Is CRISPR the Antidote to Mankind’s Problems?

In 2019, for the first time in U.S. history, doctors used a CRISPR-based genetic therapy to treat a volunteer with sickle cell disease (SCD). Today, that patient, Victoria Gray, is symptom-free. On December 8, 2023, the Food and Drug Administration (FDA) approved the new gene-editing treatment, called CASGEVY™ (or exa-cel), shown to alleviate SCD pain for at least one year in patients.¹ (The U.K. approved SCD CRISPR therapy one month prior, in November). These biologic drugs are a big deal because they work to alter the patient’s genome, possibly forever, and because they represent not just a therapy but a potential curative therapy—in the case of SCD, exa-cel edits a gene involved in red blood cell shape and function. The long-term implications, both good and bad, remain to be seen, but it’s clear the age of CRISPR medicine is here.

CRISPR iterations and implications

CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) gene technology first appeared in the lab in 2012,² the template derived from bacteria that store phage DNA as a memory bank of previous invaders. When a virus attacks, the bacterium initiates transcription of the genetic code, inserted between palindromic repeats. The newly made RNA molecules then guide a CRISPR-associated (Cas) nuclease to the foreign DNA, dicing it up and rendering the phage DNA useless, subsequently ending the infection.

By replicating this phenomenon in animal and human cells, scientists demonstrated how RNA could be constructed to escort nucleases, acting as molecular scissors, to specific sequences of genome and disrupting function, generating speculation that CRISPR could become a revolutionary tool in the treatment of genetic diseases.

The first iteration of CRISPR essentially chopped up specific genomic DNA stopping the effects of a genetic mutation. Newer, more sophisticated versions soon followed. There’s CRISPR base editing, or CRISPR 2.0, which targets specific DNA bases (A, T, C, or G), and can swap one base letter into another, through DNA nicks (carried out by nickases) instead of double-strand breaks.³ Theoretically, this is thought to be safer because only one strand of DNA is being cut, so the wrong gene can’t be deleted accidentally, for example. This kind of CRISPR is the basis for the current wave of clinical trials.

And there’s CRISPR 3.0, or prime editing CRISPR, still relatively new and being tested in animals, this version lets scientists replace or insert large segments of DNA.⁴ CRISPR 3.0, of course, has the biggest implications for medicine because scientists could place new genes into a person’s genome, expanding the pool of genetic disorders that could be remedied.

From a select few to entire populations

The approval of CRISPR SCD therapy for use in people ushered in a new age of life-changing medicine. But it isn’t perfect. At the moment, it’s a cumbersome ex vivo process that can be grueling for patients. Bone marrow stem cells are harvested, edited in the lab, and then replaced after the residual bone marrow has been destroyed by chemotherapy. This is severely limiting for diseases in which cells cannot be removed from the body.

The next great step would be to deliver the editing materials directly into the patient, and this comes with its own set of issues, such as dispatching the ingredients to the correct organ and cells. Research related to mRNA vaccines and delivery systems, however, has helped to accelerate the goal of generating in vivo CRISPR methods. As with mRNA vaccines, the use of lipid nanoparticles is one way to protect and transfer these bioengineering tools to their destination in the body. Others include the use of virus-like and viral particles, such as adenoassociated virus. This continues to be a topic of intense scientific research.⁵

Further understanding of how parceling CRISPR determines where it ends up in the body and the extent to which it can carry out its job, will undoubtedly lead to more treatment for more diseases and more people. CRISPR vaccines are already on the horizon.

In July, 2022, Verve Therapeutics launched an in vivo CRISPR-based clinical trial to permanently lower cholesterol levels in volunteers with familial hypercholesterolemia (FH).⁶ FH carriers often have twice the average cholesterol readout, even as children, and can experience heart attack at a young age. The study stands out because it is an early use of the newer base editing CRISPR method and because it is done with a simple injection.⁷ Subjects were inoculated directly with the biomaterials for turning off liver cell copies of PCSK9, the gene responsible for maintaining cholesterol levels in the blood. Similar to COVID vaccines, Verve’s treatment is wrapped in nanoparticles that guide contents into the targeted cells.

