections," corresponding author Vance Fowler, a professor in the Department of Medicine and the Department of Molecular Genetics and Microbiology at Duke, said in a statement. He noted that the "increasing prevalence of antibiotic-resistant staph infections has created an urgent need to better understand who is most susceptible to these difficult-to-treat S. aureus infections and why."

As they reported online in the Proceedings of the National Academy of Sciences, Fowler and colleagues from the MRSA Systems Immunobiology Group used a combination of exome sequencing, RNA sequencing, reduced-representation bisulfite sequencing, and array-based cytokine and chemokine immune cell profiling to search for suspicious genetic variants, gene expression profiles, and epigenetic patterns in blood samples from almost 70 prospectively enrolled individuals with MRSA bacteremia.

The search led to a heterozygous chromosome 2 variant — falling in an intron of DNMT3A — that was far more common in individuals with MRSA infections that did resolve compared to a matched group with persistent MRSA infections.

The team followed up on those findings with in vitro immune cell assays, small interfering RNA silencing on human macrophage cells exposed to S. aureus, mouse experiments, and more, demonstrating that the apparently protective DNMT3A variant tends to coincide with enhanced methylation at several gene regulatory sites, along with dampened IL-10 anti-inflammatory cytokine interleukin levels in the blood serum, among other host immune characteristics.

Although IL-10 contributes to host immune responses, the authors explained, past research suggests that dramatic increases in IL-10 levels can become detrimental in individuals with S. aureus infections, coinciding with poor clinical outcomes, an increased risk of tissue damage, and death, in some cases.

"Our study identifies a particular DNMT3A mutation that contributes to an increased ability to resolve MRSA infections," Fowler said, noting that this apparent resilience may be mechanistically related to "increased methylation of gene regulatory regions, and reduced levels of the anti-inflammatory cytokine IL-10."

For the analysis, the researchers sequenced the exomes of 34 individuals with persistent MRSA infections and as many individuals with resolving MRSA infections, chasing down suspicious leads with additional gene expression, methylation, and serum cytokine profiling.

When they compared protein-coding sequences from those with persistent and resolved infections, they found that just three of 34 — or less than 9 percent — of the individuals with ongoing MRSA infections had the intronic variant in DNMT3A. In contrast, 21 out of 34, or nearly 62 percent, of those who successfully ditched the multidrug-resistant bug carried one copy of the potentially protective variant.

The investigators used siRNA experiments to demonstrate a role for DNMT3A in reigning in excess IL-10 activity in human macrophage cells: knocking out the methyltransferase enzyme led to a rise in IL-10 in human macrophage cells treated with S. aureus. Similarly, results from their mouse experiments suggested that inhibiting methylation directly could boost susceptibility to S. aureus in a sepsis model.

"Using in vitro macrophage assays and murine sepsis models, we demonstrated that DNMT3A variants may alter host response to infection through increased methylation of key regulatory genes, resulting in reduced interleukin-10 production and, in turn, allowing for a more protective immune response that clears infection," the authors wrote, adding that "improved understanding of the factors predisposing to persistent MRSA bacteremia may help to discover better treatment options."