Bioengineers at UC San Diego have developed a breakthrough method for sequencing-based methylation profiling, which could help fuel personalized regenerative medicine and even lead to more efficient and cost-effective methods for studying certain diseases.
To do this, the researchers, led by Kun Zhang, a bioengineering professor in the UC San Diego Jacobs School of Engineering, developed an accurate assays for quantifying DNA methylation digitally on an arbitrary set of nonrepetitive genomic targets using padlock probes.
Zhang and his group describe the breakthrough in a recent paper published in Nature Biotechnology titled "Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming."
DNA methylation is a type of chemical modification of DNA that can be inherited and subsequently removed without changing the original DNA sequence. Current DNA methylation assays are limited in the flexibility and efficiency of characterizing a large number of genomic targets, and are extremely costly (more than $100,000). The method created by Zhang and his team will allow researchers to perform such assays at a significantly lower cost, he said.
"What we reported in this paper is a novel method that allows us to do target analysis on the subset of the genome where we think the memory could be stored," Zhang said.
"This is a generic method for the analysis of epigenome," he added. "The application to induced pluripotent stem cells is one example to demonstrate the utility of this method. The method we developed would be widely applicable to other area of biomedical sciences, such as the study of cancers or Alzheimer's disease."
Epigenetics is an emerging frontier of science that involves the study of changes in the regulation of gene activity and expression that are not dependent on gene sequence. While epigenetics refers to the study of single genes or sets of genes, epigenomics refers to more global analysis of epigenetic changes across the entire genome.
Zhang's team – which includes researchers from Harvard University, Virginia Commonwealth University and the University of Wisconsin, Madison – used their novel method to study nuclear reprogramming of differentiated adult human cells into pluripotent stem cells.
"We found that nuclear reprogramming based on the existing retroviral carriers appears to result in over-reprogramming, which will have profound implications on the use of induced pluripotent cells for personalized regenerative medicine," Zhang said. "The surprising finding is that all current similar methods seem to be over re programming so they push the cell fate too far. Once we turn the clock back we want to turn it forward again to a certain tissue type to fixed damage tissues in patients. You want to turn it back just enough. If you turn it back too far it might be hard to bring it back. We found that the first generation of (reprogramming) cocktails that people have developed is not perfect yet. One of the biggest concerns about regenerative medicine is that stem cells can cause tumors. You want to control that."
Zhang and his team are using this new method to compare the use of artificial and natural stem cells.