David Schaffer Harnesses “Directed Evolution” for Gene Therapy

March 12, 2021
Jeannine Mjoseth

Hertz Fellow and gene therapy researcher David Schaffer says he “plays Darwin” in his Berkeley lab, using high throughput genetic sequencing technology to test over a billion genetic samples for the desired biological activity. 

He mutates promising genes and selects the gene variants with the properties he’s seeking, a process called directed evolution. Thus far, he’s identified gene variants that can potentially help restore sight (in X-linked retinitis pigmentosa, choroideremia, wet age-related macular degeneration and diabetic retinopathy), repair hearts damaged by Fabry disease and improve lung function in patients with cystic fibrosis. 

Schaffer’s biggest company – 4D Molecular Therapeutics – focuses on this technology and has three clinical trials underway and two investigational new drug applications in the hopper.

“We have evolved new proteins that have the desired functions through iterative rounds of genetic diversification and Darwinian selection,” Schaffer said. “Gradually, we are climbing from the foothills to the mountains as the library of genetic variants converges from a billion variants to a small handful that are specialized for having properties of interest.” Schaffer is a professor of chemical and biomolecular engineering, bioengineering, and molecular and cell biology at the University of California, Berkeley, where he also leads the California Institute for Quantitative Biosciences.

He credits the brilliant Francis Arnold, Berkeley alumnus and winner of the 2018 Nobel Prize in chemistry, for developing the directed evolution approach. While Arnold focused on enzymes, Schaffer was the first to apply directed evolution to gene delivery viruses, using harmless adeno-associated viruses (AAV) to deliver therapy to genes.

Learn more:
Fellowship Awarded 1993
Director, California Institute for Quantitative Biosciences

“Part of the reason AAV is a harmless respiratory virus is that it’s not very good at delivering DNA to cells, even to the lungs,” Schaffer said. To improve AAV’s ability to deliver DNA medicines, Schaffer re-engineered the AAV’s protein shell using directed evolution techniques.

“We introduced diversity into the viral protein coat, which is the viral DNA delivery vehicle, in a variety of different ways. We have 40 libraries with a total of a billion different versions of the virus, each of which has a different composition in the protein shell.” After engineering a highly optimized version that can serve as a carrier for highly efficient, targeted delivery to any cell type in the body, he loads it with medicinal DNA to treat diseases that affect those cell types.

“The old joke in my field is that there are only three problems with gene therapy: delivery, delivery, delivery,” said Schaffer. “I feel pretty good about the progress we’re making – using directed evolution – to solve the delivery problem.” 

He’s also pleased with the amount of therapeutic DNA that can fit into a virus, which will be enough to treat many disorders. Furthermore, there’s a broad therapeutic window for the first diseases that he’s working on so even if the patient receives a lot of the modified AAV, it’s not going to be toxic, he said.

So far, he has targeted diseases like retinitis pigmentosa caused by a mutation in a single gene. The idea is that a patient can be permanently cured of the disease with a correct copy of the DNA that lasts for the patient’s lifetime, unlike most medications, which don’t stay in the body very long and are considered treatments, not cures. 

“The old joke in my field is that there are only three problems with gene therapy: delivery, delivery, delivery. I feel pretty good about the progress we’re making – using directed evolution – to solve the delivery problem.”
– David Schaffer

Next, he’ll tackle tougher disease targets caused by a combination of genetics and environment. “In many complex diseases, it will matter when, where and how much protein is produced. So all of a sudden you need to regulate and control the DNA medicine.” Another challenge is the increasing demand for gene therapy. 

Schaffer is using directed evolution to solve these issues. “We’re also creating and evolving large libraries of promoters – regulatory regions that control when, where and how many of our proteins are produced. Also, to really democratize gene therapy and to save the healthcare system lots of money, we need to make improvements in manufacturing. We’re engineering libraries of cells and selecting for ones that are better at producing virus. So those are two directions I’m really excited about. Like Wayne Gretzky said, we want to skate where the puck is going, not where it is.”

Without the five years of funding from the Hertz Foundation, Schaffer doubts if he would have embarked on his 27-year scientific journey into gene therapy. While pursuing his doctorate in chemical engineering at the Massachusetts Institute of Technology, Schaffer worked for his favorite professor, Doug Lauffenburger. His mentor’s research focused on understanding how signaling molecules interact with and regulate cell function.

“But we’d never attached any cargo to those molecules, so that was what I worked on during my Ph.D.,” Schaffer said. “I wanted to design delivery vehicles at the molecular level and make them better, which was really different from what the group had been doing.”

Half of Schaffer’s research focuses on “DNA as a medicine” while the other half centers on “genomes as medicines” or stem cell therapy. “The idea behind stem cell replacement therapy is that if a particular disease is wiping out a population of cells, you can teach stem cells to develop into a specific cell type and use the stem cells to mass produce a cell type that can be the basis of a replacement therapy,” said Schaffer, who served as the director of the Berkeley Stem Cell Center for 10 years. 

In Parkinson’s disease, for example, patients lose a population of cells called dopaminergic neurons, which can be mass produced using stem cells. The same is true for replacing medium spiny neurons in Huntington’s disease. “Outside of nervous system disorders, you can think about replacing heart muscle cells that died in a heart attack, or insulin-producing beta-cells that die due to Type 1 diabetes. There are a lot of ways in which stem cell replacement therapy could potentially repopulate and rebuild tissues.”

The arc of Schaffer’s science trajectory began in childhood when his father, a basic biochemist, would sit Schaffer and his sister on his lap and read to them from anatomy and microbiology textbooks. “He’d make up little rhymes so that we would remember vocabulary words. For example, to help us remember scapula – the shoulder blade – he would say stuff like ‘scapula backula.’”

Schaffer’s family ended up at different points on the spectrum of therapeutic development. “My dad spent his career trying to understand the mechanisms of disease while my mother ran phase 1-4 clinical trials at Novartis and Sanofi to improve the efficacy of drugs to treat human disease. My sister is a practicing pediatrician so she’s the one prescribing the drugs. I’m an engineer and wanted to create the technologies that people like my mom would test in the clinic. I ended up at the interface between academia and industry, creating new kinds of technology platforms and then playing a role in trying to get them out to the industry, on their way to the clinic.”