Beam Therapeutics Develops Inlaid Base Editing Technique for SCD

Beam Therapeutics is testing a new form of CRISPR-based technology called inlaid base editing to modify cells from patients with sickle cell disease (SCD).

Base editing uses fusions of a deaminase and CRISPR-Cas ribonucleoprotein to allow programmable installment of transition mutations without double-strand DNA break intermediates. “The breadth of potential base editing targets is frequently limited by the requirement of a suitably positioned Cas9 protospacer adjacent motif,” the study authors wrote in The CRISPR Journal. “To address this, we used structures of Cas9 and TadA to design a set of inlaid base editors, in which deaminase domains are internal to Cas9.”
Researchers at Beam Therapeutics developed this tool to shift the “activity windows” of the original base editors, which often landed too far away from the genes of interest, enough to land within range of the SCD hemoglobin gene.

While there are still risks of guide-independent off-target effects, the authors believe inlaid base editing might be safer than the classic CRISPR technique because it doesn’t break DNA in two, but nicks open one strand of the double helix to swap in a single letter for another. The safety of gene therapies for patients with SCD has been under increased scrutiny following a U.S. Food and Drug Administration (FDA) clinical hold on LentiGlobin after two patients with SCD developed acute myeloid leukemia and myelodysplastic syndromes, respectively. However, an investigation was unable to confirm a link between LentiGlobin and the cancers.

At the 2020 American Society of Hematology Annual Meeting in December, Beam Therapeutics presented data showing the technique was used to successfully edit more than 70% of blood progenitor cells from a patient with SCD.

“Doing this kind of engineering does really broaden the scope of the available tools,” said Daniel Bauer, MD, PhD, associate professor at Harvard Medical School and director of gene therapy at Boston Children’s Hospital, who was not involved with the study. “It’s encouraging to see that we’re not too far off a point where almost any spot in the genome could be base edited.”

Sources: STAT, April 20, 2021; Chu SH, Packer M, Rees H, et al. Rationally designed base editors for precise editing of the sickle cell disease mutation. The CRISPR Journal. Apr 2021. 169-177.