Dr. Philip Dubé of Taconic Biosciences presented a recent webinar on genetically engineered models (GEMs) of colitis, which are widely used for preclinical research on inflammatory bowel disease (IBD). Although a wide array of GEM colitis models exist, Dr. Dubé focused on a few models which are both most commonly used and most useful for drug discovery. He discussed the relevance of the disease mechanism in each model and covered important experimental considerations based on both his long personal experience using colitis mouse models as well as feedback from pharma and biotech researchers in the field.
Time constraints prevented discussion of all submitted questions during the Q&A period. We present a full Q&A here, including the great discussion between Dr. Dubé and moderator Dr. Terina Martinez regarding the parallels between IBD and Parkinson's research.
You can go through that same exercise: predictive, face and construct validity. Is DSS very predictive? In this case, DSS doesn't respond to many therapeutics. To my knowledge, the only therapeutic that works consistently as a positive treatment control in DSS is something like cyclosporine A. A lot of the biologics don't work. It's a very acute model. You can make that more clinically relevant, potentially by doing it in a chronic fashion. But it's kind of more of a repeated injury model.
From the perspective of drug development in the for-profit sector, people just aren't willing to face going to clinic solely off of DSS data. I showed the increasing spectrum that these companies are using to evaluate their therapeutics. They're going to still do DSS because it's cheap and quick, but in addition to that, they're going to use as many models as they can to really get good confidence that there isn't something specific to any one model that would lead you to think that your drug is either going to be successful or unsuccessful.
Ultimately, just like in people, we know that there is a relationship and cross-talk between the genetic background and the microbiome driving disease. There's no real straightforward way to tease those apart. So it depends on how much you want to invest in in teasing apart that mechanism. Co-housing is an imperfect solution but it is an approach. We know that co-housing animals together when possible can at least normalize their fecal microbiome. Whether or not you're getting normalization at the luminal surface is probably another question — there's some data that co-housing is not effective. I mentioned just transferring dirty bedding, and that's a quick and dirty solution. Other, more complex approaches include cross fostering between different lines and going right to germ free. If you go right to germ free, you take that out of the equation and then you can normalize your microbiome across different genotypes and different groups. I think that is ultimately going to be the the gold standard in figuring out the contribution from those two different factors.
What does that mean for your research? When you bring this into even the cleanest pharmaceutical vivarium, the microbiome there tends to be much more diverse versus that at our clean-room production facilities. Our production practices require stringent personal protective equipment including powered air purifying respirators with strict environmental controls. That helps in a number of respects. It allows us to be able to produce large numbers of these animals to do studies. The fact that you're switching them from a very, very clean environment to a slightly less clean environment and exposing them to more microbiota probably helps accelerate the disease. Kind of like a light version of the germ-free. We've come across this issue in breeding with other types of models. One of the more notorious models in this regard is the SAMP1Yit spontaneous colitis model. That model will in a very similar fashion to the Il10 knockout develop spontaneous disease, but it's really hard to breed them unless you keep them germ-free. That's typically what has to be done for that particular model and it's not a scientific rationale. It's a practical concern of simply being able to produce enough mice to do your study.
Time constraints prevented discussion of all submitted questions during the Q&A period. We present a full Q&A here, including the great discussion between Dr. Dubé and moderator Dr. Terina Martinez regarding the parallels between IBD and Parkinson's research.
Dextran sulfate sodium (DSS) colitis model
Q: One thing that really struck me about the wide spectrum of the different models for colitis, from the chemical induced in the rapid acute models versus the chronic and spontaneous — it actually parallels a field that I'm familiar with, which is Parkinson's disease. That is another disease that is attributed to a complex interaction between genetics, and environment with insidious onset and a wide variety of pathology. For Parkinson's, the toxin model MPTP was first identified in the early 1980's and became the most popular model in Parkinson's, because it's very fast, it's very acute, specific, it's easy to reproduce, and you can do it anywhere. That seems to be kind of similar to the DSS or chemical-induced model in the colitis fields. When you look at the number of publications in Parkinson's, MPTP has the most publications, but I would argue that potentially it isn't the most translationally relevant. Can you speak to the fact that in the colitis research publications, chemically-induced acute models may have a larger footprint, but do you think that that necessarily translates there better utility or wider adoption?
