Very few scientists pioneer a disruptive technology once during their career; fewer manage to do it twice. But Giuseppe Ciaramella, PhD, president and CSO of Beam Therapeutics, is moving closer to that exclusive club as his company blazes a path in the development of precision genetic medicines. His first disruption? Working to develop mRNA vaccines at Moderna.

His second might be the work described in a new paper in The CRISPR Journal, in which Ciaramella and colleagues present a redesigned base editor that affords greater flexibility in targeting genetic diseases such as sickle-cell disease (SCD).

Beam Therapeutics burst onto the genome editing scene in 2017 with a platform centered around base editing—a genome editing mechanism that alters one base at a time. Base editors are fusions of a deaminase and a Cas enzyme. A nucleotide conversion is the result of the editing process and can occur via a C-to-T base editor (CBE) or an A-to-G base editor (ABE). Base editors alter DNA precisely, efficiently, and avoid double-stranded breaks with few off-target effects.

One of the differentiating features and strengths of base editing, notes Nicole Gaudelli, PhD, leader of the gene editing technologies platform group at Beam, is its ability to “programmably, and predictably, directly convert single-letter misspellings in the genome to a desirable base, without reliance on HDR [homology-directed repair] mechanisms.”

For all its inherent advantages, base editing has hurdles that need clearing when being applied to genetic engineering. One such limitation is access to particular sites in the genome, which depends on the location of the protospacer adjacent motif (PAM) sequence—a short DNA sequence that is required for Cas9 to target an editing window. The location of the PAM site could create a situation where the target nucleobase resides outside the activity window of the base editor.

Beam developed a workaround for the PAM problem by embedding the TadA deaminase—which typically hangs off the N or C terminal end of the Cas9—inside. In doing so, they created a new class of base editors known as inlaid base editors (IBEs).

In a new paper published today in The CRISPR Journal, Beam shows that genome editing with IBEs converts a pathogenic sickle cell hemoglobin allele to a naturally occurring variant. The details are presented in the paper, “Rationally Designed Base Editors for Precise Editing of the Sickle Cell Disease Mutation.” The goal of the larger program, known as Beam 102, is to provide a treatment for people with SCD through base editing the human genome.

Sliding the editing window   

This work provides an improvement to the base editing toolbox, notes Anna Cereseto, PhD, professor, University of Trento, Italy, because IBEs offer the opportunity to “slide” the window of action through repositioning of the deaminase domain in the base editor.

Why does repositioning the deaminase domain have such an effect? Ian Slaymaker, PhD, senior scientist at Beam and co-corresponding author of the new paper, tells GEN that the previous generation of base editors were all based on either N or C terminal fusions. They would “bounce around,” he explains. By placing the deaminase into the Cas9, he notes, researchers can steer the active site around the Cas9 and decide where the deamination is going to occur in the DNA, “without relying on steric happenchance.” Ciaramella asserts that doing this creates a “completely novel base editing architecture compared to what we had developed in the past.”

Nicole Gaudelli
Nicole Gaudelli, PhD

With IBEs, Gaudelli says, Beam has further advanced its capability to shift the editing window, “enabling access to nucleobases previously un-editable with our foundational editors.” The IBEs, together with the foundational base editors, allow the flexibility to select the optimal precision editor “to target nearly every adenine or cytosine base within a protospacer window, given a reasonably proximal PAM.”

Using this new configuration of the deaminase, notes Donald B. Kohn, MD, professor, Microbiology, Immunology and Molecular Genetics, Pediatrics, and Molecular and Medical Pharmacology at the University of California, Los Angeles, “may represent an important improvement in the activity of base editors.” He adds that the data in the paper “look good,” but, “it needs to be assessed further against more alleles and in various cell types to know how robust is the improvement in activity and specificity.”

Delivery delayed, for now

The advancement of base editors “still needs an efficient delivery system,” notes Cereseto. Base editors, she adds, are large cargos that are difficult to deliver. In vivo base editing has been performed with adeno-associated viruses (AAVs), which requires the base editing complex to be split in two, thus decreasing the efficiency of co-delivery of the two halves; nanoparticles, she adds, are not efficient as viral vectors yet.

Beam works on delivery, notes Ciaramella, as much as they work on base editing. That said, for Beam 102, delivery is not as much of a hurdle. Because this is an autologous cell-based therapy, the cells will be removed from the patient and sent to a central manufacturing site, where the editor and the guide will be introduced into the cells through electroporation.

But Beam’s portfolio does include in vivo gene editing programs. Ciaramella tells GEN that they “understand that delivery is essential in order to translate this wonderful technology into real medicines.” As such, he says, they invest as heavily in delivery as they do on the payload. In addition to AAV discovery, Beam recently acquired a company called Guide Therapeutics which has an expertise in technology that allows for rapid screening of novel lipid nanoparticles by virtue of DNA barcodes.

It’s about more than sickling

This work is Beam’s second program focused on SCD. Beam 101, which is on track for an IND filing later this year, is designed to treat SCD by upregulating the fetal form of hemoglobin.

In the paper, the researchers describe how they used the IBE to precisely convert the single-letter, disease-causing mutation implicated in sickle cell disease, into a natural occurring allele in human population, called the “Makassar” variant, notes Gaudelli. “Our adenine base editor strategy for the treatment of sickle cell disease,” she adds, “with our Makassar edit approach, can eliminate the pathogenic global protein without causing double-stranded breaks as is required for HDR-based strategies.”

The biology of red cells with the benign Hb Makassar variant seems to not cause sickling, notes Kohn, based its natural occurrence in a few people. But further study will be needed on the overall effects on erythropoiesis, red blood cell survival in vivo, and ultimately clinical findings for the patients. That said, Kohn, who is an author on a paper in the same issue (April 2021) of The CRISPR Journal, on site-specific insertion of the BTK cDNA as a treatment for X-linked agammaglobulinemia, thinks the approach Beam used to treat SCD is “very exciting.”

“It’s not just sickling,” notes Haihua Chu, PhD, senior scientist at Beam Therapeutics, and first author on the paper. Chu, who will continue driving this program toward the clinic, envisions future studies testing whether these cells can engraft and recapitulating hematopoiesis. Those are the kind of studies, he notes, that will convince clinicians that this sort of therapy will be a potential cure for the disease.

These studies are ongoing for Beam 102 and will follow the path of Beam 101, which has laid the foundation from animal model to manufacturing. Eventually, the company hopes to have two trials in SCD, each with its own mechanisms of action to treat SCD.

When will Beam 102 move into the clinic? Ciaramella did not give a date, but he notes that it is not too far behind Beam 101. Beam thinks that it is likely that their treatments will be among many genome-editing treatments available to SCD patients in the future. Ciaramella notes that the “sickle cell disease therapeutic field is likely to expand very significantly.” He welcomes the expansion, and notes that patients deserve to have more than one option at their disposal.