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New Technology Developed Helps Personalized Medicine
August 18, 2015

A new technology that will dramatically enhance investigations of epigenomes, the machinery that turns on and off genes and a very prominent field of study in diseases such as stem cell differentiation, inflammation and cancer, is reported on recently in the research journal Nature Methods.

The examination of epigenomes requires mapping DNA interactions with a certain protein in the entire genome. This epigenomic characterization potentially allows medical doctors to create personalized treatment of diseases by understanding the state of a patient, making the forecast, and tuning the treatment strategy accordingly. However, such tests require a huge number of cells. At one point, the study of in vivo genome-wide protein-DNA interactions and chromatin modifications required approximately 10 million cells for an individual test. This enormous requirement practically ruled out such analysis on patient samples.

Virginia Tech Professor of Chemical Engineering Chang Lu, at left, and his student Zhenning Cao work in the lab. Lu is holding a microfluidic chip used in the study.

For well more than a decade, Chang Lu, a professor of chemical engineering at Virginia Tech, has worked on the development of tools to effectively analyze living cells with the long-term goal of gaining a better understanding of a range of diseases. In his lab, Prof. Lu and his students develop small microfluidic devices with micrometer features for examining molecular events inside cells.

The latest breakthrough comes from Prof. Lu’s collaboration with Kai Tan at the University of Iowa, a systems biologist and associate professor of internal medicine. Together, they demonstrated that a technique called microfluidic oscillatory washing based chromatin immunoprecipitation (MOWChIP-Seq) allows analysis of epigenomic modifications using as few as 100 cells. The description of this advance is in the Nature Methods paper.

The National Institutes of Health, along with a seed grant from Virginia Tech’s Institute for Critical Technology and Applied Science, funded this work.

“The use of a packed bed of beads for ChIP allowed us to collect the chromatin fragments with a very high efficiency. 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” Prof. Lu said.

The entire MOWChIP process takes about 90 minutes as opposed to many hours that conventional ChIP assays took.

Virginia Tech Intellectual Properties has filed a utility patent on MOWChIP-Seq on the behalf of Prof. Lu.

This story can be found on the Virginia Tech News website.

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