Crohn's Disease Podcast

Are We Any Closer to Intestinal Gene Therapy in Crohn's Disease?

Peter Higgins, MD, PhD; Judy Cho, MD


May 24, 2022

This transcript has been edited for clarity.

Peter Higgins, MD, PhD: Hello. I'm Dr Peter Higgins, and welcome to Medscape's InDiscussion series on Crohn's disease. Today we'll be discussing gene therapy trials. Given the recent successes with sickle cell anemia, how far away are we from intestinal gene therapy in Crohn's disease? First, let me introduce my guest, Dr Judy Cho. Dr Cho is professor of pathology, molecular, and cell-based medicine at Mount Sinai in New York, where she is the dean of translational genetics and director of the Charles Bronfman Institute for Personalized Medicine. Dr Cho's many important discoveries include early work on identifying NOD2 and the IL-23 receptor as risk alleles for Crohn's disease. Welcome to InDiscussion, Judy. Just to get us started, what is it about researching and treating inflammatory bowel disease (IBD) that first drew you to this field?

Judy Cho, MD: It was during my GI fellowship at the University of Chicago. What's great about IBD is you're treating a very specialized disorder. You're making a positive impact in patients. And because it affects teenagers and young adults, you're really functioning as a primary care physician. That was back in the days that I was actively seeing patients. In addition, the GI tract is very accessible, so you can actually study the tissues involved. And then I really started getting into genetics when a lot of the colon cancer genes were being discovered.

Higgins: Great. Certainly a lot of understanding of the mechanisms of IBD has come out of this genetic research through the consortium that you lead. I got interested in this very recently after seeing some really amazing results of several forms of gene therapy for sickle cell anemia in a couple of recent publications that have been remarkable. And as someone who trained in a sickle cell center during residency at Duke, I for many years held out hope that gene therapy could make a difference for sickle cell patients. That variance, of CRISPR-Cas techniques, really seems to be making serious headway in recent publications. Very recently some of my more science-savvy patients ask me when some version of gene therapy will be available for Crohn's disease, which is an interesting and complicated question because it's not quite the same or as simple as sickle cell. There could be a number of barriers to overcome before this could become a viable approach. I think it might only be available for some patients, if ever. So I wanted to sit down with an expert in IBD genetics and talk through what the road to gene therapy for Crohn's disease might look like in the near future. Judy, let's start with the very recent data on gene therapy in sickle cell anemia. Can you explain for us how this gene therapy was done, how there were two different approaches, and how successful these initial clinical trials have been for sickle cell patients in preventing hospitalizations in sickling crisis?

Cho: Thanks for bringing up these examples, because these are very exciting new approaches for gene therapy to treat. What is the single gene disorder with sickle cell? It's a single base pair substitution in the hemoglobin B gene, and one of the things about sickle cell is it obviously has tremendous morbidity and mortality. It really does have a major effect. And so targeting and trying to treat the specific molecular defect for sickle cell anemia is very logical but not easy. Two back-to-back New England Journal articles (Frangoul et al, Kanter et al) used two different molecular approaches for treating sickle cell. And it's based upon a very interesting clinical observation, which is that the hemoglobin that's present in adults involves genes that are coded by two different gene areas: hemoglobin A and hemoglobin B in adults. But that's different in the prenatal and fetal time, where you have hemoglobin A and hemoglobin F. And so the observation is, well, you always have the genetics that you have. But yet sickle cell tends not to present right away because you have remaining hemoglobin F. So the observation that hemoglobin F can be protective against these sickle cell anemia patients who carry the hemoglobin B mutation was the important clinical observation, and that actually formed the basis for some of the treatments to induce hemoglobin F in patients who then subsequently go on and present with sickle cell anemia.

There's a particular transcription factor called BCL11, which normally serves to repress the expression of hemoglobin F. And so with both of these approaches, one using CRISPR, the other one using lentiviral transduction, both increased the expression of hemoglobin F, thereby reducing the complications of sickle cell that you typically see. So when you carry the hemoglobin B mutation, what that does is it has the tendency to sickle the red blood cells, and you can see a lot of the complications that you typically see with sickle cell anemia, including a lot of clotting complications or thromboembolic complications. By enhancing hemoglobin F, you actually can reduce side effects. And as you pointed out that in addition in one of the papers, they actually replaced it with a normal copy of hemoglobin B. So both of these studies are involved. They're promising. They're incredibly transformative. And most importantly, the side effects: These were chronic effects. They were able to reduce the complications of those thromboembolic diseases.

