Shining a bright light on the reprogramming process

HSCI work broadens understanding of iPS creation

New discoveries have had an impact on the field of stem cell and regenerative biology comparable to that of the creation of induced pluripotent stem cells (iPSCs). The discovery of a process by which mature human cells can be reprogrammed to assume an embryonic-like state opened an entirely new way for researchers to study human disease and cell fate determination. And now HSCI Principal Faculty members Konrad Hochedlinger, PhD, and Chad Cowan, PhD, have published new findings with significant implications for both the understanding and use of iPSCs.
The Hochedlinger lab studies the processes underlying cellular reprogramming, with a focus on the iPSC process. Building upon their own previous research, which identified cell populations with specific cell markers indicative of iPSC generation, Hochedlinger and his team have gained important insights into the mechanisms that underlie iPSC formation.
First, the group observed that the reprogramming process is marked by two distinct periods of gene expression. “The first [period] is maybe not so surprising,” said Hochedlinger. “You turn on these reprogramming factors and a lot of changes are expected. But the second [period] seems to indicate that the cells are ready to acquire pluripotency.” Furthermore, the team noticed a definite hierarchy of molecular changes regulating cellular reprogramming. Interestingly, Hochedlinger said, “The reprogramming process, which is artificial, seems to recapitulate in reverse what’s going on during normal differentiation.” 
The researchers also found that cells that resisted the effects of reprogramming, “refractory” cells, express transcription factors at much lower levels than those cells which become iPSCs. “One reason why reprogramming is so inefficient is because the reprogramming factors you put into an adult cell somehow become dampened in expression in a large fraction of the cells,” said Hochedlinger.
Collectively, these findings illuminate the reprogramming process in greater detail than before, as most previous studies have been limited to the initial stages of cellular response to reprogramming factors. With this increased level of detail, researchers may be able to improve the reprogramming process to make it more efficient, faster, and capable of generating higher-quality iPSCs.
While the Hochedlinger lab was working to answer fundamental questions regarding the processes involved in the production of iPSCs, Chad Cowan’s lab was addressing a fundamental problem with the use of iPSCs in disease-centered research: given the inherent variability among iPS cell lines, how can any particular cell line serve as a control? 
Cowan’s team approached this problem by comparing the cell lines of identical twins, or, more specifically, identical twin cell lines. Utilizing the recently developed technology of genome editing with engineered nucleases, Cowan and his colleagues used a special type of engineered nucleases, transcription activator-like effector nucleases (TALENs), to create identical twin iPSC lines. TALENs can be engineered so that they can recognize any sequence in the genome, bind themselves at either end of that sequence, and then cleanly cleave the DNA allowing scientists to insert or remove specific genes. “By using these genome-editing tools, [we] can vastly improve our ability to alter the genome in any location, and in any way, we want.” The Cowan lab chose to use this technology to alter the genome to isolate and study mutations linked to increased risk of heart attack, diabetes, or obesity.
By applying technology such as TALENs to stem cell biology, researchers can investigate diseases in ways not previously possible, broadening their focus beyond specific cell types to all cells implicated by a biological process. Cowan explained, “I think that it’s really opened the door to do much more exciting disease-oriented biology, because you’ve got the appropriate control and you’ve got the ability to understand any genetically-associated disease risk.”