Genomic analysis gives new insights into cellular reprogramming

A cross-disciplinary team of Harvard University, Whitehead Institute, and Broad Institute researchers has uncovered significant new information about the molecular changes that underlie the process by which adult cells can be reprogrammed to a stem cell-like state. Their findings are published online on May 28, 2008, in the journal Nature.

“We used a genomic approach to identify key obstacles to the reprogramming process and to understand why most cells fail to reprogram,” said Alexander Meissner, Assistant Professor in Harvard’s new inter-school Department of Stem Cell and Regenerative Biology and Associate Member of the Broad Institute, who led the multi-institutional effort.

“Currently, reprogramming requires infecting somatic cells with engineered viruses,” continued Meissner, who is also a member of the Principal Faculty of the Harvard Stem Cell Institute. “This approach may be unsuitable for generating stem cells that can be used in regenerative medicine. Our work provides critical insights that might ultimately lead to a more refined approach,” he said. 

Previous work had demonstrated that four transcription factors — proteins that mediate whether their target genes are turned on or off — could drive fully differentiated cells, such as skin or blood cells, into a stem cell-like state, known as induced pluripotent stem (iPS) cells. Building off of this knowledge, the researchers examined both successfully and unsuccessfully reprogrammed cells to better understand the complex process.

“Interestingly, the response of most cells appears to be activation of normal ‘fail safe’ mechanisms”, said Tarjei Mikkelsen, a graduate student at the Broad Institute of Harvard and MIT and first author of the Nature paper. ”Improving the low efficiency of the reprogramming process will require circumventing these mechanisms without disabling them permanently.”

The researchers used next-generation sequencing technologies to generate genome-wide maps of epigenetic modifications — which control how DNA is packaged and accessed within cells — and integrated this approach with gene expression profiling to monitor how cells change during the reprogramming process. Their key findings include:

• Fully reprogrammed cells, or iPS cells, demonstrate gene expression and epigenetic modifications that are strikingly similar, although not necessarily identical, to embryonic stem cells.

• Cells that escape their initial fail safe mechanisms can still become ‘stuck’ in partially reprogrammed states. By identifying characteristic differences in the epigenetic maps and expression profiles of these partially reprogrammed cells, the researchers designed treatments using chemicals or RNA interference (RNAi) that were sufficient to drive them to a fully reprogrammed state. One of these treatments, involving the chemotherapeutic 5-azacytidine, could improve the overall efficiency of the reprogramming process by several hundred percent.

“A key advance facilitating this work was the isolation of partially reprogrammed cells,” said co-author Jacob Hanna, a postdoctoral fellow at the Whitehead Institute, who recently led two other independent reprogramming studies. “We expect that further characterization of partially programmed cells, along with the discovery and use of other small molecules, will make cellular reprogramming even more efficient and eventually safe for use in regenerative medicine.”