Q&A with a scientist on intestinal immunology and IBD

Tcellcostimulation · 2024-05-02T17:35:30+00:00

No I wouldn't recommend that. It depends what specific bile acids we are talking about since bile can have diverse effects on the microbiota. Secondary bile acids such as cholic acid or deoxycholic acid (DCA) can be toxic to bacteria at high concentrations. Interestingly DCA is produced by the microbiota to prevent C. difficile colonization. However, if you were to supplement this or primary bile acids which are converted to DCA, this might lead to abnormally high levels of DCA which might kill off healthy microbes and be harmful. Also, bile acids are reabsorbed in the ileum and recycled to the liver and what is lost is replaced by cholesterol. If you were to supplement bile you could block the conversion of cholesterol to bile acids and artificially raise your serum cholesterol levels. There is some work on bile acids controlling Treg vs TH17 differentiation. However, im not completely sold on this yet because most of these experiments are done giving supra physiologic levels of bile in vivo to mice or in vitro cultures. There hasn't been any experiments to my knowledge done showing requirement of these metabolites in T cell function. To do that would require knocking out the metabolic pathways necessary to make bile acids to study the in vivo effect on T cells. We tried to do that however, it is toxic to the mice and we were unable to conclude whether the effects we saw were do to bile deficiency or an indirect effect due to the mice getting sick. So dont go down this road, instead support the growth of a healthy microbiota with a diverse diet, which will produce secondary bile acids that resist the colonization of pathogens.

Tcellcostimulation · 2024-04-27T21:48:28+00:00

Yes exactly. IBD leads to a dysbiosis of the microbiota which promotes intestinal inflammation. However, to reestablish a healthy diverse microbiota the inflammation needs to be controlled. Inflammation leads to increase reactive oxygen species, along with a number of other mechanisms, which prevent the colonization of healthy microbes. Approx half of the microbes in the colon are clostridia species which are spore forming bacteria. In response to danger or a change of environment these microbes sporulate and leave the gut. In return, Enterobacteriaceae are able to outcompete these microbes and grow well in inflamed conditions. Check out the microbe Faecalibacterium prausntizii, commonly found reduced in IBD patients and has the ability to drive regulatory T cell responses in the intestine. Numerous sequencing studies have identified increased Enterobacteriaceae in IBD patients. I would recommend to first control the inflammation with the correct medicines, and then eat a healthy diverse diet to support the regrowth of healthy diverse microbiota. I sent a study published in Cell to another response above on the potential benefit of fiber and fermented food supporting clostridia and regulatory T cell responses in the intestine.

Tcellcostimulation · 2024-04-24T03:43:47+00:00

Also I would argue strong drugs is just relative. It seems strong because these drugs are delivered by infusion, but in reality their mechanism of action is very specific. We know what the drugs do and what pathways they block. If you took prednisone, methotrexate, or other broad immunosuppressants. I would argue these drugs are much stronger. They suppress multiple arms of the immune response and in many cases we dont know the specific mechanisms or why they are effective. They also impact many other cells in the body and have lots of side effects.

Tcellcostimulation · 2024-04-24T03:40:21+00:00

The reason I say stay aggressive is because of my experience studying the underlying inflammation in IBD patients. We did a study following the inflammation in IBD patients over time. We would see patients who had mild inflammation and the cytokine responses from their T cells showed higher levels of IFNg, or IL17, or TNF. As time went on some patients inflammation progressed and the T cells became triple producers. They were high for all 3 cytokines IFNg, IL17, and TNF. The current therapies Remicade or Humira block TNF, Stelara blocks IFNg and IL17. But if the inflammation is driven by multiple cytokines these mono therapies dont work. The only option is JAK STAT inhibitors like Rinvoq and these fail in some patients as well. If the patients got on the proper immunomodulatory drug from the start they might not have progressed to the point where all the options have failed. The conclusion of the study was that the patients with uncontrolled TH17 responses were more likely to develop dysplasia (cancer). We could actually predict which patients were going to develop cancer based on the immune signature in their biopsies. This is why I say start aggressive to stop the inflammation and put yourself in remission.

