Researchers develop novel techniques to understand stem cell reprogramming and differentiation

By Sathya Achia Abraham

Virginia Commonwealth University is part of two national research teams that have developed epigenetic profiling technologies that may prove useful tools for researchers studying stem cell reprogramming and differentiation.

The two studies, both published online in the Advance Online Publication issue of Nature Biotechnology this week, are a collaboration between researchers based at Harvard Medical School, MIT, the University of California at San Diego, the University of Wisconsin-Madison and the VCU Center for the Study of Biological Complexity and the Department of Computer Science in the VCU School of Engineering.

“In stem cell reprogramming adult cells can be reprogrammed to become induced pluripotent stem cells, which are like embryonic stem cells, and can be further induced to become a specific cell type,” said Yuan Gao, Ph.D., an assistant professor in the Department of Computer Science in VCU’s School of Engineering and the VCU Center for the Study of Biological Complexity in the Life Sciences, who co-led one of the studies and contributed significantly to the other.

“Researchers are interested in reprogramming stem cells because terminally differentiated cells, such as skin cells, can be taken from a patient and reprogrammed into induced pluripotent stem cells. Induced pluripotent stem cells can then be further induced to the specific cell types that can potentially cure disease,” he said.

For example, clinicians could one day treat various blood and immune disorders by injecting stem cells destined to grow blood and immune-system cells, much like bone marrow transplant, without the fear of rejection, Gao said.

The research teams have made two technological advancements in quantifying DNA methylation levels – a process that is important in epiegentic regulation. Epigenetics refers to the study of the modifications of DNA and the surrounding proteins found in chromosomes that turn genes on and off and that can be passed on after cell division in an individual. Traditionally, researchers have focused their attention on changes to the DNA base code as being responsible for altered gene expression in disease.
 
According to Gao, in the first paper by Deng et al., the team used the padlock probe approach to specifically capture a subset of genomic targets for single-molecule bisulfite sequencing and to quantify DNA methylation at single-nucleotide resolution.

In the second paper by Ball et al., the team developed a bisulfite padlock probes approach and methyl sensitive cut counting approach to quantify DNA methylation and demonstrated that results from both approaches are highly correlated.

“By applying the two methylation quantification methods to profile the methylation patterns in different human cell lines, we find the interesting pattern of gene body methylation in highly expressed genes. Our results also support previous findings that genes with promoters containing an intermediate level of CpG density have the highest expression related differences in promoter methylation,” said Gao. CpG is the site where methylation takes place.

Bin Xie, a senior research associate, from the Gao Lab contributed to both studies.

This work was supported by grants from the National Institutes of Health.