This therapy was designed with a specific population in mind, and may end up being a life-long cure (in monkeys, 60% had lower cholesterol a year later). But there are broader implications. Someday, a simple shot may be available to the general population to lower cholesterol—heart disease is the leading cause of death across gender and ethnicity groups in the U.S.

Homing in on cell subtypes in the body

Earlier this year, Jennifer Doudna, co-inventor of CRISPR-Cas9 genome editing, and her lab reported a precision-targeted delivery method that allows for in vivo gene editing in animals.⁸ Using monoclonal-antibody tagged enveloped delivery vehicles (EDVs) filled with the requisite components, T cells are reprogrammed into CAR-T cells in humanized mice. Although a proof-of-concept study, it represents a critical step in a delivery method that would eliminate the need to engineer CAR-T cells ex vivo and destroy a patient’s bone marrow and immune system before administering the edited cells. Because EDVs can be decorated with more than one kind of antibody fragment or targeting ligand, cell delivery specificity is greatly enhanced. There is also less uptake by non-targeted cells, such as those in the liver, which minimizes side effects.

CRISPR and the world around us

Other CRISPR-based therapies are currently in development for chronic conditions, infections, and inflammatory disease. The expectation is that with research and time, CRISPR will become available to everyone, not just a select few, with the delivery less invasive and costly. The tool is not solely being directed toward the human genome, either. At the Innovative Genomics Institute, researchers are aiming CRISPR-mediated modifications at nearly every kind of microbe, in and around us.⁹ Reengineering the genetic code in bacteria could lead to less antibiotic resistance or healthier complex microbiomes in people (and even soil). Agricultural research aims to reduce methane production by cattle, which would have a big impact on greenhouse gas emissions. Other uses include CRISPR-modified meat, such as recently FDA-approved pork.¹⁰ Ready or not, CRISPR is rapidly infiltrating every sector that touches our lives and hopefully it is the long-awaited answer to the many internal (and external) ailments from which we suffer.

References

1. https://www.fda.gov/news-events/press-announcements/fda-approves-first-gene-therapies-treat-patients-sickle-cell-disease

2. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science (New York, N.Y.), 337(6096), 816–821. https://doi.org/10.1126/science.1225829

3. Ledford H. (2023). CRISPR 2.0: a new wave of gene editors heads for clinical trials. Nature, 624(7991), 234–235. https://doi.org/10.1038/d41586-023-03797-7

4. Scholefield, J., & Harrison, P. T. (2021). Prime editing - an update on the field. Gene therapy, 28(7-8), 396–401. https://doi.org/10.1038/s41434-021-00263-9

5. Mohammadian Farsani, A., Mokhtari, N., Nooraei, S., Bahrulolum, H., Akbari, A., Farsani, Z. M., Khatami, S., Ebadi, M. S., & Ahmadian, G. (2024). Lipid nanoparticles: The game-changer in CRISPR-Cas9 genome editing. Heliyon, 10(2), e24606. https://doi.org/10.1016/j.heliyon.2024.e24606

6. https://www.vervetx.com/our-programs/verve-101-102

7. Kasiewicz, L. N., Biswas, S., Beach, A., Ren, H., Dutta, C., Mazzola, A. M., Rohde, E., Chadwick, A., Cheng, C., Garcia, S. P., Iyer, S., Matsumoto, Y., Khera, A. V., Musunuru, K., Kathiresan, S., Malyala, P., Rajeev, K. G., & Bellinger, A. M. (2023). GalNAc-Lipid nanoparticles enable non-LDLR dependent hepatic delivery of a CRISPR base editing therapy. Nature communications, 14(1), 2776. https://doi.org/10.1038/s41467-023-37465-1

8. Hamilton, J. R., Chen, E., Perez, B. S., Sandoval Espinoza, C. R., Kang, M. H., Trinidad, M., Ngo, W., & Doudna, J. A. (2024). In vivo human T cell engineering with enveloped delivery vehicles. Nature biotechnology, 10.1038/s41587-023-02085-z. Advance online publication. https://doi.org/10.1038/s41587-023-02085-z

9. https://www.audaciousproject.org/grantees/innovative-genomics-institute

10. https://www.fda.gov/news-events/press-announcements/fda-approves-first-its-kind-intentional-genomic-alteration-line-domestic-pigs-both-human-food