Komor’s first trick was to find a way to block an enzyme that “rips out uracils like nobody’s business.” So she fused a third component to the base editor—an inhibitor of uracil DNA glycosylase, or the ripper. It shifted the balance a bit but not as much as she hoped. And then one day, she had an epiphany while talking to a colleague in the lab kitchen. “It just came to me,” she recalls. “Oh my God, we’re working with an endonuclease!” Although she was working with a “dead” form of Cas9, it was still a nuclease that cleaves DNA. By replacing a single amino acid in the enzyme, Komor could restore a “nickase” function that would clip one strand of the double helix. By nicking the G-containing strand (leaving the U intact) she could trigger the cell’s DNA repair machinery to fix the G rather than the U nucleotide.
When Komor told Liu about her brilliant idea, he started swearing: he’d wanted to start writing up the paper for fear of being scooped. But Komor’s idea was obviously worth trying. “How quickly can you do it?” Komor spent Christmas 2015 back home in California drafting the manuscript, editing it on Christmas Day, and even foregoing her ten-year high school reunion. The Nature reviewers initially gave the paper a rough ride on technical grounds, and it was rejected. Komor worked tirelessly to rebut each of the criticisms, while Liu phoned the editor, Angela Eggleston, to appeal. The revised paper was accepted and eventually published in April 2016.12 When I asked Komor why they chose Nature, she laughed. “Where else would we send it?!”
As Komor was developing the first C-to-T base editor (CBE), Gaudelli grew increasingly interested in her friend’s research. After much internal debate, she decided to abandon her own project, switching instead to try to develop a novel base editor that could do the reverse reaction—an A-to-G base editor. This would be a more useful setup for medical applications as about half of the known pathogenic mutations in human genes involve mutations of a G to A. (Indeed, there is a high spontaneous mutation rate involving the deamination of cytidines de novo to uracil, resulting in an erroneous T:A basepair.) Developing a system that could reverse this common source of human mutation could have a profound medical benefit. There was one small problem however: Gaudelli didn’t have any starting material.
Liu had one unbreakable rule in his lab that had endured more than fifteen years: never start a project by evolving the starting material. But Gaudelli didn’t have much choice: there was no natural enzyme that deaminates A to G in DNA.II Undaunted, Gaudelli trained her sights on a bacterial enzyme called tadA, which works on RNA, not DNA. With nothing to lose, Gaudelli performed a slightly crazy experiment—evolution in a test tube to try to generate the desired properties.III The first round of evolution yielded a mutation that enabled the altered enzyme to tackle single-stranded DNA instead of RNA as its substrate. The mutation was in the precise location that Gaudelli would have expected. She sent a quick slide to Liu, who started swearing again. “Holy—, this is our smoking gun,” he replied.
Several rounds later, Gaudelli had evolved a potent A-base editor, or ABE. She was also able to demonstrate the ability to modify mutations in genes responsible for hereditary diseases including hemochromatosis and sickle-cell disease. Like Komor, Gaudelli’s base-editing exploits also earned her a first-author paper in Nature.13 By now, rival journal editors were visiting Liu to solicit hot papers like Gaudelli’s. It sailed through peer review over a long weekend. Researchers around the world immediately jumped on the base editing bandwagon.14
Looking back, Gaudelli took an almost ludicrous gamble but she pays tribute to the nurturing environment in Liu’s lab and her “Hulkbuster” of a boss, who “just makes you feel invincible.”15 She could have had any faculty position she wanted, but she elected to join Beam Therapeutics, a new biotech company Liu cofounded with his comrades in arms, Feng Zhang and Keith Joung. Gaudelli started to think about the friends and family base editing might eventually help. “What if one of those people was my father? My grandfather? What if that was a hypothetical child of mine?”
A friend of Liu’s, a pediatric oncologist at Stanford named Agnieszka Czechowicz, came up with the company’s name. She texted Liu her suggestion—Beam—which evokes a laser, a precision technology. “It also happens to stand for ‘Base Editing And More’,” she pointed out.
“What’s the ‘more’?” Liu asked.
“I’m sure you’ll figure it out,” she replied.16
Several Liu and Zhang postdocs, including Fei Ann Ran, have followed Gaudelli’s path to Beam’s facility in a building next to Novartis’s R&D headquarters in the former Necco candy factory. In 2019, CEO John Evans took Beam public, raising a tidy $180 million, which will help them build a new headquarters in the heart of Kendall Square.
In less than five years, base editing had evolved from a speculative postdoc proposal to a pair of landmark Nature papers, rapid uptake in labs around the world, and a public biotech company. The creation of base editors is an impressive feat of chemistry. As Liu told me: “These molecular machines have to search the genome for a single target position, open up the DNA, perform chemical surgery directly on a base to rearrange the atoms—then do nothing else [except] defend the edit from the cell’s fervent desire to undo them.”17
The first two base editors offer a means to edit “all the easy mutations,” says Komor. Liu anticipates “there’ll be a library of base editors and you’ll pull out the book that matches exactly what you need.” That choice will be influenced by the desired edit, the sequence context, off-target effects, and so on. In March 2020, Liu underscored that prediction: working in collaboration with Jennifer Doudna’s group, another postdoc, Michelle Richter, unveiled a new-and-evolved version of the A base editor that was six hundred times more active than Gaudelli’s original.18 Just as with CRISPR-Cas9, base editors are prone to cutting at off-targets. But scientists are working fast to improve their specificity. To keep this in perspective, note that in each of your 10 trillion cells, the genome is constantly mutating. Hundreds of times a day, a C is mutated to a U, which if left unchecked, would become a C-to-T mutation.
It will be years before a base editing drug is available, with many hurdles to climb to get there. Komor, who is now a university professor in her beloved Southern California, sees great promise in not just treating symptoms, but “curing the disease.” That’s what I’d expect her to say, but Liu’s group has already used base editing to correct a mouse model of a rare but devastating genetic disease. Progeria, or Hutchinson-Gilford progeria syndrome, is a dominantly inherited disease caused by a single-base mutation in the laminA gene that results in extreme premature aging. The mutant protein, called progerin, wreaks damage in the aorta and other tissues. Affected children rarely live beyond fifteen years of age.
Liu partnered with NIH director Francis Collins, who years earlier had developed a mouse model of the disease carrying the human progeria mutation. Liu’s team delivered the base editor via a pair of AAV vectors, using a molecular Velcro to splice the components together once inside the cell. The ABE corrected the mutation and squashed production of progerin. In the treated mice, cells regained their normal shape, and the aorta was restored to near-normal health. Stunningly, the treated mice look healthy and live longer than the progeria mice. How much longer Liu couldn’t exactly say—for the good reason they were still alive. “We’re really excited,” Liu said, moving forward “carefully but quickly” to advance this revolutionary treatment from mice to boys and girls.19