South Lake Union skyline
The collaboration between ISCRM and IPD is based in the thriving Seattle biotech hub of South Lake Union.

Designed Regeneration is a story about very small solutions to very big problems. It takes place in Seattle, at the University of Washington, home to the Institute for Stem Cell and Regenerative Medicine (ISCRM) and the Institute for Protein Design (IPD).

The plot, which involves lab-grown cells, manmade proteins, and the most urgent health threat in a century, feels like science fiction. In fact, it is a very real, and very promising example of the spirit of innovation and collaboration that have defined UW Medicine and the Pacific Northwest for decades.

And, in an exciting twist, the partnership known as DREAM (Designed Regeneration for Medicine) just received a significant grant from the Department of Defense that will allow ISCRM and IPD to push the boundaries of medicine together – starting with COVID-19.

Stem Cells and Biological Pathways

ISCRM Wordle
Since 2008, ISCRM researchers have been confronting many of the deadliest and costliest human diseases.

Since 2006, hundreds of biologists, engineers, physicians, and other specialists in more than 130 ISCRM-affiliated labs have been using stem cells as tools of discovery and treatment to fight heart disease, Alzheimer’s, diabetes, muscle disorders, and other conditions impacting billions of people worldwide.

Stem cells, the cells that give rise to almost all other cells, enable organisms to develop, grow, and replenish tissue lost to injury, disease, and natural attrition. In regenerative medicine, researchers use stem cells to study diseases, to test drugs in labs without involving humans or animals, and, in some cases, as therapies in patients.

Hannele Ruohola-Baker, PhD is a Professor of Biochemistry and an Associate Director of ISCRM. Her lab studies what makes stem cells tick. “Our goal is to answer questions about the fundamental biology of stem cells,” says Dr. Ruohola-Baker.  “We study how nature makes a human from a single cell, a fertilized egg, and how to protect and ultimately unleash that same potential in stem cells by teaching them how to survive, stay young and differentiate, and what causes diseases to arise when these processes are abnormal.”

Regulating Biological Pathways

Of particular interest to the Ruohola-Baker Lab are biological pathways –  the chemical telegraph systems proteins and other molecules use to relay instructions within cells or between cells.  Wound healing, metabolism, and gene regulation are all controlled by biological pathways. One such pathway, known as Tie2, is a key part of this story.

Faculty headshot of Hannele Ruohola-Baker, PhD
Hannele Ruohola-Baker, PhD, is a Professor Biochemistry and Associate Director of ISCRM

Through ongoing research that began in fruit flies before shifting to human stem cells, Dr. Ruohola-Baker and her team have helped to demonstrate the importance of the Tie2 pathway to stem cells and to the growth and maintenance of blood vessels. That raised a question. Is it possible to regulate this pathway – and therefore build stronger vessels?

Yan Ting (Blair) Zhao, a graduate student in the Ruohola-Baker Lab, believes it is. Zhao, who is based in the School of Dentistry, explains that a pair of genes, Ang1 and Ang2, signal cells to turn on or turn off angiogenesis (or blood vessel formation) via the Tie2 pathway – in other words, to speed up or slow down blood vessel development, respectively.

“We’re using a computationally designed protein to analyze the regulation of Tie2 and to understand why Ang1 and Ang2 lead to such different outcomes,” says Zhao. The key, according to Zhao, who conducted her investigation with Shally Saini, a visiting scientist in the Ruohola-Baker Lab, is the number  of binding mechanisms – known as F-domains – that activate the receptors on the surface of cells.

Magnified image of a protein molecule
Magnified image of the designed protein scaffold that, in lab experiments, accelerated wound healing and vascular stabilization by activating the Tie2 pathway. F-domains are shown in purple. Designed protein scaffold components are shown in gray.

More than six F-domains seems to stimulate increased blood vessel stability or repair, while fewer F-domains is a marker of Ang2-like action – resulting in destabilized blood vessels. Far from being an evil twin, however, Ang2 provides a vital service by cutting off unwanted blood vessel growth, initiating normal vascular remodeling, and, at other times, recruiting immune cells to fight off infection.

