Epigenomic analysis typically requires millions of cells, making it difficult to acquire the needed cells for a test from patient samples. Researchers have now addressed this problem, coming up with new technology that requires just 100 cells for an assessment.
Examining epigenomes require mapping out interactions in the DNA involving a certain protein. It's a very thorough look at the epigenome that paints an accurate picture of the current state of a patient and this allows doctors to produce highly personalized treatment for diseases. Unfortunately, studying in vivo protein-DNA interactions across the genome as well as chromatin modifications called for about 10 million cells for a single test. This was a number that made it impossible to start analyses using patient samples already on hand.
In a study published in Nature Methods, Zhenning Cao and colleagues showed how research done by Chang Lu, also one of the authors of the study, has resulted in the development of tools that can analyze living cell samples effectively. Specifically, Lu was able to produce in his lab small microfluidic devices fitted with micrometer features that can examine cell events at the molecular level.
Lu demonstrated with Kai Tan a technique known as microfluidic oscillatory washing based chromatin immunoprecipitation (MOWChIP-Seq), which allowed epigenomic modifications to be analyzed using dramatically less cells compared to the previous requirement.
The study received funding support from the National Institutes of Health and the Institute for Critical Technology and Applied Science at Virginia Tech. In behalf of Lu, the Virginia Tech Intellectual Properties has also filed a patent on the technique that was developed.
Lu explained that using a packed bead bed allowed the researchers to collect chromatin fragments in a highly efficient manner while effective washing removed debris and undesired molecules from the sample to guarantee purity.
"These two factors constitute a successful strategy for epigenomic analysis with extremely high sensitivity," he added.
The conventional method of assessing epigenome interactions usually lasts for many hours while the MOWChIP process will only need around 90 minutes to finish. According to the researchers they are planning to continue their research by exploring how the technology can be used to study other changes in the epigenome associated with cancer and inflammation.
Bing He and Changya Chen also contributed to the study.
