Embryonic cells use Yamanaka factors to defy developmental "gravity"
Waddington's Landscape
February 20, 2021
By Christopher Vaughan
It has long been an accepted principle of development that cells give rise to other cells that have the same or less potential for producing various kinds of tissues. Embryonic stem cells can give rise to blood stem cells and neural stem cells, but neural stem cells will never give rise to blood and immune cells outside of the laboratory. Conrad Waddington nicely illustrated this process with his famous landscape showing a ball, representing a cell, that can roll down a hill and funnel into one valley or another (one cell fate or another). But once it has chosen the blood and immune path, for instance, a cell can’t jump the ridge to the next valley over and become a muscle cell, for instance. In nature, it is thought, cells’ fates are progressively restricted--anything else would be like a ball starting to roll uphill.
Now, however, researchers in the laboratory of institute scientist Joanna Wysocka, PhD,with some help from the lab of institute director Irv Weissman, MD, have shown that some cells in the early can effectively defy epigenetic gravity, rolling up Waddington’s landscape and becoming more pluripotent instead of less. And perhaps just as surprising, the cells do it using factors that Shinya Yamanaka previously showed could create pluripotent cells in the lab. Yamanaka’s work, which garnered him the Nobel prize, had never been shown to operate developing organisms. Wysocka and her colleagues published their work recently in the Journal Science.
The Wysocka lab has long been studying an early embryo cell group called the neural crest, focusing on a particular portion that gives rise to the face. Cells in the neural crest have already chosen their path down Waddington’s landscape to become ectoderm, which gives rise to cells in the nervous system. This ectodermal tissue should not be able to give rise to muscle, bone and connective tissue, which usually come from another type of tissue called mesoderm.
“There were some ideas about how neural crest cells could give rise to the very different kinds of cells in the face, such as perhaps there was small subset of cells that had retained their pluripotency and ability to produce mesenchymal tissues, “Wysocka said.
The insight to what was going one came after the researchers stared doing single-cell RNA sequencing on cells in the neural crest, allowing them to look at what proteins particular cells were making at different times in development.
Joanna Wysocka, PhD
Famed writer Issac Asimov once said that the most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny …' Antoine Zalc, PhD, a postdoctoral fellow in Wysocka lab and lead author on the Science paper, noticed something that at first seemed like an odd coincidence. “I was giving a talk on our data and I pointed out that, strangely enough, these neural crest cells were producing Oct4 and Nanog,” Zalc said, naming two of the widely known factors that Yamanaka showed could be used to transform mature cells into pluripotent cells in the lab.
Wysocka prompted him to follow up on this observation, and after much more single cell sequencing and analysis done with Rahul Sinha, PhD and medical student Gunsagar Gulati of the Weissman lab, they showed that a small subset of cells in the neural crest could express Yamanaka factors themselves and reverse the differentiation process, turning themselves into cells that could give rise to the kinds of cells they were unable to produce before. For just a bit, Waddington’s ball can indeed defy gravity and roll itself uphill.
“It’s also amazing to me that the cells do this using the Yamanaka cocktail of factors,” Wysocka said. “You would think that if increasing pluripotency is possible, there might be many other ways of doing it, but this suggest that there is something universal in the four factors that is hard to accomplish in other contexts.”
The researcher now wonder what this means for our understanding of development and other biological processes. “This work is a game-changer,” Weissman said.
“The developmental neural crest is somewhat unique, but I wonder if this reactivation of earlier gene programs happens in other instances, like in regeneration, for instance,” Wysocka says.
"This is evidence of how teamwork between computational and bench biologists can lead to exciting discoveries.
Wysocka notes that there have been observations that sometimes Yamanaka factors like Oct4 have been spotted in cancer cells, and it has been discounted as an inconsequential sign of how dysregulated cancer cells have become. “We are now thinking that perhaps, in some contexts, expression of these factors in cancer cells might help them adapt and colonize new niches,” she said.
The researchers note that further work must be done to understand the molecular process that is going on in the neural crest cells in reaction to the Yamanaka factors. Understanding more thoroughly how nature uses these factors may lead to new capabilities and more precise control of their use in the lab.
The researchers also note that this work is a testament to the benefits of interdisciplinary research. “Overall, this project greatly benefited from the collaboration between different labs and disciplines,” said Gulati, who is pursuing an MD degree while also earning a PhD in cancer biology with a strong emphasis in computational biology. “It is evidence of how teamwork between computational and bench biologists can lead to exciting discoveries.”
Other Stanford researchers involved in the work were Tomek Swigut, a senior scientist in the Wysocka lab, and Daniel Wesche, a graduate student in the ISCBRM program.
The departments of Chemical and Systems Biology and Developmental Biology were also involved in the research.