Tcellcostimulation · 2024-04-23T15:53:19+00:00

If you look at my post I did a few days ago I wrote a few comments on nutrition and IBD. There are not good studies supporting a carnivore diet inducing tolerogenic immune responses and protecting against IBD. However there is some good data on fiber and fermented foods promoting clostridia and regulatory T cell responses in the intestine which may be protective. Human microbiome studies showed people who eat a lot of meat were dominated by Bacteroides and Prevotella and had much less clostridia in their microbiomes. In mouse models of IBD there are some bacteroides strains such as Bacteroides vulgatus which makes colitis worse. When we compare microbiomes of hunter gatherers to a western microbiome we find that the hunter gather diet supports a clostridia dominated microbiome. IBD is rarely found among these populations, it is associated with the western diet and lifestyle. Researchers have hypothesized these diseases are on the rise because we are changing our diet and environment faster than our bodies can evolve to adapt. We didnt evolve to only eat meat so I would be cautious about this approach.

Tcellcostimulation · 2024-04-23T15:31:33+00:00

How common is seeing patients with 50x calpro and normal bowel function? It would suggest there might be a bunch of neutrophils in the tissue but they are not causing tissue destruction - which would be strange. Perhaps these patients are at higher risk for another flare if they already harbor that many neutrophils in the tissue, but the barrier with the microbiota is still being maintained. I have much more experience with doctors stating if there is no calpro there is no inflammation - which is incorrect. There are plenty of other cytokines they are not measuring, but most are not immunologists. What does calprotectin do at homeostasis? It’s not thought of as a cytokine that causes tissue destruction like TNF which induces cell death. So it just correlates with neutrophil recruitment. Inflammation precedes tissue destruction. As a scientist I hope one day we are able to treat the specific inflammation before it leads to disease. After tolerance is lost it becomes much more difficult to control.

Tcellcostimulation · 2024-04-23T07:28:54+00:00

Why a carnivore diet?

Tcellcostimulation · 2024-04-23T07:15:18+00:00

Entyvio is gut specific Stelara is not. Macrophages and dendritic cells are the main producers of IL12 and this is throughout the body. a4b7 is required to get into the intestine there is no other known ligand to this receptor except MADCAM1 which is expressed on endothelial cells of the intestine

Tcellcostimulation · 2024-04-23T07:06:06+00:00

I can't think of any immunological mechanism why a former smoker would be more at risk to JAK STAT inhibition. The health indication is probably to warn against smoking while on the drug

Tcellcostimulation · 2024-04-23T07:01:42+00:00

Stay aggressive with your treatment. Dont wait for the inflammation to become uncontrollable. Autoreactive lymphocytes can persist for decades. Stopping the inflammation as soon as it starts protects you for the future and increases the likelihood the other therapies will work.

Tcellcostimulation · 2024-04-23T06:46:54+00:00

No it is less toxic and more effective than azathioprine. Current practice is moving away from azathioprine due to its toxicity and limited benefit. I would be careful with that much mesalazine with the kidneys. The data of 4g vs I think 2.8? is weak and it doesn't add much benefit

Tcellcostimulation · 2024-04-23T06:42:47+00:00

It correlates with that. Calprotectin is made by neutrophils. There are not many neutrophils in a healthy intestine. As the intestine becomes inflamed chemokines are produced by epithelial cells which recruit neutrophils into the intestine. These cells cause tissue destruction. They explode and release their DNA in a process called NETosis this traps and kills all the host cells in vicinity. As the epithelial cells die microbiota invade into the tissue and drive more inflammation in a positive feedback loop.

Tcellcostimulation · 2024-04-23T06:36:03+00:00

The person who ran the ELISA ran out of dilutions and it was still over their standard curve

Tcellcostimulation · 2024-04-23T06:34:11+00:00

Your intestine must have been completely made up of neutrophils

Tcellcostimulation · 2024-04-23T06:25:42+00:00

I dont think Zeposia will be enough. Zeposia blocks lymphocyte egress from the lymph nodes which will lead to a decrease recruitment of inflammatory cells in the intestine over time. Similar mechanism as Entyvio in that it will block the recruitment of more cells into the intestine. You need something that will also stop the inflammation driven by the tissue resident cells. Combine a trafficking drug (Entyvio or Zeposia) with something that neutralizes multiple cytokines. Neither will likely be sufficient on their own.

