Portions of this story were written by written by Ian Haydon, Institute for Protein Design
Broadly speaking, the term stem cell refers to a category of cells that give rise to other cells in the body by replicating and differentiating in response to different kinds of cues. Scientists have learned to turn stem cells into many cell types, including heart cells, muscle, kidney cells, neurons, and blood vessels.
While the ability to program stem cells in lab has opened up exciting possibilities for research and therapy, the process is also time-consuming, expensive, and prone to inconsistent results.
One reason stem cell-derived cultures tend to be imperfect is that the growth factors used to nurture the cells contain naturally occurring cells and proteins. This may sound good on a carton milk, but in the lab these ingredients tend to be unstable and degrade quickly, requiring frequent replenishment by hand.
Hannele Ruohola-Baker, PhD is a professor of biochemistry and an associate director of the Institute for Stem Cell and Regenerative Medicine (ISCRM) in University of Washington School of Medicine. For the last few years her lab has been collaborating with their counterparts in the Institute for Protein Design (IPD) to create and test synthetic solutions to problems just like this.
Now, using computer-designed proteins, researchers from ISCRM and IPD have shown they are able to direct human stem cells to form new blood vessels in the lab. This milestone in regenerative medicine offers new hope for repairing damaged hearts, kidneys, and other organs. Their findings appear in the journal Cell.
“Whether through heart attack, diabetes, and the natural process of aging, we all accumulate damage in our body’s tissues. One way to repair some of this damage may be to drive the formation of new blood vessels in areas that need healthy blood supply restored,” said Ruohola-Baker, a senior author of the study. “This collaboration is a case of a biological need propelling a technological advance that could have real-world therapeutic benefit for patients.
Dr. Ruohola-Baker adds that with this investigation, a code has been cracked. For the first time, designed proteins have been used to direct stem cells to become the endothelial cells that form the walls of arteries, a breakthrough that will help scientists model diseases and regenerate this type of blood vessel.
“The outcome is a novel tool for controlling cell fate,” says Ashish Phal, a PhD student in the Ruohola-Baker Lab and a lead author of the study. “The innovation is a computer-designed component that is much easier to make and less time-intensive to manage than current methods of stem cell culturing, including vascular differentiation, which was our focus.”
Growth factors play key roles in tissue development, wound healing, and cancer. By binding to receptors on the outside of cells, these molecules drive changes inside. Researchers have for decades attempted to repurpose natural growth factors as regenerative medicines with some limited success, but many of these experimental treatments have failed due to imprecision.
“We set out to create custom proteins that would engage with cellular growth factor receptors in extremely precise ways. When we made these molecules in the lab and treated human stem cells with them, we saw different kinds of vasculature develop depending on which proteins we used. This is a whole new level of control,” explained Natasha Edman, a lead author of the study and recent graduate of the UW Medical Scientist Training Program.
The researchers used computers to design ring-shaped proteins, each targeting up to eight fibroblast growth factor receptors. They found that by varying the size of the rings and other protein properties, they could control how stem cells matured under laboratory conditions.
The resulting vascular networks were functional and mature. They formed tubes, healed when scratched, and absorbed nutrients from their surroundings as expected. When transplanted into mice, these tiny webs of human blood vessels grew connections to the animal’s circulatory system within three weeks.
ISCRM faculty members Chuck Murry, Beno Freedman, and Ying Zheng are also authors of the study. “We definitely took advantage of the fact that ISCRM is very collaborative,” says Phal. He points to Thomas Vincent, a PhD student in the Freedman Lab who helped the researchers demonstrate that the designed proteins promoted blood vessel growth in mice.
“This study shows that custom proteins with exquisite biological functions can be created by design. This will help scientists understand biology and ultimately prevent and repair disease,” said senior author David Baker, a Howard Hughes Medical Institute Investigator, professor of biochemistry, and director of the Institute for Protein Design at the University of Washington School of Medicine.
Phal emphasizes the broad potential of the findings. “We decided to focus on building blood vessels first, but this same technology should work for many other types of tissues. This opens up a new way of studying tissue development and could lead to a new class of medicines for spinal cord injury and other conditions that have no good treatment options today.”
Acknowledgements:
This research was performed at the Institute for Protein Design and Institute for Stem Cell and Regenerative Medicine at UW Medicine and included collaborators from New York University School of Medicine, Tehran University of Medical Sciences, Yale University School of Medicine, Brotman Baty Institute for Precision Medicine, and Allen Discovery Center for Cell Lineage Tracing.
This work was supported by The Audacious Project, Open Philanthropy, Nordstrom-Barrier Directors Fund, Institute for Protein Design Breakthrough Fund, Brotman Baty Institute, Institute for Stem Cell and Regenerative Medicine Fellows Program, Howard Hughes Medical Institution (GT11817), American Heart Association (19IPLOI34760143), Human Frontier Science Program (LT000880/2019-L), Simons Foundation (SF349247), New York State Assembly, National Institutes of Health (T90DE021984, R01GM097372, R01GM083867, 1P01GM081619, COF220919, U24 GM129539, P30 GM124169, S10OD018483), National Institute of General Medical Sciences (R35GM128777, R35GM150919), National Institute on Aging (R01AG063845, U19AG065156), National Heart, Lung, and Blood Institute (U01HL099997, UO1HL099993),
Department of Defense (PR203328 W81XWH-21-1-0006), Department of Energy, and European Molecular Biology Organization (ALTF191-2021).