You can go through that same exercise: predictive, face and construct validity. Is DSS very predictive? In this case, DSS doesn't respond to many therapeutics. To my knowledge, the only therapeutic that works consistently as a positive treatment control in DSS is something like cyclosporine A. A lot of the biologics don't work. It's a very acute model. You can make that more clinically relevant, potentially by doing it in a chronic fashion. But it's kind of more of a repeated injury model.
From the perspective of drug development in the for-profit sector, people just aren't willing to face going to clinic solely off of DSS data. I showed the increasing spectrum that these companies are using to evaluate their therapeutics. They're going to still do DSS because it's cheap and quick, but in addition to that, they're going to use as many models as they can to really get good confidence that there isn't something specific to any one model that would lead you to think that your drug is either going to be successful or unsuccessful.

Q: Do you know if DSS per se has a direct effect on microbiota?
The role of the microbiome in colitis
Q: Here's a question that relates to how you mentioned the potential interest in exacerbating a gene effect with chemical induction. This question gets at the interaction of genes and microbiome. How would you distinguish the effect of the gene mutation and the microbiome, and the relative importance in a given model?
Ultimately, just like in people, we know that there is a relationship and cross-talk between the genetic background and the microbiome driving disease. There's no real straightforward way to tease those apart. So it depends on how much you want to invest in in teasing apart that mechanism. Co-housing is an imperfect solution but it is an approach. We know that co-housing animals together when possible can at least normalize their fecal microbiome. Whether or not you're getting normalization at the luminal surface is probably another question — there's some data that co-housing is not effective. I mentioned just transferring dirty bedding, and that's a quick and dirty solution. Other, more complex approaches include cross fostering between different lines and going right to germ free. If you go right to germ free, you take that out of the equation and then you can normalize your microbiome across different genotypes and different groups. I think that is ultimately going to be the the gold standard in figuring out the contribution from those two different factors.
Q: Do you offer germ-free Mdr1a knockout animals?
Q: Which model would you suggest to study the role of microbiome in ileocolonic Crohn's disease?
Q: What is the difference between germ-free B6 and germ-free BALB/c Il10 knockouts?
Q: What makes BALB/c Il10 knockouts more sensitive?
Q: Fecal matter transplants induced colitis in the Il10 deficient germ-free mice on the C57BL/6 background. What was the source of the fecal matter? Is fecal matter/microbiota from C57BL/6 conventional mice sufficient to induce colitis or do you need microbiota from conventional BALB/c mice?
Logistical challenges presented by spontaneous colitis models
Q: The phenotype in Il10 knockouts occurs relatively early. How can you breed and maintain those animals for commercial production while avoiding welfare and production problems?
What does that mean for your research? When you bring this into even the cleanest pharmaceutical vivarium, the microbiome there tends to be much more diverse versus that at our clean-room production facilities. Our production practices require stringent personal protective equipment including powered air purifying respirators with strict environmental controls. That helps in a number of respects. It allows us to be able to produce large numbers of these animals to do studies. The fact that you're switching them from a very, very clean environment to a slightly less clean environment and exposing them to more microbiota probably helps accelerate the disease. Kind of like a light version of the germ-free. We've come across this issue in breeding with other types of models. One of the more notorious models in this regard is the SAMP1Yit spontaneous colitis model. That model will in a very similar fashion to the Il10 knockout develop spontaneous disease, but it's really hard to breed them unless you keep them germ-free. That's typically what has to be done for that particular model and it's not a scientific rationale. It's a practical concern of simply being able to produce enough mice to do your study.
Selection of the most appropriate IBD model
Q: IBD is a multigenic disease with mutations in a number of genes modulating susceptibility and severity of disease, combined with environmental factors. In many cases, the specific etiology for patients is unknown. Which model mimics more closely the development of human pathology? Can any single mouse gene knockout recapitulate this?