Form follows function in the latest chapter of a fruitful collaboration involving two University of Washington research centers – the Institute for Stem Cell and Regenerative Medicine (ISCRM) and the Institute for Protein Design (IPD).
In this case, the integration of form and functions refers to a technology in which computer-designed proteins drive the assembly of antibody proteins into well-defined structures known as nanocages that outperform mother nature in helping the body cope with diseases.
These spherical nanocages, designed by scientists from IPD, supercharge the antibodies by clustering them, increasing their potency, and making them more effective at combating many deadly diseases and disorders, including cancer and COVID-19, that have proven difficult to treat or cure.
Antibodies are naturally programmed to target specific molecules, such as a virus, and neutralize the threat by binding to the surface of the pathogen. Other types of antibodies are capable of regulating cell-to-cell communication pathways that control a wide range of biological functioning.
How signaling pathways function and control regeneration is a topic of interest for Hannele Ruohola-Baker, PhD, a Professor of Biochemistry and Associate Director of ISCRM. Under the banner of Designed Regeneration for Medicine (DREAM), the Ruohola-Baker lab has partnered with IPD researchers over several years to translate protein design technology into therapies that might someday help patients in clinical settings.
The DREAM researchers have been especially interested in the Tie2 pathway, which plays an important role in blood vessel growth and maintenance. Diseases like COVID-19 can significantly impair blood vessel health, leading to dangerous conditions, like sepsis. The Tie2 pathway, which is regulated by proteins known as Ang1 and Ang2 have also allowed the ISCRM and IPD investigators to test the efficacy of protein design.
Yan Ting (Blair) Zhao, a graduate student in the Ruohola-Baker Lab has teamed up with her IPD counterparts to show that the expression of Ang1 and Ang2 is related to the number of binding mechanisms, known as F-domains – that activate receptors on the surface of cells, a finding that influenced the design of a protein scaffold engineered to modulate the Tie2 pathway, a potentially life-saving intervention, say, for patients experiencing severe inflammatory responses to viral attacks.
Zhao’s Tie2 research has helped set the foundation for the nanocage technology, which is described in a cover story in the journal Science. IPD investigator Robby Divine, a graduate student in the Department of Biochemistry, is the study’s lead author. (Among the listed authors are ISCRM faculty members Julie Mathieu and Hannele Ruohola-Baker, along with the following members of the Ruohola-Baker lab: Yan Ting (Blair) Zhao, a graduate student in the Department of Oral Health Sciences in the UW School of Dentistry, and visiting scientists Shally Saini and Infencia Xavier Raj.)
Divine explains the novelty of the antibody nanocages. “What makes these nanoparticles unique is that they are built with antibodies as structural and functional components. That makes the nanocages easier to produce, because antibodies are so readily available.”
The paper in Science describes the proteins that assemble antibodies into nanocages, demonstrates that the proteins will form in a lab just as a computer model would predict, and illustrates several applications of the technology. That last part, says, Divine benefited most from the DREAM partnership with ISCRM.
“When it comes to signaling applications, ISCRM has the knowledge. If I can make a protein that might be useful or interesting to study, possibly for translational value, they bring the expertise in biology and in designing experiments that teach us more about signaling pathways, like Tie2.”
Ruohola-Baker offers the ISCRM perspective.
“Protein design allows us to use what nature has provided and takes it a step farther. Our bodies make antibodies to fight antigens. Here we make antibodies work better through the use of small, designed, self-assembling proteins that, like a magnetic toy, attract the antibodies through their Fc-region to high-valency structures. We then show that these novel designed forms contribute to more effective regeneration and greater potency against cancer.
That’s a combination of IPD innovation and ISCRM’s expertise in regenerative medicine.”
Infencia Xavier Raj, a visiting scientist, echoes Ruohola-Baker. “I’m amazed by the thought of using nanocages with natural elements to target specific pathways, like Tie2, that play an important role in so many diseases,” says Raj, who performed experiments to understand how to make the technology more efficient and how to apply it on a broader scale.
Much of Raj’s work was done in the early month of the COVID-19 pandemic, when safety guidelines required her to be alone in the lab. “It was hard,” she recalls. “There was nobody there to talk to, to guide me. But there was also a motivation to come to the lab, to do my research, to do the science, to do something that will benefit mankind.”
Shally Saini joined the Ruohola-Baker lab as a visiting scientist from India, specifically to work on protein design in stem cells, and to explore the use of the technology to develop cancer treatments. Saini, whose motivation as a cancer researcher is fueled by the loss of several family members to the disease, hopes to improve the outlook for cancer patients by making existing antibodies more effective. “There are cases of antibody drugs that targeted some cancer cells, but ultimately failed because the cancer cells developed resistance. We were able to show that nanocage technology can be used to generate more complete cancer cell death while preserving healthy cells.”
Joining Saini on the cancer front was Mathieu, who earned her PhD in France studying the TRAIL pathway, which plays a role in the programmed cell death of cancer cells. As an ISCRM postdoc Mathieu further showed that TRAIL pathway plays an important regulatory role in reprogramming cells to a stem cell state. “Using these designed proteins for the next generation of cancer therapy is very exciting,” says Mathieu, now an Assistant Professor in Comparative Medicine. “I believe we can develop new ways to activate cell death and overcome drug resistance by binding more antibodies to TRAIL receptors. This could be a big step forward for cancer research.”
Zhao, whose research on the Tie2 pathway produced insights fundamental to the development of the nanocages, remains focused on the mechanisms driving the molecular changes generated when clusters of Tie2 receptors are bound to F-domains on cell surfaces. Because blood vessel stability is a critical issue in so many diseases, understanding the interplay of designed proteins and the Tie2 pathway could have broad implications for human health.
Indeed, it is the versatility of the nanocages that energizes the DREAM researchers. “The most exciting aspect of this technology is that it is so simple to swap different antibodies into the assemblies. We envision many new treatments emerging from this one common tool,” said senior author David Baker, Professor of Biochemistry and Director of the UW Medicine Institute for Protein Design.