Programmable gene editing with CRISPR/Cas systems has finally arrived at the clinic but there are still problems to solve
May 17, 2024
Last week’s issue of The New England Journal of Medicine published the results of two clinical trials that led the FDA to approve the very first gene therapy based on CRISPR gene editing. The treatment is for sickle cell disease and is called, under the completely inscrutable conventions of pharmaceutical naming is called exagamglogene autotemcel (Casgevy is the commercial name). This first CRISPR treatment follows a number of other gene therapies, which were first approved beginning in 2017, the year gene therapy became a reality. The arrival of CRISPR therapy represents in one sense an enormous milestone in medicine: for the first time, medical scientists have used a “programmable” gene editing technology to directly edit a patient’s DNA to cure disease, in contrast to the more common viral vector-based gene therapies. The fact that CRISPR DNA editing is relatively easy to target means that we should expect many more CRISPR therapies, and indeed there are many in the pipeline. But, as I’ll discuss below, the case of Casgevy also shows that therapeutic gene editing still hasn’t quite achieved what scientists have long hoped for. Fixing broken genes to cure disease is still very hard.
Finally a treatment for the first ‘molecular disease’
It’s fitting that the first CRISPR therapy is for sickle cell disease, which was the very first disease for which a pathological state was linked to a molecular change in a specific protein. Sickle cell disease is caused by a genetic variant in the β-hemoglobin gene, which in turn produces an aberrant protein called “hemoglobin S” in red blood cells. Under low oxygen conditions (when deoxygenated blood is flowing through the veins back to the lungs), hemoglobin S polymerizes and contorts blood cells into a stiff, “sickle” shape, which in turn leads to blocked blood vessels, excruciating pain, and regular visits to the hospital to deal with these recurrent circulatory crises. When patients die of this disease, they are often only in their 40’s or 50’s.
In 1949, Linus Pauling, Harvey Itano, S.J. Singer, and Ibert Wells tracked down the molecular cause of sickle cell disease in a now classic paper titled “Sickle cell anemia, a molecular disease.” They found that the β-hemoglobin protein of sickle cell patients was more positively charged than that of normal patients, which was a clue that a specific change in the protein sequence was responsible for the disease. They also found that otherwise healthy people with a mild form of “sickling” blood cells had both kinds of β-hemoglobin, the positively charged version and the normal version. This fit perfectly with a new genetic study of sickle cell disease by James Neel, who argued that sickle cell disease was caused by a recessive mutation (i.e., you need two copies of the mutation to get sick), and that heterozygous people with only one copy of the mutation were healthy. It was the heterozygotes who in Linus Pauling’s study had both kinds of β-hemoglobin.
Figure 1 from Linus Pauling, et al., Science (1949) 110:543-458 showing a charge difference in hemoglobin between sickle cell disease patients and healthy controls.
In 1957, Vernor Ingram worked out that hemoglobin S had a single amino acid substitution, glutamic acid to valine, that was responsible for its abnormal behavior. With this paper, sixty-seven years ago, scientists had for the first time pinned down a specific, disease-causing genetic change that could, in principle, be reversed by gene editing. Over the decades, scientists have discovered thousands genetic variants that underlie a wide range of diseases, many of which could be, in principle, corrected to cure the disease. Without the development of accurate, easy-to-design, in vivo gene editing technology, what’s been an obvious possibility for the better part of a century has been impossible in practice.
Gene editing to cure disease is still not easy
Casgevy to treat sickle cell disease is an amazing advance, but how it works still highlights some key limitations of the technology, notably this: it’s still hard to correct a mutation by editing it with CRISPR directly. It is much easier to use CRISPR to delete some DNA rather than replace it with a corrected sequence. And so Casgevy doesn’t work by correcting the disease-causing, single base-pair mutation in the β-hemoglobin gene directly. Instead, this particular gene therapy is a bank shot: CRISPR is used to reactivate a different hemoglobin gene, fetal γ-hemoglobin, which normally stops being produced in the first twelve months after birth.
It’s been known for some time that having fetal hemoglobin around prevents the pathological β-hemoglobin S gene from polymerizing into the toxic structures that cause red blood cells to sickle. And so the Casgevy strategy is to switch the fetal γ-hemoglobin genes back on by switching off another gene, BCL11A, which represses fetal γ-hemoglobin. Casgevy does this via CRISPR deletion of a regulatory DNA region (called an “enhancer”) that controls the expression of BCL11A. Basically, Casgevy deactivates the activator of the deactivator of fetal hemaglobin, which in turn inhibits the polymerization of hemoglobin S. Welcome to molecular biology.
The lesson here is that, as impressive as the first CRISPR therapy is, it’s still not as simple in practice as gene editing is in concept. We’re still not directly correcting pathogenic mutations.
Delivering gene therapy to individuals and populations
Receiving Casgevy is expensive and arduous. A sample of the patient’s blood stem cells is collected and edited ex vivo, then re-infused into the patient, much like CAR-T cells for cancer treatment. The procedure is essentially a bone marrow transplant in which the patient’s unedited cells are killed and replaced with the edited cells. It’s a difficult treatment that is challenging for the patient and requires a lot of expensive medical care. The results however are astonishing. Before receiving Casgevy, patients in the study routinely ended up in the hospital multiple times a year – in some cases, up to nine times annually on average. Of the 30 patients who completed the full twelve-month follow up, not a single one was hospitalized after treatment. Similar results were observed for Casgevy-treated patients with β-thalassemia, a related blood disorder.
Gene therapy is a cure for disease, not just a treatment. You receive it once, and, if all goes well, you never need treatment again. But it’s not a cheap cure – the wholesale price of Casgevy is $2.2 million dollars. So will people who need it be able to get it? Casgevy was developed by Vertex Pharmaceuticals and CRISPR Therapeutics. However, the key scientific discoveries needed to make Casgevy work were made in part with NIH funding:
- The GWAS that associated the regulator BCL11A with fetal hemoglobin expression
- The study showing BCL11A is a direct regulator of fetal hemoglobin
- The study that identified the BCL11A enhancer that is targeted by Casgevy
- The study showing that inactivating BCL11A corrects sickle cell disease in mice.
And of course for more than half a century before that, public funding was critical for working out the molecular mechanisms underlying sickle cell disease, as well as for the discovery and development of CRISPR technology.
The question of who gets access to expensive gene therapy is even more urgent in the case of sickle cell disease, because the disease overwhelming affects people with African ancestry — in the U.S. that means Black Americans. The persistence of the harmful sickle cell mutation is a literally a textbook example of “balancing selection”, in which people with one mutant copy of a gene and one wild-type copy have an advantage over people who don’t carry the mutant copy at all. As a result, a disease-causing mutation is preserved in the population by natural selection. People who carry one copy of the hemoglobin S mutation have greater resistance to malaria, and, as predicted by evolutionary theory, this mutation is most common in those parts of Africa where malaria is most endemic. Thanks to their African ancestry, Black Americans are much more likely to carry the hemoglobin S mutation. Overall the estimated incidence of sickle cell disease among newborns in America is about 1 in 2,000, while among Black Americans the incidence is over five times higher, 1 in 365. In American, sickle cell disease patients are overwhelmingly black.
We now have an amazing $2 million cure for a genetic disease that primarily kills economically vulnerable Black Americans who live in states and counties that are the least equipped to provide the medical care these patients need. The first CRISPR gene therapy is a long-awaited achievement in medicine, but if it’s going to have a historic impact, we also need to solve the problem of getting these therapies to the people who need them.