Higgins: It's pretty amazing that a single treatment has produced results out to 2 or 3 years and essentially taken people who are having sickle cell crisis about once a month and basically eliminated those with a single treatment. And I think that's what's gotten some of my science-savvy patients excited about: Wow, could I get one treatment and essentially eliminate my Crohn's flares? You mentioned specifically that sickle cell is a single gene. What makes Crohn's disease less attractive as at least a first case for gene therapy?

Cho: Crohn's disease is a polygenic disease. For most cases where you have disease onset in the teenage years or young adulthood, we believe it's caused by many, many genetic variants acting together. Now, in some cases of very-early-onset IBD, you can have a single gene disorder that we think largely drives these diseases. These single gene diseases usually present very early, either in the neonatal period or in early childhood, and probably two of the most important pathways that are involved in these single gene forms of Crohn's are the loss-of-function mutations interleukin 10 as well as a loss-of-function mutation in a gene called Xiap, or XIAP X-linked inhibitor of apoptosis, which is downstream of NOD2 signaling. But for most polygenic forms of IBD, the biggest effect mutation is in the gene that we discovered, together with Gabriel Nuñez at the University of Michigan as well as investigators from France, that these loss-of-function mutations in the bacterial sensing gene NOD2 confer the highest risk in European ancestry Crohn's disease.

Higgins: And how common is NOD2 in European ancestry Crohn's disease? Is that a large percentage of patients or not that many?

Cho: It's probably a little bit over a third. So probably somewhere between 35% and 40% of those with European ancestry Crohn's disease carry at least one copy of a disease-associated NOD2 risk allele. And if you carry one copy of these loss-of-function NOD2 variants, it increases your risk of developing disease by about 1.5-fold to twofold. If you carry two copies or are a compound heterozygote of the NOD2 risk alleles, it increases your risk anywhere from eightfold to 12-fold.

Higgins: That's a fair number of people. It certainly wouldn't be the majority who might, in theory, be eligible for some NOD2 direct gene therapy. Now, this is pretty different because in addition to the immune cells, which obviously come from the bone marrow, the gut is affected. Would it be appropriate to have a lentivirus focused on the bone marrow or the gut? Or would you need both?

Cho: That's a great question. One of our colleagues here at Mount Sinai, Louis Cohen, is actively studying this, together with support from the Helmsley foundation. And for years, Louis and Jean-Frederic Colombel had started a bone marrow transplant effort in the most severe Crohn's patients who had basically failed every form of existing biologics. It was kind of out of desperation. The bone marrow studies have actually shown beneficial effects, which is great. The bad news is that the disease comes back. And so if you take those two things together, what you might then consider is that if we believe that it's the NOD2 deficiency from the hematopoietic stem cells from the bone marrow. If you think that's what's really driving disease, then by using these types of approaches — CRISPR, lentiviral — you may actually have a long-lasting effect. The challenge is that you want to start this in some of the sickest patients with Crohn's disease. It's too early to say whether it's going to make the difference, but the fact that you actually have transient benefit in bone marrow transplantation in some sets of these very sick Crohn's patients indicates that this might be a positive approach.

Higgins: I've seen a few IBD patients in the Midwest who've had bone marrow transplants and have done well for a while. The data for Northwestern were very interesting. They reported that most of the patients were able to be drug free in remission for 3-5 years, but it was interesting that the ones who recurred early tend to be smokers. So there's an environmental factor, and as much as anything, it's felt like they were resetting the immune system, not necessarily changing the immune system. Whereas doing this CAS CRISPR on NOD2 might actually change their immune system so they wouldn't recur. Does that seem reasonable?

Cho: Exactly. We published a paper last year. We describe some of the mechanisms of blood monocytes, which ultimately are coming from the bone marrow in terms of how these blood monocytes may have abnormal cellular differentiation, resulting in an increased risk for Crohn's disease. And so if we think the defect really is blood monocytes and with trafficking to the intestine being altered, it does make sense to try to do gene therapy of these hematopoietic stem cells. It should be stated, however, that there's a substantial literature that NOD2 is expressed in Paneth cells as well, and Paneth cells are important cells in the intestinal epithelial crypt bases that secrete a variety of antimicrobial peptides. So certainly, a bone marrow transplant would not correct those types of defects.