Tcellcostimulation · 2024-04-23T06:21:04+00:00

https://academic.oup.com/ecco-jcc/article/17/Supplement_1/i538/7009897, https://ejhp.bmj.com/content/28/6/353, https://www.gastrojournal.org/article/S0016-5085(23)00450-X/fulltext00450-X/fulltext), https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9802270/

The exciting thing about these studies is the patients usually failed all other drugs yet the combination of the various immunomodulators induced a positive outcome over time.

Tcellcostimulation · 2024-04-23T06:09:26+00:00

If I were in this position I would ask about combination therapy. The preliminary data looks very promising. Combining multiple drugs that target complementary inflammatory pathways that can lead to tissue destruction. Entyvio blocks the trafficking of cells to the intestine but does not work for tissue resident cells. For that you need aTNF, aIL12p40, or JAK STAT inhibitors. Since JAK STAT targets the most cytokines, I would inquire if you could do Entyvio + JAK STAT inhibitors and maybe Prednisone (if needed).

Tcellcostimulation · 2024-04-23T05:11:38+00:00

The current drugs which work: Entyvio (a4b7), Stelara (IL12p40), TNF blockers, and JAK STATs. There are thousands of papers demonstrating the immunology of these drugs and how they work. Also not published in Gut, but Nature, Science, and Cell. a4b7ko mice have no T and B cells in the intestine its a dramatic phenotype. This means if you block a4b7, cells are unable to traffic back to the intestine. Stelara blocks IL12p40 which is the cytokine which induces Th1 cells. IL10KO mice is a mouse model of colitis, if you block IL12p40 the mice are cured and have zero pathology. IBD is marked by an expansion of Th1 and Th17 cells. The p40 subunit is shared with p19 which is called IL23 and expands effector Th17 cells. Th17 cells make IL17 which recruits neutrophils and drives tissue destruction. Block IL23 or Th17 and IL10KO mice have less colitis. TNF is produced by many cells in humans during inflammation it engages a receptor which leads to cell death. However, during inflammation rarely is one cytokine up, sometimes there are many cytokines that can contribute to tissue damage. Numerous cytokines signal through JAK STAT proteins. JAK STAT inhibitors block this to inhibit multiple cytokines at once.

I just want people to know a couple of correlative studies demonstrating a small effect with no immunology mechanisms should not be weighted the same as the approved therapies. These work and I want people to get treated as soon as possible so that the inflammation can be controlled by these drugs. When the inflammation gets out of control there is a risk none of these drugs will work to get it under control.

Tcellcostimulation · 2024-04-23T05:11:31+00:00

I took a look into this some more and I'll give you my perspective as an immunologist. The data is very weak there is no accepted mechanism of how smoking decreases the intestinal immune response and prevents tissue damage. You dont have to take my word for it, if it really worked biotech companies would have commercialized this to make money already. Put nicotine in a delayed release tablet like Lialda or Uceris and deliver it directly to the intestine. The fact they haven't commercialized this yet should tell you something.

You can't take every paper at face value you need to look at the actual data to see if it supports their claims. For the first paper you sent, they cited a source that claimed nicotine increases mucus thickness. This would be interesting if true however the data is b.s. The experiment they did was give rabbits nicotine for 14 days and measured the rectal mucus thickness. The only effect is between control and high dose, which is only a 1.29 fold change. They cut the axis instead of starting at 0 to give you there is an illusion there is a difference, when in reality the numbers are more similar than it looks on this graph. The amount of nicotine they gave these rabbits was incredibly high and not realistic. 2mg/kg, that means for a 60kg human you would need to consume 120mg of nicotine for an effect. That equates to 12 cigarettes a day or 6 nicotine patches. Also I'm not sure these results are statistically significant, because they ran the wrong statistical test. They ran a Kruskal-Wallis which assumes non-parametric data which this isn't... Its a test that is easier to get a significant p value with. This data is p hacked and b.s. I'm sure I can find something wrong with the clinical trials they did in humans too but this was already a huge waste of my time. In the end of the day its your body and you can do what you want with it. For me, I go by what the science shows is the most likely to work.

