David Liu Speeds Up Evolution of Therapeutic Proteins

Using viruses to evolve useful molecules isn’t new. David Liu has made that approach far more practical and powerful by speeding up the process from years to weeks with a technique called phage-assisted continuous evolution (PACE) that uses the M13 bacteriophage with a 10-minute lifespan.

Just as bacteria infect humans and other creatures, bacteriophages are viruses that infect bacteria. They are the biosphere’s most widely distributed and diverse entities. Phages are ubiquitous and can be found wherever bacteria exist, such as soil or animal intestines. The M13 bacteriophage infects the E coli bacteria.

Proteins are becoming the focus of promising new therapies. One of the most efficient ways to create new proteins with potentially therapeutic function is by using viruses undergoing directed evolution to produce a naturally occurring protein that can perform specific tasks like binding to cancer cells, either to prevent their replication or to mark them for destruction by T cells. Directed evolution is an essentially random process that takes place at the DNA level. It depends on the screening mechanism to enhance the likelihood of creating a useful protein.

“The speed of conventional protein evolution is a bottleneck,” says David Liu, a professor of chemistry and chemical biology at Harvard University who led the research group that developed PACE. “Efforts to create proteins with tailor-made properties will be maximally useful if methods to create them can operate on a truly practical timescale.”

The idea of using a phage life cycle to achieve rapid evolution was suggested by Kevin Esvelt, the graduate student in Liu’s group who led the PACE project. Arriving at the basic form of PACE took over five years.

“I think it’s fair to say that maintaining faith in the potential significance of the project and in the feasibility of our approach over more than five years was probably the most important challenge to overcome,” says Liu.

PACE allowed Liu’s group to produce 200 rounds of evolution in a single week to generate a protein with the desired property. Using conventional techniques the process would have taken years. PACE links the desired function to the production of a substance the virus must produce to keep from being screened out. If a virus emerges with a version of the target protein that performs the desired function, it is allowed to complete its life cycle and its offspring can infect other E. coli bacteria to continue on with subsequent rounds of evolution continually and automatically.

The PACE technique can be easily replicated by other researchers because it uses only readily available components. Liu believes one of its most promising applications is to rapidly evolve specific therapeutic antibodies to treat cancer and autoimmune diseases. Current directed evolution methods can only produce such molecules through years of costly effort.

“We think there are two main areas where PACE can be enabling.” says Liu. “The first is in evolving proteins or nucleic acids that possess a combination of desirable properties that might be difficult or impossible to access using conventional macromolecule engineering or evolution approaches.

“The second area is answering some basic science questions about the nature of molecular evolution that really require hundreds or thousands of rounds of evolution, such as Steven Jay Gould’s curiosity about “replaying the tape of life” — namely, if one attempts many times the same evolutionary trajectory over thousands of cycles of evolution, how many different outcomes does one obtain?”

Evolutionary research that might take a decade with conventional setups could be completed in two weeks using PACE.

David Ruchien Liu was born June 12, 1973 in Riverside, California. David’s parents had immigrated from China and met in graduate school at UCLA. His father is an aerospace engineer and his mother is a retired physics professor who had taught physics at U. C. Riverside.

“I enjoyed a good childhood with plenty of playing and studying,” recalls Liu. “I went to a strong public high school. Since my childhood years, science has been an important and enjoyable part of my life. Of course having loving parents who were scientists established a very supportive environment for fostering my interest in science!”

Liu graduated 1st among 397 seniors from Riverside Poly High School. While in high school he participated in a high school-university program in conjunction with UC Riverside. In June 1994 he graduated summa cum laude from Harvard College with a BA in chemistry, finishing 1st out of 1,641 students.

In 1997, while a third-year PhD student at Cal, Liu read Jerry Joyce’s paper on ligase ribozyme continuous evolution and was inspired to seek techniques to evolve proteins continuously. He earned a PhD in organic chemistry from UC Berkeley in May 1999. That year he began his Harvard teaching and research career as an assistant professor.

Liu is an Investigator for the Howard Hughes Medical Institute. He has published 85 research papers and scientific articles since 1992. He holds 9 U.S. and international patents.