Krishanu Saha is an associate professor of biomedical engineering. In his research, Saha uses genetic tools like CRISPR—sometimes referred to as a “molecular scissors”—to study and create personalized medicines and therapeutics. He’s been using CRISPR in his lab since shortly after its discovery in 2012, and now teaches UW-Madison engineering students about it. Saha is also a member of National Institutes of Health Somatic Cell Genome Editing Consortium. In this interview, Saha explains how CRISPR works and discusses recent developments in the field.
Q: What, broadly speaking, is CRISPR? How does it work?
A: CRISPR is a tool to change the code of genes within our body. CRISPR is an acronym for “clustered regularly interspaced palindromic repeats.” That’s a description of the DNA in which CRISPR was originally identified in a bacteria. These repeating sequences essentially encoded RNA and proteins that defended the bacterial genome against invading pathogens. Engineers and biologists have repurposed and re-engineered this system using the Cas9 protein to work in human cells.
Very small mutations in the human genome can cause disease. CRISPR is a way to precisely target those changes that may be pathologic and, in some cases, fix them to a healthy version of the code.
It works through two components. One is a protein component—the “scissors”—that can cut both strands of DNA. The other is a short piece of customizable RNA. In laboratories, we can create little stretches of RNA that tell the protein component of CRISPR where to cut. So where there’s a mutation you’re trying to address, you craft RNA, put it together with the protein, and then the CRISPR system targets the mutated portion of the genome.
Q: CRISPR has made headlines for a number of exciting developments lately. In December, the FDA approved a CRISPR-based treatment for sickle cell disease. Earlier in 2023, there were reports about its potential for protecting chicken flocks against bird flu. What do you think these sorts of advancements mean for the field as CRISPR moves more into the public eye?
A: These are, no doubt, big milestones for the field. Ever since CRISPR’s discovery as a gene-editing tool in 2012, there’s been a question mark about whether it could ever really be used in medicine. And now we’re seeing that the answer is clearly yes: There are at least 45 patients in trials for the sickle cell treatment and for many of them it seems to be working fairly well so far. Everyone hopes that the efficacy of these gene therapies remains high and durable, and in theory, we anticipate that these types of therapies could be effective for a lifetime.
So it could be a one-time procedure that leads to a lifetime of therapy. And I think that durability and efficacy is reflected in the price of these therapies. As the news was coming out, I think one question the public immediately asked was, “When can I get access to this?” Especially for something that could be helpful to so many people who need it. Cost and access are going to be important parts of this going forward. Certainly, the CRISPR field has been anticipating this, given the cost of gene therapies that did not involve CRISPR. So there are a lot of questions and challenges still to solve related to gene therapies and healthcare access writ large.
With the bird flu example, that is another recognizable application of CRISPR—for combating infectious disease in livestock. That was another question mark: taking this molecular system from bacteria and not only putting it into humans, but putting it into agricultural organisms. Would that be useful for some applications? It seems like there is potential for that.
Q: What about CRISPR therapies makes them so precise and potentially long-lasting?
A: I think the precision of the approach has some distinct advantages for certain inherited conditions. For example, a National Institutes of Health consortium that I’m a part of has a project to inject CRISPR directly into an infant’s body to treat spinal muscular atrophy, or SMA. There is a treatment for this condition using traditional gene therapy, and it works by flooding the cells with healthy genes. However, as the infant grows, the copies of those healthy genes can’t keep up, and the durability fades. There are also some dosage limitations because there are some tissues that don’t normally need that gene that are exposed to it through the gene therapy vector.
With CRISPR, we can go in and we can precisely change specific copies of the gene. So we’re not relying on external copies of the gene traditionally used in gene therapy. Instead, we’re letting the body express the gene at the right cell at the right level, because we’ve used this tool to precisely fix the mutation. So if we can make this type of change in the original mutation, it will be copied to “daughter” cells as a person grows, and the hope is that will lead to more durable changes and long-lasting therapeutic effects. At its core, we’re trying to change as little as possible and let biology and the body do the work of figuring out when and how to express those proper copies of the genes.
“At its core, we’re trying to change as little as possible and let biology and the body do the work of figuring out when and how to express those proper copies of the genes.”
Krishanu Saha
Q: What additional CRISPR-based treatments are coming in the next five to 10 years?
A: A huge proof of concept is that we can put CRISPR into a cell, do it safely, and have a therapeutic outcome.
There are several more treatments in development. Some target the liver for metabolic conditions. Within our consortium, there are programs targeting the brain, the eye and muscles, and our goal is to open up clinical trials within four to five years. We’re thrilled to develop this approach not as individual drugs that have to be developed for every single different mutation that might occur, but more as a platform. What that means is we have a base and if a physician diagnoses a mutation in a patient, a customized CRISPR drug can be rapidly developed for that person.
There seems to be some interest in this approach from the FDA. There’s some precedent in the cell therapy space and the vaccine development space where they’re changing components to keep up with a new variant without requiring full-blown testing. But it’s a tricky position for a regulator to be in so we’ll have to see how things continue to shape up over the next few years.
Q: CRISPR discussions usually are adjacent to concerns about safety and ethics. What do you see as risks or ethical concerns with CRISPR? Is it safe to use?
One of the questions the FDA is tasked with is determining whether it’s safe. The FDA has put things like the sickle cell treatment through trials and continues to monitor that. For things like embryo editing, I don’t know that the FDA thinks about those questions, as that’s a domain largely outside of its purview. Other countries, like Germany, ban those types of applications of genetic manipulation. One of the projects we’re working on is trying to understand how differing views have emerged on the same technology.
One new worry that has come recently is the idea of genetic variation. It came up during the FDA advisory committee meetings for the sickle cell treatment because there was a genetic variant identified in African American populations that could potentially provide an off-target site for CRISPR. That variant was not represented in many of the reference genomes that have been built on other populations—namely white populations—that are used to evaluate safety. Of course, the principal target population for sickle cell treatment in the U.S. is African Americans (sickle cell disease in the U.S. is most common in African Americans).
I think this is a welcome interrogation to how we think about genetic variation with CRISPR. It’s a question that may be very specific to the exact type of cell you’re using CRISPR in, the target population you’re doing it in, and the disease or mutation you’re addressing, so I don’t think there’s an easy answer to this challenge. But recognizing it and thinking about frameworks to address it is something that’s in progress and that is, ultimately, a good thing.
Featured image caption: Associate Professor Krishanu Saha discusses CRISPR during an interview. Saha researches CRISPR, which can be used to modify pieces of genetic code within our cells. Photo by Joel Hallberg.