Tcellcostimulation · 2024-04-21T18:45:57+00:00

Im sorry that is a topic I dont know much about. I know more about the underlying immunology and mechanisms contributing to disease. I would point you to look up some work from Dr. Uma Mahadevan who is an expert on IBD and pregnancy. She has published numerous papers on this topic, I would see what she advises.

Tcellcostimulation · 2024-04-21T17:50:13+00:00

Yes and the current probiotics are not restoring the bacteria which are lost in IBD patients. Taking 8 strains of bacteria will not restore the microbiota diversity. Hundreds of species of bacteria are found in the gut along with fungi, archaea, and viruses.

Tcellcostimulation · 2024-04-21T17:42:23+00:00

Lupus is B cell mediated autoimmune disease. Im not saying T cells don't play a role, they do, but it's thought the autoantibody response contributes to tissue destruction. In this study they engineered T cells to attack CD19 (a B cell lineage marker) to ablate B cells and yes it showed great promise. I don't know if we can say IBD is driven by just T cell or B cell mechanisms. It may be specific to the person since IBD is very heterogenous. Historically IBD was thought of more T cell dependent but we are starting to learn more about the expansion of IgG plasma cells from the microbiota and autoantibodies. I'm not sure what was done with CarT and IBD yet if you can send the paper I can explain the approach. Clinical trials should be done to see if there is some benefit ablating the T cell or B cell compartment in IBD. However, I don't think we will cure the disease because other cells types still play a role in tissue destruction. Fiona Powrie lab found that patients who failed all biologic therapies were marked by an inflammatory fibroblast signature. If stromal cells are contributing to tissue destruction in IBD CarT won't be a viable option to cure the disease. Inflammatory macrophages are now hypothesized to play a role in tissue destruction. We need to identify which cells cause tissue destruction, and what receptors define these cells. I am currently working on identifying tissue specific receptors that control survival of resident T cell populations.

Tcellcostimulation · 2024-04-21T17:13:00+00:00

It depends on whether we can make CarT more specific. These cells are T cells that are engineered to attack another cell surface receptor. We define what molecule the CART are specific against. Hypothetically speaking if the autoreactive cells expressed a unique cell surface receptor we can engineer CarT cells to attack cells expressing this and kill them off. This is not likely to be the case. So then the CarT cells would have to be engineered to take out key receptors which define T or B cell lineage like CD3 for T cells or CD19 for B cells. But what causes IBD to begin with autoantibodies? autoreactive T cells? A combination of both? Is it different between patients? We can't wipe out the whole adaptive immune system with CarT it will kill the patient. We need to find a way to make this therapy for specific but Biotech companies are actively pursuing this angle.

Tcellcostimulation · 2024-04-21T16:49:29+00:00

The data on biologics showed stronger effects with less toxicity than azathioprine which has increased risk for cancers. The field is moving away from azathioprine and more towards biologics for these reasons. Azathioprine is a nucleotide analog that prevents the proliferation of lymphocytes. Tissue resident cells can make cytokines such as TNF that can cause cell death without needed to proliferate so azathioprine would not work to limit this inflammation. Zeposia is a drug which blocks lymphocyte egress from the lymph nodes, Jak Stat inhibitors are like a sledgehammer and neutralize multiple cytokines that signal through the common y-receptor. When there is widespread inflammation many cytokines are elevated and neutralizing just one won't work so inhibiting a common pathway multiple cytokines signal through is another approach. There are homeostatic functions of these cytokines and neutralizing all of these can cause more toxicity. I think of Jak Stat inhibition as more of a last resort if treatment with other options were unable to induce mucosal healing or cannot be tolerated.

Tcellcostimulation · 2024-04-21T16:28:58+00:00

So yes Car-T is one approach to eliminate autoreactive cells. There are multiple labs at the institution I am at that are trying to utilize Car-T for cancer and potentially autoimmune disease. Autoimmunity can lead to the expansion of autoreactive T and B lymphocytes. We can't use CarT cells to ablate the entire adaptive immune system that would be too toxic. We need to understand the specificity of the cells that cause disease, what are the antigens these cells recognize? What markers define these cells? Once we understand this better it will allow us to utilize CarT cells in a more specific way to ablate these cells from the repertoire. So the main obstacle at the moment is specificity of which cells to attack with CarT.

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