Next Generation CRISPR

FDA approval of the first CRISPR therapeutic, Vertex’s Casgevy (exagamglogene autotemcel), was hailed as a milestone in the ongoing effort to correct genetic diseases with one-time treatments. But it isn’t likely to unleash a flood of new gene-editing therapies anytime soon. Of the more than 300 CRISPR-based therapies in the development pipeline, 88 percent are in the earliest stages of development, with the majority still in preclinical testing.

I believe two actions are critical to advance CRISPR medicines. First, we need to encourage the development of new technologies as tools for improving the accuracy and safety of gene editing. Those tools include everything from new editing processes, to novel enzymes and plasmids, to improved delivery vehicles. Second, we should use these to create CRISPR platform technologies – a collection of fine-tuned gene-editing components that meet stringent performance criteria and can be readily deployed for the development of therapies for multiple diseases.

Let’s first touch on the challenging task of improving CRISPR editing. CRISPR involves knock-outs; a method for removing DNA sequences using a Cas enzyme and guide RNA, and knock-ins; the insertion of therapeutic DNA sequences into the genome. Improving the efficiency of these processes and minimizing off-target effects are two of the challenges that researchers are focused on solving. And they are making encouraging headway.

One area of innovation is improving the long-preferred method for knock-in, homology-directed repair (HDR), which is precise but often inefficient. Alternative methods emerged recently, including microhomology-mediated end joining (MMEJ), which utilizes a different set of cellular machinery than HDR and results in inserting the desired knock-in by very short stretches of homology at the sites of double-stranded DNA breaks created by programmable nucleases. This method has been shown to be two- to three-times more efficient than HDR. Another advantage is that MMEJ is active in all phases of a “cell cycle,” the process by which a cell grows and divides. This provides more opportunities for introducing corrective genes into patient genomes, potentially broadening the universe of diseases that can be targeted with CRISPR.

The problem is, CRISPR knock-in is an inherently error-prone process. There is a lot of innovation in this field – particularly in perfecting different forms of DNA that could result in more efficient, accurate knock-ins. For example, researchers are investigating single-stranded, linear, and supercoil forms of DNA.

Another encouraging recent development involves novel enzymes designed to drastically reduce the CRISPR error rate. They include dCas9 fusions that can improve targeting, nickases that can improve efficiency by broadening the HDR targeting range, Cas9 variants, and non-Cas9 nucleases.

Improving the delivery of CRISPR is also a top priority. Delivering next-generation versions of modified CRISPR nucleases through testing alternative delivery methods to adeno-associated virus (AAV) enables delivering larger CRISPR payloads to specific tissues and organs beyond the liver, which is where most gene-editing therapies are delivered today. Alternatives include extracellular vesicles and virus-like particles, both of which show promise in their ability to carry large cargos into a variety of target cells. The successful development of small-sized plasmid DNA backbones that are free of antibiotic markers, such as Nanoplasmid vectors, lowers the risk of post-delivery toxicities and transgene silencing. Delivering CRISPR enzymes in mRNA form could also improve efficiency and reduce off-target editing.

Ultimately, CRISPR innovations should be developed as core platform technologies, so developers can deploy them to different disease settings. The idea would be to take a CRISPR system that’s approved by regulators to treat one disease and simply swap one DNA edit for another to tailor it to a new disease. The FDA is onboard with this strategy. Earlier this year, the FDA published draft guidance for its proposed Platform Technology Designation Program. Platforms could include delivery mechanisms, nucleic acid sequences, vectors, or even combinations of these and other technologies. By allowing CRISPR developers to apply their platform innovations across different diseases, the platform designation could help streamline the regulatory approval process, bringing CRISPR solutions to patients much faster – and at a lower cost.

If we can come up with platform solutions that improve the efficiency, accuracy, and safety of CRISPR, I have no doubt that gene editing will usher in the next wave of cures.