Getting CRISPR to the Clinic

In November 2023, the U.K. Medicines and Healthcare Products Regulatory Agency (MHRA) approved the first CRISPR-based therapy. This endonuclease—targeted to the gene of interest by clustered regularly interspaced short palindromic repeats (CRISPR)—and CRISPR-associated protein 9 (CRISPR-Cas9) method can be used in treatments by editing a patient’s disease-causing DNA. Specifically, MHRA approved Vertex Pharmaceuticals’ Casgevy (exagamglogene autotemcel) to treat sickle cell disease and transfusion-dependent ß-thalassemia. A few months later, the U.S. Food and Drug Administration (FDA) approved this treatment for the same diseases. These approvals, though, only marked the beginning of how CRISPR will impact treatments and patients.

As of mid-October 2024, clinicaltrials.gov listed nearly 60 studies involving CRISPR-Cas9. As Eric Kmiec, PhD, executive director and chief scientific officer at the Gene Editing Institute at Delaware-based ChristianaCare, said, “CRISPR has been a part of many of the novel treatments for cancer already, specifically as a tool to reengineer the antibody or the T-cell for cell therapy or immunotherapy.”

As explained here, CRISPR is being vastly improved as a treatment for cancer and offers promise in treating other gene-based diseases.

Precision placement

Although a day at the beach can be relaxing, it’s also dangerous. The danger comes more from the sun than from sharks circling offshore. In fact, most melanomas arise from exposure to the sun’s ultraviolet light.

As in any treatment, getting a melanoma drug to its target forms the foundation of efficacy and safety. Nonetheless, meeting that objective is not always easy. “Systemic delivery of any sort of biomolecular drug induces severe side effects and ignites drug resistance, and it always will,” Kmiec explained. “We focus on directly delivering CRISPR to tumors to disable genes involved in the development of cancer-drug resistance.” In this way, Kmiec emphasized, he and his colleagues can “attack the problem of extensive side effects and the development of drug resistance at its genetic core.”

Despite just getting started with this approach, Kmiec’s team is seeing what he calls “outstanding results in animal models.” Taking a direct-delivery approach of getting immunotherapies to melanoma tumors is key. “If you don’t do that, you’re just simply adding greater drugs with more side effects to patients who eventually fail, because they’re simply so unhealthy from the treatment [that] they quit the research trial,” he said. “We think the combination of our genetic approach coupled to pharmaceuticals is a winning formula, especially when you can deliver it directly to the tumor.”

In particular, Kmiec’s team is targeting mutations in the BRAF gene, which appear in about 50% of people who have melanoma. Of those with melanoma and a BRAF mutation, 90% have a mutation called BRAF V600E. Although effective BRAF inhibitors are available for patients with a BRAF V600E mutation, most melanomas become resistant to these drugs, often through the development of a mutation in the NRAS gene. So, Kmiec’s team created a CRISPR-based method that restores sensitivity to inhibitors in cells with mutations.

“By disabling genes that the tumor uses to fight off standard care, including pharmaceuticals, we can reduce the amount needed for effective cancer care,” Kmiec says. “BRAF inhibitors are classic examples of effective drugs that eventually become ineffective because of a unique genetic mutation.”

The scientists also developed methods that reduce off-target effects of the CRISPR-based treatment. For instance, Kmiec’s group used a proprietary, in-house algorithm to identify a unique site within the NRAS gene that produces low off-target effects.

“The work has been surprisingly effective, and what’s most important is that we’ve identified two Cas proteins that can be designed to act only on the tumor cells and leave healthy cells unchanged and unedited,” Kmiec noted. “The effect is the restoration of sensitivity to BRAF inhibitors, and the tumor cells selectively die while the healthy cells thrive, which we think is a good step forward.”

Mutations and the brain

Although many therapeutic applications of CRISPR target cancers, this technology can be used in other areas of healthcare. One of those areas might turn out to be brain-related disorders.

“One of the most striking findings in autism, as well as in other neurodevelopmental disorders, is that mutations in many genes can lead to the disorders,” said Joseph Buxbaum, PhD, director of the Seaver Autism Center for Research and Treatment at the Icahn School of Medicine at Mount Sinai. “CRISPR provides a rapid means of disrupting, downregulating, or upregulating specific genes to understand their function in a high-throughput manner.” CRISPR can therefore be used to explore how mutations, and the impact of other genes on overlapping and converging pathways, are linked to the pathobiology of neurodevelopmental disorders.

Studying such mutation-based effects in the brain requires tools that improve the analysis of information. One tool that Buxbaum and his colleagues use is Perturb-seq, which combines CRISPR-based gene perturbations with single-cell sequencing of RNA. “This is a very useful tool for high-throughput studies because you can carry out studies where—in a large mixture of cells—each cell receives a specific guide RNA against a specific gene of interest,” Buxbaum explained. “And that specific cell will have that specific gene perturbed.” Then, barcoding can be used to examine the RNA sequence and determine which guide RNA was taken up by a given cell.

“In other words, you can know which gene was disrupted and the impact of that disruption on gene expression in that cell,” Buxbaum said. “What this means is that one can take a library of guide RNAs against many genes and work out conditions where each cell takes on only a single guide RNA—on average—and then look at the consequences of disrupting each of those many genes on a cell-by-cell basis.”

As an example, studies by the Autism Sequencing Consortium, which Buxbaum co-directs, have identified over 200 genes strongly implicated in the risk of autism. About half of those genes regulate the expression of other genes. Buxbaum and his colleagues picked 70 of these regulatory genes and made a library of guide RNAs to independently impact each gene in different cells, and then applied Perturb-seq. “At the end, we had sufficient data from disruption of 60 genes, and by sequencing single cells that had a perturbation in one of those 60 genes, we can begin to understand the impact of perturbing that autism gene on neurodevelopment,” Buxbaum said.

