By Kevin Davies, PhD
LOS ANGELES – David Liu, PhD, the Harvard University and Broad Institute chemist leading the development of base and prime editing technologies, began his American Society of Gene and Cell Therapy (ASGCT) presidential symposium keynote in humorous vein.
That morning, Liu had breakfast with his parents, both non-life scientists, who live in the Los Angeles area. He told them he was in town to give an important lecture. How big would the audience be, they asked? Possibly in the thousands, Liu responded. It was unclear if his parents were surprised or impressed. But to leave no doubt, Liu took out his phone and quickly filmed the packed audience—definitely in the thousands—as proof. From there, Liu was all business, delivering a tour de force presentation crammed with data that left little doubt as to the clinical promise of precision editing.
The goal of human genome editing, Liu said, is to install, correct, and modify all types of pathogenic mutations. CRISPR-Cas9 has already proven its worth in the clinic (and won a Nobel Prize), but most genetic diseases arise from loss-of-function mutations. “They require precise gene correction rather than gene disruption,” Liu said. Using Cas nucleases for gene correction remains challenging because they don’t have the ability to engineer a specified nucleotide change.
As is well documented, some seven years ago, Liu’s lab embarked on a quest to develop precision editing tools, building on the programmability of Cas9 to engineer point mutations. As described in successive papers in Nature, Liu’s lab developed cytosine base editors (CBEs) and adenine base editors (ABEs). (He also co-founded Beam Therapeutics together with Feng Zhang and Keith Joung, who received the ASGCT Achievement Award a few hours earlier.)
Over the past two years, base editing has shown considerable promise in preclinical animal model studies. Among the early success stories Liu mentioned are:
- The rescue of sickle cell disease (SCD) in mice using a bespoke ABE to convert the SCD betaglobin point mutation to a benign variant (Hb Makassar). Transplanting these gene-edited cells into mice rescued all disease phenotypes.
- Development of an ABE to correct the mutation underlying progeria, a genetic disease characterized by premature aging. AAV9 delivery shows phenotypic rescue in mouse models.
- As reported in March, a base editing strategy to treat spinal muscular atrophy, the leading genetic cause of infant mortality. Although there are three FDA-approved SMA drugs, they don’t fully restore levels of the defective SMN1 protein. Base editing offers the prospect of a one-time permanent treatment. Liu and colleagues meticulously tested dozens of different gene-editing strategies to target the related SMN2 gene to restore functional SMN protein levels. An ABE approach fully restored SMN levels and can be delivered via dual AAV9 vector into mouse models, again leading to phenotypic rescue.
Liu said there are four base-editing clinical trials currently underway, including the use of ABE to install rare mutations in gamma-globin gene to restore fetal hemoglobin production in SCD patients. Late last year, Verve Therapeutics dosed the first familial hypercholesterolemia patients for an in vivo trial targeting the PCSK9 gene.
Perhaps the most exciting result involving base editing, reported last year, is the clinical work of Wasim Qasim at the Great Ormond Street Hospital in London. Qasim’s team used a base editing CAR-T therapy to treat a young English girl, Alyssa, with T-cell leukemia. She received CAR-T cells in which base editing was used to introduce three specific gene edits. Her leukemia is in full remission, 11 months following her treatment.
In short, Liu said, the remarkable journey of base editing in just six years from the first publication to a successful clinical intervention is a tribute to the 3,000 labs and more than 4,000 publications in the field. Liu gave special thanks to Addgene, the non-profit repository for gene editing reagents that has helped democratize the field.
Liu’s lab was the first to develop a related technology called prime editing in 2019, in research led by Andrew Anzalone, MD, PhD. (See our recent exclusive interview with Anzalone on “Close to the Edge”, transcribed in our sister journal GEN Biotechnology.)
“We’ve developed improved prime editing systems,” Liu said. In collaboration with Britt Adamson and Jonathan Weissman’s lab, Liu’s team screened several hundred DNA repair genes to evaluate how each perturbation impacts prime editing outcomes. The results, published in 2021 in Cell, spotlighted cellular mismatch repair as a natural process contributing to undesirable edits. Cellular mismatch repair is a process that acts on heteroduplexes with 1–2 mispaired bases. Liu’s group exploited this knowledge by designing prime edits to install additional benign mutations near the target prime edit. This insight from basic research substantially improves prime editing efficiencies, Liu said, and is now routinely in use to design pegRNAs.
Several other molecular tricks have been identified to enhances prime editing efficiency. The cumulative benefit is that the latest generation of prime editors exhibit an order-of-magnitude improvement in efficiency and specificity compared to the original editors designed just four years ago.
Prime editing has the flexibility to introduce any possible base edit, but that is not all it can do. Liu described early studies showing the removal of triplet repeats in trinucleotide repeat disorders such as fragile X syndrome and Huntington’s disease.
Prime editing has also been used in an ex vivo approach to rescue SCD in mice. Four months after transplantation in an animal model, prime editing did not impair stem cell engraftment or differentiation. This shows “the feasibility of one-time treatment, minimizing the undesired consequences of double-stranded [DNA] breaks,” Liu said. Meanwhile, other investigators have reported promising in vivo prime editing studies in animal models of retinitis pigmentosa and phenylketonuria.
Although these early studies are impressive, Liu stressed there is still much to be learned about the mechanism and safety of prime editing. It is a newer technology with a larger molecular footprint and more complex mechanisms than other forms of genome editing, he said. Nevertheless, through one of his other companies, Prime Medicine, prime editing is anticipated to reach the clinic next year.
These advances, Liu said, “give me hope that one day, we’ll have a say in our genetic futures, so we’re not so beholden to the misspellings in our DNA.”