Not surprisingly, the ability to regulate the Tie2 pathway has been a holy grail for medical researchers.  The experiments in the Ruohola-Baker Lab suggest the quest may lead to even better outcomes: Zhao found that the synthetic protein scaffold was capable of promoting wound healing more effectively than naturally occurring Ang1 and Ang2.

Building Proteins From Scratch

Zhao is not the only University of Washington researcher curious about the possibility of controlling the Tie2 pathway.  Ariel Ben-Sasson, a Senior Fellow in the Baker Lab in the Institute for Protein Design, uses computational methods to create 2D arrays of proteins. Rather than reproduce proteins that exist in nature, Ben-Sasson uses computers to build proteins from scratch for specific functions.

Ariel Ben-Sasson
Ariel Ben-Sasson is a Senior Fellow in the Baker Lab in the Institute for Protein Design

Ben-Sasson is the lead author of a paper, published in the journal Nature, that describes this work. Dr. Ruohola-Baker and Logesh Somasundaram, a visiting scientist in her lab, are co-authors of the paper; the lead investigator is David Baker, PhD, a Professor of Biochemistry and the Director of IPD. The study was also conducted in partnership with the Derivery lab at the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK.

“We know that combinations of proteins have more functional possibilities and applications than any single protein, says Ben-Sasson. “I design practical, stable materials that can be used to solve problems in simple ways.  These materials are built to interact intimately with cells and to apply forces that act on cells – for example, to activate and regulate the Tie2 pathway.”

In the case of the Tie2 pathway, Somasundaram and Ben-Sasson have figured out how to cluster Tie2 receptors at certain locations on the surfaces of cells. This ability to localize cell behavior to a certain point at a certain time is crucial for cell biologists or tissue engineers who want to direct cells to differentiate – or to block biological activity.

Ben-Sasson offers an analogy.  “You can compare it to a brain-computer interface. To do that, you need precise tools that connect the computer to the brain all the way down to the individual cells. Traditionally, that’s done with very thin wires. Protein design lets us build tools out of biological parts that can target cells and influence them. It’s a totally new means of cellular manipulation.”

David Baker
David Baker, PhD is the Director of the Institute for Protein Design, a Professor of Biochemistry, and a Howard Hughes Medical Institute Investigator

In the case of the Tie2 pathway, Ben-Sasson is particularly interested in the binders that cluster receptors that, in turn, either turn on or off the blood vessel growth Zhao studies as a biologist. “We have a protein scaffold that can control a biological process,” says Ben-Sasson. “That, combined with ISCRM’s expertise in stem cell biology and modeling, is what adds up to a new technology.”

Dr. Baker echoes Ben-Sasson. “It’s very exciting to think what we can accomplish by pairing advances in protein design and stem cell biology. We’re particularly interested in designing proteins that have therapeutic utility for regenerative medicine. The DOD grant accelerates our partnership with ISCRM at a critical time for public health.”


Combating COVID-19

There is a good reason ISCRM and IPD are keen to regulate pathways like Tie2. Something like an on/off switch for Tie2 could help physicians control one of the deadliest aspects of COVID-19 – the body’s own inflammatory response to infection. In this cytokine storm the immune system goes into overdrive, ultimately doing lasting damage to the organs it is trying to protect from the virus.

High resolution image of designed scaffolds
Tie2 receptor concentrates (purple) where the designed sheets (green) form at the cell membrane, activating signaling and cytoskeletal rearrangements (gold).

ISCRM and IPD are now ready to show that their designed regeneration technology could help physicians combat COVID-19 by modulating the inflammatory response. “Designed regeneration is the use of synthetic proteins to heal patients at the cellular level,” says Dr. Ruohola-Baker. “We believe everything we have learned from Blair, Ariel and others about regulating biological pathways with designed proteins has the potential to save many lives by minimizing the danger of sepsis.”

