Personalized medicine could get a push forward from a new technique that reduces the number of cells needed for epigenomic analysis from millions to just 100.
Investigation of epigenomes requires mapping DNA interactions with a certain protein in the entire genome. This allows doctors to get a fuller picture of the state of the patient and dial-in on a personalized treatment strategy. However, the large requirement — about 10 million cells for a single test to study in vivo genome-wide protein-DNA interactions and chromatin modifications — made it impractical for doctors to perform such analysis on collected patient samples.
In his lab Chang Lu, study author and professor of chemical engineering at Virginia Tech, and his students designed a small microfluidic device with micrometer features that can examine cells at a molecular level.
The technique, called microfluidic oscillatory washing based chromatin immunoprecipitation (MOWChIP-Seq) came from a collaboration of Lu and study author Kai Tan, a systems biologist and associate professor of internal medicine at the University of Iowa. The research was published Tuesday in the journal Nature Methods.
The technology makes the process of assessing epigenome interactions faster — about 90 minutes compared to conventional ChIP assays that took multiple hours, according to a news release.
“The use of a packed bed of beads for ChIP allowed us to collect the chromatin fragments with a very high efficiency,” Lu said in the release. “At the same time, effective washing for removing undesired molecules and debris guarantees the purity of the collected molecules. These two factors constitute a successful strategy for epigenomic analysis with extremely high sensitivity.”
Next up the team plans to use the technology to study changes in the epigenome associated with cancer and inflammation.
The research was funded by the National Institutes of Health and Virginia Tech’s Institute for Critical Technology and Applied Science.
Virginia Tech filed a U.S. utility patent on the technology on behalf of Lu.