A team of MIT chemical engineers reports that they have developed a fast and reliable technique for detecting methylated genes linked to cancer. They believe their method could offer a new way to choose the best treatment for individual patients.

“It’s pretty difficult to analyze these modifications, which is a need that we’re working on addressing. We’re trying to make this analysis easier and cheaper, particularly in patient samples,” said Hadley Sikes, Ph.D., the Joseph R. Mares assistant professor of chemical engineering and the senior author of a paper (“Evaluating the sensitivity of hybridization-based epigenotyping using a methyl binding domain protein”) describing the technique in Analyst.

“Hypermethylation of CpG islands in gene promoter regions has been shown to be a predictive biomarker for certain diseases,” wrote the investigators. “Most current methods for methylation profiling are not well-suited for clinical analysis. Here, we report the development of an inexpensive device and an epigenotyping assay with a format conducive to multiplexed analysis.”

In some cancers, a DNA-repair gene known as MGMT is turned off when methyl groups attach to specific locations in the DNA sequence, namely, cytosine bases that are adjacent to guanine bases. When this happens, proteins bind the methylated bases and effectively silence the gene by blocking it from being copied into RNA.

“This very small chemical modification triggers a sequence of events where that gene is no longer expressed,” explained Dr. Sikes, adding that current methods for detecting cytosine methylation work well for large-scale research studies, but are hard to adapt to patient samples. Most techniques require a specific chemical step, bisulfite conversion: The DNA sample is exposed to bisulfite, which converts unmethylated cytosine to a different base. Sequencing the DNA reveals whether any methylated cytosine was present.

However, this method doesn’t work well with patient samples because you need to know precisely how much methylated DNA is in a sample to calculate how long to expose it to bisulfite, according to Dr. Sikes.

“When you have limited amounts of samples that are less well defined, it’s a lot harder to run the reaction for the right amount of time. You want to get all of the unmethylated cytosine groups converted, but you can’t run it too long, because then your DNA gets degraded,” she pointed out.

Her team’s novel approach avoids bisulfite conversion completely. Instead, it relies on methyl binding domain (MBD) protein, which is part of cells’ natural machinery for controlling DNA transcription. This protein recognizes methylated DNA and binds to it, helping a cell to determine if the DNA should be transcribed.

The other key component of Dr. Sikes’ system is a biochip coated with hundreds of DNA probes that are complementary to sequences from the gene being studied. When a DNA sample is exposed to this chip, any strands that match the target sequences are trapped on the biochip. The researchers then treat the slide with the MBD protein probe. If the probe binds to a trapped DNA molecule, it means that sequence is methylated.

The binding between the DNA and the MBD protein can be detected either by linking the protein to a fluorescent dye or designing it to carry a photosensitive molecule that forms hydrogels when exposed to light. This technique, which cuts the amount of time required to analyze epigenetic modifications, could be a valuable research tool as well as a diagnostic device for cancer patients, noted Andrea Armani, Ph.D., a professor of chemical engineering and materials science at the University of Southern California, who was not part of the research team.

“It’s a really innovative approach,” Dr. Armani says. “Not only could it impact diagnostics, but on a broader scale, it could impact our understanding of which epigenetic markers are linked to which diseases.”

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