The effort to develop and test designed regeneration approaches to preventing and treating COVID-19 will be fueled in part by a $3.4 million grant from the Department of Defense. According to Ruohola-Baker the funding is critical because it will enable the research team to show that this computer-assisted take on medicine is safe and effective in the fight against COVID-19 and future viruses.

Dr. Ruohola-Baker and her ISCRM colleagues Drew Sellers, PhD and Ying Zheng, PhD, both Associate Professors of Bioengineering, have already shown in stem cell-derived tissue that synthetic proteins are capable of repairing leaky blood vessels – one example of the friendly fire an inflammatory response can inflict on the body – and can reduce neurodegeneration in mice with brain injuries.

How would a designed regeneration treatment work in the hospital? For a patient at-risk for sepsis, relief could come in the form of a protein scaffold delivered into the body, where it would bind to Tie2 receptors on the surfaces of distressed cells and act as a regulator to help care teams take control of the inflammation by directing the pathway in whichever direction restores the body to a healthier state.

COVID-19 image
ISCRM and IPD are developing designed regeneration approaches to treating and preventing COVID-19 infections.

The Department of Defense grant will also allow ISCRM and IPD to test the viability of proteins designed to protect cells from infection in the first place. In November 2020, an article in Science described a protein designed to bind to the spikes that allow the virus to bind to the surface of cells. DOD funding will enable ISCRM and IPD to test the safety of these proteins, which could potentially become a more cost-effective and efficient antibody than traditional vaccines.

According to Dr. Ruohola-Baker, who is a co-PI on the DOD grant, the goal is to make a double hit, combination therapy by designing mosaic scaffolds that will neutralize the virus and heal sepsis at the same time.  Furthermore, mosaic scaffolds can target the treatment to correct cells. The strategy will be tested in differentiated stem cells and in stem cell-derived kidney organoids grown in the lab of the grant’s other co-PI, Dr. Beno Freedman, PhD, Associate Professor of Medicine and Nephrology.

Preserving Blood Vessel Health

Preserving or restoring blood vessel health by regulating the Tie-2 pathway could give physicians entirely new ways to treat COVID-19, heart disease, and diabetes, and even mitigate the downstream effects of strokes, including Alzheimer’s disease.

The healing potential of designed regeneration reaches farther still, explains Dr. Baker. He points to an induced biological process known as trans-differentiation. “We’re now asking whether we can design proteins that control stem cell differentiation. If we can design proteins that cause cells to switch their fates, that would have huge medical implications at a fundamental level.”

Dr. Ruohola-Baker underscores the translational potential of the project, which has received an Innovative Project Award from the American Heart Association.  “We know we can reprogram adult cells to an undifferentiated stem cell  state, and then differentiate them forward. The breakthrough would be to use designed proteins to signal a differentiated cell to become another kind of cell without going backwards. For example, we could coax fat or scar cells to become muscle cells without having to put any new cells in the body.”

In another crossover investigation, ISCRM faculty member Julie Mathieu, PhD, Assistant Professor of Comparative Medicine, is exploring the use of a designed protein technology that interacts with antibodies to activate a pathway, known as TNF alpha. This pathway induces cell death in cancer cells. Mathieu is also a co-investigator on the Department of Defense grant, along with ISCRM colleagues Dr. Freedman, and Hongxia Fu, PhD, Assistant Professor of Medicine and Hematology.

For all the exciting potential, the investigators note that the thriving partnership came about serendipitously, in part because of the same virus it is now attempting to treat and prevent. In an era of social distancing, it was a need for elbow room that led IPD, which is based on UW’s main campus, to set up a satellite operation in ISCRM lab space.

“In many ways, the collaboration emerged just from ISCRM and IPD researchers working in proximity to each other,” says Baker. “Everything sped up after that. We’re very grateful to ISCRM for sharing their space and for their partnership.”


This research was supported by the UK Medical Research Council, UK Engineering and Physical Sciences Research Council, Wellcome Trust,Human Frontier Science Program, Howard Hughes Medical Institute, US National Institutes of Health, US Department of Energy Office of Basic Energy Sciences Biomolecular Materials Program at Pacific Northwest National Laboratory, Medimmune, and Infinitus.