Advancing the development of CRISPR platform technologies

Advances in CRISPR technologies promise to accelerate the burgeoning pipeline of gene-editing therapies and broaden access to these disease-altering therapies.

The Food and Drug Administration approval in December 2023 of the first CRISPR therapeutic, Casgevy to treat sickle cell, came 11 years after the discovery of the revolutionary gene-editing technology. And it took nearly 10 months after approval for patients to start receiving infusions of the drug, as they waited for their insurers to approve the treatment, which came to market with a $2.2 million list price.[i]

Now there are an estimated 300 CRISPR therapies in the pipeline, most of which are in early development for a range of diseases,[ii] including diabetes, HIV/AIDS and several types of cancer.[iii] How can we speed these innovations to the patients who need them—and ensure they are brought to market at prices that are sustainable?

Improving CRISPR with new technologies will alleviate shortcomings, such as off-target editing. And these new tools can be used to create CRISPR platform technologies that can be applied to the development of future gene-editing therapies for multiple diseases, shrinking development timelines and reducing the time and costs associated with bringing gene-editing therapies to patients. This is a strategy that the FDA declared its support for in 2024, when it published its draft guidance for the Platform Technology Designation Program, which would allow CRISPR innovators to streamline development by applying nucleic acid sequences, delivery vectors and other new technologies across therapies for multiple diseases.[iv]

CRISPR developers can work hand-in-hand with CDMOs to accelerate workflows using currently available tools, as well as to adopt next-generation technologies to improve gene-editing processes. As these systems are perfected in preclinical and clinical trials, CDMOs can help transform them into platform solutions that can be used to develop future CRISPR therapies.

Solving CRISPR’s challenges

Casgevy uses CRISPR/Cas9 to “knock out” part of a gene responsible for making fetal hemoglobin. Normally this gene, BCL11A, shuts off after birth and adult hemoglobin takes over, but in people with sickle cell, abnormal hemoglobin causes red blood cells to become misshapen, resulting in blockages. Knocking out part of BCL11A allows the body to continue making fetal hemoglobin, which helps raise the number of blood cells that don’t sickle.[v]

The Cas9 enzyme has been the preferred tool for cutting DNA since the advent of CRISPR, but it’s not necessarily the best choice for all gene-editing applications. One challenge of Cas9 is that it must be delivered at a specific point in the cell’s cycle. The Cas9 process is often inefficient and it can cause unpredictable off-target editing.

Recently developed enzymes are offering alternatives that can reduce the CRISPR error rate and improve efficiency. They include dCas9 fusions, which are deactivated mutants of the enzyme that can improve targeting, and non-Cas9 nucleases such as Cas12a, which enable targeting of genomic sites that may not be reachable with Cas9. Aldevron developed a high-fidelity Cas9 nuclease, which was designed to reduce off-target effects and increase editing efficiency. This nuclease was used in early research by Stanford University researchers who helped develop the CRISPR process that later became Casgevy.

Some CRISPR therapeutics that are in the pipeline require not just knocking out parts of the genome, but also knocking in therapeutic genes. The most widely used knock-in strategy is homology-directed repair (HDR), which can be inefficient. One promising alternative method in development is microhomology-mediated end joining (MMEJ), which involves inserting short stretches of homology at sites where programmable nucleases create double-stranded DNA breaks. MMEJ is up to three times more efficient than HDR,[vi] and it is active in all phases of the cell cycle, providing more opportunities for introducing therapeutic genes into patients’ genomes. That could make it possible to address a wider universe of diseases with CRISPR.

The future of CRISPR

The utility of CRISPR has so far been restrained by the commonly used delivery method adeno-associated virus (AAV), which is limited in the size of the cargo it can carry, the cells it can target and the risk of causing immunogenic reactions. CRISPR developers and CDMOs are investigating promising alternatives to AAV delivery. They include extracellular vesicles and virus-like particles, both of which are showing promise for their ability to carry larger cargos than AAVs typically can, and to target cells beyond the liver.[vii] Researchers are also investigating delivering CRISPR enzymes in mRNA form, which could improve efficiency and lower the risk of off-target editing.

Improvements have also been made in plasmid DNA backbones needed to carry CRISPR into target cells for the knock-in process. Novel plasmid DNA backbones are smaller than traditional plasmids, and they are free of antibiotic markers. These attributes lower the risk of toxicities and transgene silencing.[viii] Single-stranded DNA is also emerging as a promising technique for knock-in that can improve efficiency and lower the risk of unintended recombinations and toxicities.

As these CRISPR innovations are perfected, CDMOs will be able to work with developers to establish platform technologies and apply for FDA approval under the new Platform Designation Program. Then, in the future, they’ll be able to take an approved CRISPR system for one disease and swap out DNA edits to tailor that system to different diseases. This is the promise of platform technologies: They’ll streamline the development and regulatory approval for future CRISPR therapies, ultimately bringing cures to patients much faster, and lowering costs in the process.

About the author: Venkata Indurthi, Ph.D., is the Chief Scientific Officer of Aldevron, a Danaher Life Sciences company that works with CRISPR innovators from early research through clinical use, providing custom nucleases, next-generation plasmid vectors, RNP complexing and analytic services, and more. He has been a member of the Aldevron team since he received his doctorate in pharmaceutical sciences from North Dakota State University, Fargo, ND, in 2016.