Buxbaum and his colleagues explore neurodevelopment with induced pluripotent stem cells (iPSCs) to track their development in two- and three-dimensional models of the brain, such as organoids. This produces a complicated analytical challenge because the perturbations could completely change brain function. “Imagine, for example, if a perturbation may change the ratio of excitatory to inhibitory neurons in the brain, or may alter the timing of the development of an excitatory or inhibitory neuron,” Buxbaum said. “Separating these kinds of clear developmental impacts is an emerging challenge.”

As one way of analyzing such complex information, scientists could use structural topic modeling (STM), which “treats cells as ‘books’ and the expression of distinct genes in that cell as ‘words,’” Buxbaum explained. For example, if you had a computer algorithm that could count the number of specific words in two books, then “you could develop a metric that tells you how similar the two books are in terms of topics,” Buxbaum said. “If both books have many words associated with geopolitics, for example, they would be more similar by this metric than a book that had many words about geopolitics and another book that has many words about maintaining a healthy garden.”

Led by Xuran Wang, PhD, an assistant professor at the Seaver Autism Center, Buxbaum and his colleagues apply STM to neurodevelopmental disorders. “Some of the genes in the cell will be more highly expressed when the cell is becoming an excitatory neuron, versus an inhibitory neuron,” he said. “Other genes will be more highly expressed when a cell is differentiated and reaching terminal differentiation as a mature neuron.” Even more possibilities exist, making analysis complicated. “By using the gene expression from Perturb-seq as words, and assigning ‘topics’ to each cell, we can begin to find convergence of different genes and see how they might impact aspects of neurodevelopment,” Buxbaum said. “And importantly, we do this in an unbiased way, allowing the words to speak for the cells, in the sense that we allow different biological processes—for example, cell fate and developmental trajectory—to vary naturally, and we don’t constrain things, which is done in most of the current approaches.”

Using such methods, Buxbaum and his colleagues identified converging pathways in genes related to autism spectrum disorder, but many of these genes are yet to show any convergent mechanisms. “This means, first, that we need to expand our models and analyses to better capture brain development, but also highlights the critical importance of precision medicine in autism,” Buxbaum said.

One day, precision medicine for neurodevelopmental disorders could include CRISPR-based treatments. “The same technology that allows us to manipulate gene expression in preclinical studies allows us to manipulate genes in vivo,” Buxbaum said. “Ultimately these mutations may be correctable using CRISPR editing, which we are still far away from, but modulating the expression of genes is perhaps a nearer goal.”

Buxbaum is already thinking about how CRISPR-based treatments might work. For example, if a disorder arose from a loss-of-function mutation in a gene, CRISPR might be used to upregulate the expression of the healthy, second copy of that gene. In that way, “we would get more RNA and protein, which is likely to ameliorate the impact of the mutations,” he said.

Is economic equity possible?

Although treatments based on CRISPR promise to offer extensive benefits to patients, many of them won’t be able to afford it. For example, Casgevy costs about $2 million.

“Although the treatment is priceless for the patient who is cured, the cost of Casgevy is astronomical from a lay perspective,” said Jon Rueda, PhD, a postdoctoral fellow at the University of Basque Country in Leioa, Spain, and lead author of a 2024 article about CRISPR pricing in The CRISPR Journal. “This price was not surprising, though, because we have—sadly—gotten used to multi-million dollar prices for gene therapies in recent years.”

When asked why Casgevy is so expensive, Rueda emphasized that it cannot be simply explained. That said, he provided an overview. “To summarize it very hastily, the cost mainly reflects the following: Casgevy is a therapy that cures patients while saving health systems and insurers the cost of lifelong treatment, and pharmaceutical companies want to recoup the investment in the development of this particular therapy and previous unsuccessful therapies.” In addition, he pointed out that the price of Casgevy depends on other potentially costly factors like highly skilled labor, vector production, and safety and efficacy controls.

For now, Casgevy can only help some patients regardless of the price. First of all, it’s only approved for specific groups of people even within those who have sickle cell disease or ß-thalassemia. Even if this treatment gets approved for more diseases, only some people will get it. “The high cost greatly limits the potential users,” Rueda said. “It is clear that this cost can be a significant financial barrier, even in high-income countries.”

That leaves a crucial question for today and tomorrow’s CRISPR-based therapies: Can they be made more affordable? “Very talented people are coming up with different views on how to make CRISPR affordable, but I don’t think there is a single magic bullet,” Rueda said.

In fact, CRISPR-based treatments are not alone in high cost. “The prevailing research ecosystem is prioritizing the private profit-making of start-ups, which often build on previous basic science research funded by public money,” Rueda explained. “I believe that the development of gene therapies for people with rare diseases should be a public goal and that it should also go beyond the patent wars.”

In today’s biopharmaceutical market, the process of making foundational changes is very complicated, but worth pursuing. “Setting a price that divides the threshold between the affordable and the unaffordable would be subject to multiple problems,” Rueda stated. “But most people would find it very far from their common sense for an affordable therapy to have a multi-million dollar price tag.

Mike May is a freelance writer and editor with more than 30 years of experience. He earned an MS in biological engineering from the University of Connecticut and a PhD in neurobiology and behavior from Cornell University. He worked as an associate editor at American Scientist, and he is the author of more than 1,000 articles for clients that include GEN, Nature, Science, Scientific American, and many others. In addition, he served as the editorial director of many publications, including several Nature Outlooks and Scientific American Worldview.