Higgins: So if we figured out that we needed to correct the Paneth cells and we wanted that to be lasting, would we actually have a gut-focused lentivirus or an orally ingested lentivirus that would try to change the stem cells in the crypts?

Cho: It's an interesting idea. Each one of the crypts has its own stem cell history. It's an interesting question because one of the features of Crohn's disease is it tends to be very focal. And so you could even envision kind of local therapy. But in my opinion, the first step to try would really be those hematopoietic stem cells similar to the sickle cell stores.

Higgins: Yeah. I was impressed. And I don't know if it was beginner's luck, but the folks doing sickle cell were able to change hemoglobin expression in the neighborhood of 99% of cells for a really long time with a single treatment. Do you think, though, with the way NOD2 works or at least as well as we understand it today, even if we got 50% correction or 80% correction, would that potentially be enough to change the phenotype?

Cho: I think so. Absolutely. And again, the genetics give us some insight into this. If you have one defective allele vs two defective alleles. I think the 50%-80% correction of the hematopoietic stem cells — I would guess again; we're just guessing right now — would have a substantive positive impact.

Higgins: And I would imagine the NOD2 homozygotes, the folks who tend to get very early disease — often in their pre-teen years — and tend to have stricturing and really complicated disease are probably the ones that would benefit the most. I would imagine that a single CRISPR-Cas would probably modify the 3' end of NOD2 and just cover multiple versions of NOD2 defects.

Cho: Yes, most of the mutations in NOD2 are in the 3' part of the gene. It's a part of the gene that actually senses a bacterial product. So it's that failure to sense correctly. I do actually think molecularly that approach makes sense when you try to get all three of the major NOD2 mutations because they're all in that same area of the gene.

Higgins: So theoretically, you might have one cassette that you would swap out for the 3' end of NOD2.

Cho: That's exactly right.

Higgins: We talk about Crohn's as a polygenic disease, and obviously sickle cell is a lot easier. They made one change that was spectacularly successful, but occasionally you can run into somebody who's got a NOD2 mutation. IL23R mutation, ATG16L, IL10 — you name it. Does it seem reasonable that if we see success with NOD2, it might help that portion? But if they have multiple hits, we may not take care of the whole story. How many hits, as far as we know, does the average Crohn's patient have?

Cho: We can't answer that precisely. The other thing is that there's such a thing as winner's luck. NOD2 was kind of the first gene we associated outside of the MHC (major histocompatibility complex) associated with IBD. So winner's luck means that you're going to find the biggest effect genes first. And as we find more and more loci that are associated, there have smaller effects. So the hope would be that if you kind of hit a few of the biggest ones which you've listed — NOD2, IL23R, the autophagy pathway — that actually might be enough because you're just kind of tipping over and you're passing some type of threshold. And the final point we'll make about IL23R is that most of us, probably myself and yourself included, are walking around with what is the risk allele. And that is actually why the association with IL23R is particularly interesting; about 1 out of every 7 European ancestry individuals are heterozygous carriers for a protective allele. So you might think, well, yeah, that's why not just make everyone a protective allele. And obviously that's being targeted now by therapies that are presently approved for IBD to block the IL-23 pathway.

Higgins: So I'm thinking about whether the big genes are probably the top three or four. What percentage of Crohn's patients who are on biologics and have pretty bad disease have one of those big four?

Cho: Probably the majority. It's actually a very exciting vision you have there, Peter. Why not correct all the big three or four and be done with it?

Higgins: I don't know technically how easy it is with a bone marrow transplant to do multiple edits where we'd be editing NOD2 with one construct, IL23R with a different one, ATG16L with a third. But if that were technically possible, you might have kind of a general approach to the majority of Crohn's patients.

Cho: I think it's an exciting vision. I think if we can get the first one done, why not do the top three to five? That opens up the question of how much of the risk is conferred by stromal cells, the epithelial cells, as opposed to the hematopoietic stem cells? But it is an exciting vision that I hadn't really thought of seriously. But why not do it? If you're going to do it…

Higgins: Yeah, it's really interesting. And I've found the bone marrow literature really interesting because it's a very blunt instrument and they're still doing trials in the UK, continuing with bone marrow transplant for severe Crohn's. But if we could do it in a much targeted way with a lot fewer side effects, it would be pretty amazing.

