A crowning achievement in understanding head development

How does a stem cell decide what to be when it grows up? Stem cells are remarkable for their ability to differentiate into all manner of specialist cell types, but the genetic instructions that map out their destinies are generally mysterious.

To better understand the versatility of these cells, scientists from the Crump Lab at the University of Southern California (USC) created a series of atlases over time to map the molecular decisions by which a particular type of stem cell commits to forming specific tissues in developing zebrafish.

Their research, published in Nature Communications­, tracks the fate of cranial neural crest cells (CNCCs), which not only form most of the skull and facial skeleton in all vertebrates ranging from fish to humans, but also can generate everything from gills to the cornea.

The researchers hope their findings may provide new insight into normal head development, as well as craniofacial birth defects.

“CNCCs have long fascinated biologists by the incredible diversity of cell types they can generate,” says Gage Crump, professor of stem cell biology and regenerative medicine at USC’s Keck School of Medicine.

“By studying this process in the genetically tractable zebrafish, we have identified many of the potential switches that allow CNCCs to form these very different cell types.” 

Led by postdoc Peter Fabian, the team of scientists permanently labelled CNCCs with a red fluorescent protein, then tracked which cell types originated from these dyed CNCCs throughout the lifetime of zebrafish.

They then used an approach known as “single-cell genomics,” to identify the complete set of active genes and the organization of the DNA across hundreds of thousands of individual CNCCs.

Making sense of such an enormous data set required the team to develop a new computational tool to make sense of it.

“We created a type of computational analysis that we called ‘Constellations’, because the final visual output of the technique is reminiscent of constellations of stars in the sky,” says Fabian.

“In contrast to astrology, our Constellations algorithm really can predict the future of cells and reveal the key genes that likely control their development.”

Through this new bioinformatic approach, the team discovered that CNCCs do not start out with all the information required to make the huge diversity of cell types. Instead, only after they disperse throughout the embryo do CNCCs begin reorganizing their genetic material in preparation for becoming specific tissues. Rather than fates written in the stars, the final destinies of CNCCs are shaped directly by their surrounds.

Constellations accurately identified genetic signs that point to these specific destinies for CNCCs. Real-life experiments confirmed that Constellations correctly pinpointed the role of a family of “FOX” genes in facial cartilage formation, and a previously unappreciated function for “GATA” genes in the formation of gill respiratory cell types that allow fish to breathe.

“By conducting one of the most comprehensive single-cell studies of a vertebrate cell population to date, we not only gained significant insights into the development of the vertebrate head, but also created a broadly useful computational tool for studying the development and regeneration of organ systems throughout the body,” says Crump.