Stem cell reprogramming mystery close to being solved

Australian researchers have discovered new evidence in the decade-long mystery concerning stem cell reprogramming — a process by which cells from mature tissues of the body, such as skin, can be deliberately converted into stem cells.

Stem cell reprogramming could theoretically give scientists the capacity to create any type of tissue for transplantation or for the repair of damaged organs, thus holding immense potential for regenerative medicine. However, the ability to carry out cell reprogramming depends on the use of proteins called transcription factors, which help switch specific genes ‘on’ or ‘off’.

In 2006, Japanese researchers discovered the capability of a specific set of four transcription factors to turn mature cells into induced pluripotent stem cells (iPSCs) — a breakthrough that won them a Nobel Prize. Yet more than a decade later, it is still not understood clearly how these reprogramming factors worked.

“You don’t need to know about mechanics to drive a car from A to B, but if something goes wrong or you want to improve the car’s performance, then you do need to know how a car works in order to fix or improve it,” said Associate Professor Jose Polo from Monash University’s Biomedicine Discovery Institute and the Australian Regenerative Medicine Institute.

Associate Professor Polo recently published two studies related to this mystery in the journals Cell Reports and Cell Stem Cell. A third paper, published in Nature Methods, characterised and established a protocol for creating a form of human iPSCs called naïve cells, which closely resemble the first cells of a human embryo.

The Cell Reports study builds on landmark research into iPSCs that Associate Professor Polo conducted in 2012 which described a ‘roadmap’ of what was happening in the process of reprogramming fibroblasts (skin cells) into stem cells.

“Before our 2012 study it was a black box about how the fibroblasts used for reprogramming became iPS cells — we traced the roadmap of what happened,” Associate Professor Polo said.

In this new work, the team found that the roadmap was not the same for every cell type. Using fibroblasts, neutrophils (white blood cells) and keratinocytes (another skin cell type) from animal models, the researchers revealed that the route to pluripotency depended on the original cell type.

Monash biologist Dr Christian Nefzger, co-first author on the paper, said the findings have important implications, noting, “Studying how different cell types convert into pluripotent stem cells revealed that we need to look through different lenses to comprehensively understand and control the process.”

The Cell Stem Cell study, co-led by Professor Ryan Lister from The University of Western Australia and the Harry Perkins Institute, meanwhile unveiled how the four reprogramming transcription factors go into areas of the genome and make specific genes that are encoded in the DNA accessible.

“Genes and other instructions encoded in the DNA sequence are required to build a functional cell,” explained Professor Lister. “But DNA can be switched between an open accessible state and a closed compressed state, which alters how the cell can utilise the underlying DNA sequence.

“This is referred to as chromatin, a complex of DNA and proteins that forms chromosomes within the cell nucleus and that influences how information stored in the DNA sequence is used by the cell.”

The researchers used advanced genome analysis techniques to watch how the chromatin was reconfigured throughout the cell reprogramming process, from specialised cells into iPSCs. “Through this,” said Professor Lister, “we were able to see in great detail how some cells reprogram successfully, while others don’t, and learn how to improve the efficiency of the conversion process.”

“This has unveiled areas of the chromatin and transcription factors that previously we didn’t know were important in pluripotency,” Associate Professor Polo added.

“In a very simplified version, we found that the reprogramming factors open other areas on the chromatin, while the transcription factors that control the skin get ‘lost’ in these areas, forget to control their own genes and get shut down.

“In this way, the reprogramming factors can open the areas involved in the pluripotency program.

“Now that we know they’re significant, we can study these areas in more detail and see what role they may play in development, regeneration or even cancer.”

According to Associate Professor Polo, the researchers’ findings may pave the way in the future for tissues to be regenerated within the human body rather than in the laboratory, for the production of ‘synthetic cells’ with properties tailored to the needs of researchers or clinicians, or for the production of drugs that mimic these factors.

“Through our molecular analyses we were able to better understand and consequently improve the reprogramming process, which is essential if we want to eventually move this technology into clinical applications,” said Dr Anja Knauppco, co-first author from Monash University.

Artwork designed by Scot Nicholls, scot@ancientlakes.com.au