UK Team Identifies Genes Involved in NaÏve Pluripotent Stem Cells Reprogramming

Researchers in the United Kingdom have used a genome-wide functional screen to identify factors used in naïve stem cell reprogramming. By describing critical regulators of the process, the findings advance potential for more efficient and faster generation of human naïve pluripotent stem cells (PSCs).

PSCs are a useful tool for investigating how cells specialize to make every tissue of our body. They come in two different states—primed and naïve. Both types of PSC can self-renew and differentiate into new cell types, but they have distinct functions and molecular characteristics.

The majority of reprogramming experiments generate primed PSCs, which are more developmentally advanced than naïve PSCs.  Naïve PSCs can be collected directly from human pre-implantation embryos, or more commonly researchers expose primed PSCs to conditions that induces them to become naïve.

But existing methods for reprogramming are inefficient and slow, preventing researchers’ from quickly producing the numbers of high-quality stem cells they needed.  This low efficiency of naïve reprogramming suggests the presence of barriers that limit cells in reaching the naïve state.  “Very little was known about what genetic and epigenetic factors are required for naïve cell reprogramming, and this knowledge gap limited the design of reprogramming conditions,” says Adam Bendall, a PhD student in Babraham Institute’s Epigenetics research program and a lead researcher on the study.

Bendall and colleagues homed in on these barriers by performing a large-scale genetic screen to identify genes that hinder and help reprogramming. They were able to identify a large number of genes that have a crucial role in naïve PSC programming but had not been previously linked to the process.

“Human PSCs in the naïve state replicate the key molecular and cellular characteristics of cells in a pre-implantation stage embryo,” says group leader Peter Rugg-Gunn. “Importantly, when naïve PSCs are encouraged to self-organize in particular conditions, they form structures that resemble an early blastocyst stage of development. By growing these cells in the lab, we can learn about the key events that happen during human development, and they have potential uses in personalized medicine. But we need to create high-quality, stable stem cell populations to be able to conduct our experiments.”

The team focused on one epigenetic complex in particular, the PRC1.3 complex, that regulates gene expression without altering the underlying DNA sequence, and which they found to be essential for the formation of naïve PSCs. Without this complex, the cells undergoing reprogramming become a completely different type of cell rather than naïve PSCs. This suggests that the activity of PRC1.3 could encourage more cells to reprogram properly, in effect lowering the barrier.

After identifying factors that promote reprogramming, the researchers also looked at those that impede reprogramming. In doing so, they identified epigenetic protein HDAC2.  “Excitingly, when we inhibited one of these factors using selective chemicals, then naïve PSC reprogramming occurred more efficiently and rapidly,” says coauthor Amanda Collier. “We’re able to look at it from both sides; we can remove the barriers and introduce the factors that push cells towards state change.”

The research improves scientists’ ability to produce human naïve PSCs and also provides details on the molecular events that occur during the cell state transition itself. Some of these molecular events are conserved in developmental regulation in human embryos.

 “By building up our tools for manipulating pluripotent stem cells, we can spend more time asking important questions about the pre-implantation embryo,” Rugg-Gunn says. “In the longer term, further improvements in working with naïve PSCs might open up the possibility for using these cells in personalized disease models or cell therapies, although this will require more research on how to differentiate naïve PSCs into specialized cell types.”

Their findings were published recently in Science Advances.