Cho: Yes, the autologous bone marrow transplants are pretty safe, but I mean, these are the sickest of the sick patients. And so that's really where you have to do these types of experiments to start with. But that's often in the cancer field how things started as well. So yes, I agree that's an exciting approach.

Higgins: So imagining a future 5 years from now, we've got effective vectors, we've got rodent trials, possibly even cotton-top tamarin trials that seem to work. Who would be the first patients, if you were hypothetically designing a trial, to approach about this kind of therapy?

Cho: Well, again, Louis Cohen is actually doing this at Mount Sinai right now for these really treatment-refractory patients. And it's exactly the same fraction we've already genotyped them. It's kind of like 30%-40% are NOD2 carriers. So it's probably a confluence of multiple risk alleles plus some environmental things as well. So there's no reason to think that the genetics are going to be any different in these refractory patients, and that's probably the group to go after.

Higgins: Makes sense. While we have many more choices with biologics, there just seems to be a group of patients who are often diagnosed before age 10 and have just dreadful refractory disease. And it does seem that identifying those folks and having this approach would be pretty effective. Do you think in terms of the monogenic IBD, XIAP and IL-10, is this going to happen, possibly even earlier?

Cho: It's a great question. It actually does make sense that that would be another cohort. I do think that it's completely logical. XIAP is definitely expressed in stromal cells as well. But that would not put me off that because they're often severe, they often have severe perianal disease — IL-10 as well. It's a great point. And to a substantial effect they're already cured by standard bone marrow transplant. But your point, that maybe a more targeted therapy may be the way to go, is interesting. And certainly for those centers that see a lot of these patients that are doing bone marrow transplants, it makes perfect sense that that should be the approach for the very small subset of IBD patients.

Higgins: Where do you think this is in terms of timeline? Obviously when you're doing science and you're trying to translate this to medicine, unexpected things will happen. But if you're trying to imagine specific trials and genes or possibly multiple genes, how far away do you think it might be?

Cho: I like that Bill Gates quote where we overestimate the change that can happen in the next 3 years and underestimate the amount that can happen in the next 10 years. I think what's going to work, we're going to know in the next 10 years.

Higgins: I certainly think of a lot of clinic patients who our current approaches are just not quite good enough for and for whom we would love to have a whole other tool in the arsenal. It's pretty amazing to think about — seeing the successes in sickle cell and thinking that this could actually happen for our Crohn's patients. In the big picture, big takeaways, I think it's reasonable that NOD2 would probably be first, that doing hematopoietic cells and doing bone marrow transplants is at least the starting point. We may not need to treat the gut directly at all, and this is actually starting to happen at Mount Sinai at least. Hopefully, if we see successes, this may not be more than a decade away with success. Yeah, fingers crossed on this one, for sure.

I want to thank you for having this conversation. I think it's a really exciting new field, and thank you for bringing your expertise in IBD genetics to share with us.

Cho: Thanks so much, Peter. It's been fun.


Sickle Cell Anemia

Crohn's Disease

Inflammatory Bowel Disease

CRISPR-Cas systems: Overview, Innovations and Applications in Human Disease Research and Gene Therapy

CRISPR-Cas9 Gene Editing for Sickle Cell Disease and β-Thalassemia

Biologic and Clinical Efficacy of LentiGlobin for Sickle Cell Disease

Causes of Crohn's disease

IL-10R Polymorphisms Are Associated With Very-Early-Onset Ulcerative Colitis

Characterization of Crohn Disease In X-Linked Inhibitor of Apoptosis-Deficient Male Patients and Female Symptomatic Carriers

A Frameshift Mutation in NOD2 Associated With Susceptibility to Crohn's Disease

Extended Haplotype Association Study in Crohn's Disease Identifies a Novel, Ashkenazi Jewish-Specific Missense Mutation in the NF-κB Pathway Gene, HEATR3

Autologous Stem Cell Transplant for Crohn's Disease

Stem-Cell Transplantation for Crohn's Disease: Same Authors, Different Conclusions?

A Myeloid-Stromal Niche and gp130 Rescue in NOD2-Driven Crohn's Disease

Expression of NOD2 in Paneth Cells: A Possible Link to Crohn's Ileitis

Role of ATG16L, NOD2 and IL23R in Crohn's Disease Pathogenesis

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