New Base Editing Tools Enhance Precision and Improve Efficiency

Base editing, a gene editing approach that chemically modifies DNA, has advanced from laboratory work to treating serious illnesses in under ten years. Developed by Alexis Komor at the University of California San Diego, base editing remains an emerging technology, and her group continues to refine it by increasing efficiency while reducing unwanted DNA changes. A key challenge is “bystander editing,” when adenine base editors (ABEs) alter not only the target adenine but also neighboring adenines, which can sometimes cause harmful effects, including cell death.

One strategy to lower bystander edits is to narrow the “editing window,” the span of DNA bases an ABE can modify. However, earlier work showed that shrinking this window often reduces desired on-target activity. Komor’s lab set out to decrease bystander editing without sacrificing efficiency, aiming for “both properties” to be optimized for therapeutic use. Mallory Evanoff, first author of the study published in Nature Biotechnology, focused on an older editor, ABE7.10, which has a narrower editing window but lower efficiency than newer ABE8.20 and ABE8e variants. While the ABE8 versions offer higher on-target activity and are widely used, including in clinical trials, they also produce more bystander edits, prompting the search for a middle ground.

ABE7.10 relies on an engineered enzyme carrying 14 point mutations identified through directed evolution in E. coli, but the specific contribution of each mutation was unclear. Evanoff used reversion analysis, restoring each mutation to its original “wild type” sequence and testing the impact in both human cells and E. coli. Some mutations behaved similarly in both systems, while others differed. Because most applications occur in human cells, Evanoff highlighted five mutations that, when reverted individually, either did not reduce or actually increased editing activity in human cells. Combining these reversions produced a “minimally evolved ABE” (ME-ABE).

The ME-ABE maintains a narrow editing window while achieving editing activity comparable to ABE8.20 and ABE8e. Komor noted that this is one of the first instances where efficiency and editing window have been successfully decoupled, reducing bystander edits without losing performance. Evanoff describes ME-ABEs as a “cuts-both-ways” tool: they can introduce specific mutations in model systems to clarify which genetic changes drive disease, and they can support development of personalized therapies. As Komor and Evanoff work on evolving base editors directly in mammalian cells, they view ME-ABEs as a starting point for others. 

“One of the great things about working in the tool development world, is that you're making something that allows other people to answer their own questions,” stated Evanoff. “These tools are going to be available for researchers who are really, really well-informed on their particular disease or their particular system and now have an ability to model a cure.”