The Impact of Gut Microbiome on Transplant or CAR T-cell Therapy 

Transcript of Presentation.

(00:01): [Susan Stewart]: Welcome to the workshop: The Impact of the Gut Microbiome on Transplant or CAR T-Cell Therapy. My name is Sue Stewart, and I'll be your moderator for this workshop. It's my pleasure to introduce today's speaker, Dr. Melody Smith.

(00:18): Speaker Introduction. Dr. Smith is a board-certified, fellowship-trained Hematologist-Oncologist and an Assistant Professor of Medicine in the Division of Blood and Marrow Transplantation and Cellular Therapy at Stanford University School of Medicine. In 2021, she established the Smith Lab, an independent lab investigating CAR T-cell biology to gain insights that may help to improve patient outcomes. Please join me in welcoming Dr. Smith.

(00:50): [Dr. Melody Smith]: Thank you, Sue, for the introduction and for the opportunity to present our research here at this seminar and symposium. I'll be talking today about the impact of the gut microbiome on transplant or CAR T-cell therapy.  

(01:13): Overview of Talk. Today we will discuss the role of the intestinal microbiome in outcomes following allogeneic hematopoietic cell transplantation (allo-HCT) or chimeric antigen receptor (CAR) T-cell therapy. We will also discuss the impact of allo-HCT and CAR T-cell therapy on the intestinal microbiome, and wrap up with interventions – such as diet and lifestyle changes – that promote a healthy microbiome.

(01:41): I'd like to begin with a brief overview of cancer immunotherapy, which are any immunotherapies that harness the body's immune system in order to fight cancer.

(02:11): In this picture, there is a plane that's flying close to the surface of the ocean. Think of this as a plane that is flying below the radar. This plane represents cancer, and this plane is flying below the ‘radar detection’ of the immune system.  

(02:33): The cells within the immune system – such as T-cells – detect malignant, or cancerous cells, to eradicate and destroy them. Cancer forms when these malignant cells form and the immune system does not detect them.

(02:52): Cancer immunotherapy, is a class of immune-based therapies that harnesses and enhances the immune system's ability to detect cancer cells. These therapies have really led to novel approaches for us to be able to fight cancer.

(03:16): This slide shows the big categories that encompass cancer immunotherapy.  

(03:28): The oldest cancer immunotherapy is the allogeneic hematopoietic cell transplantation, which is a therapy that is used primarily for high-risk and relapsed blood cancers, after chemotherapy treatment.  

(03:47): Then, there are immune checkpoint blockades which inhibit specific proteins on the cancer cells, and allow the body’s T-cells to attack the cancer cells. The first immune checkpoints were anti-PD-A and anti-CTLA-4 proteins, and now there are many others being investigated. These are most commonly used for solid tumors, but they're also used in the treatment of lymphoma.

(04:04): Finally, there's adoptive cell therapy, which encompasses both chimeric antigen receptor (CAR) T-cell therapy, as well as T-cell receptor-based therapy (TCR).

(04:15): Today I'll be focusing on allo-HCTs and CAR T therapies.

(04:24): For those who are less familiar with an allogeneic hematopoietic cell transplant (allo-HCT), here is a brief overview. During this therapy, the patient’s body is conditioned – or prepared for transplant – with total body irradiation, chemotherapy, antibodies, or a combination of these. Once their body is conditioned, and the recipient's own immune cells are ablated, then receive donor hematopoietic stem cells from a genetically matched or half-matched donor.

(05:14): These donor cells are infused into the recipient. For a conventional allogeneic transplant, the recipient receives all of the cells from the donor, and the donor’s T-cells are not removed prior to infusion. The rate of graft-versus-host disease (GVHD) in this type of conventional transplant can range from as low as 40% of recipients to 60%.

(05:42): This data from the Center for International Blood and Marrow Transplant Research (CIBMTR) showing the mortality rate one-year after transplant, indicates the leading cause of death in that first year is relapse from their disease for which the patient received the transplant, followed by death due to graft-versus-host disease.

(06:02): Graft-versus-host disease (GVHD)-related mortality has dramatically decreased over the years as we've been able to develop new therapies and strategies to more effectively treat the disease and prevent GVHD. However, relapse remains an ongoing factor in terms of post-transplant morbidity and mortality. So, much of the focus within allogeneic transplant (allo-transplant) research focuses on enhancing graft-versus-leukemia activity – which is intended to help decrease relapse – and also mitigating or decreasing graft-versus-host disease.

(06:39): Let’s discuss a brief review of CAR T-cell therapy, which is a form of an adoptive cell therapy. Why is it called a ‘CAR’? Why is it called ‘chimeric’?

(06:49): In Greek mythology, the chimera was a fire-breathing, hybrid creature that consisted of the head and body of a lion, the head of a goat, and sometimes a tail ending with a snake’s head.  

(07:24): The word ‘chimera’ simply means combining different things that are not naturally together. So, it’s chimeric because a lion, a goat, and a snake aren't usually together. Similarly, B-cell receptors, which are in chimeric antigen receptors (CAR) T-cells, are not usually in a T-cell. T-cells usually have only T-cell receptors. Therefore, it's considered chimeric because introducing a chimeric antigen receptor (CAR) into the T-cell, you're making it chimeric with a B-cell receptor as well.

(07:55): This technology to introduce the CAR into the T-cell is usually a viral-based technology. And the portion of the receptor outside of the T-cell, that binds to the antigen or the marker on the tumor, is the CAR.

(08:13): Here are the five different CAR T-cell therapies that are currently approved by the FDA. These CARs are indicated for non-Hodgkin’s lymphoma B-cell acute lymphoblastic leukemia. This slide shows their names and disease indications, and they all target the CD19 antigen of the cancer cells.

(08:43): You can see the structures of these CARs. They have quite a few similarities, but some of the internal workings and designs of these CARs vary. This is important to keep in mind, because those design differences allow the different CARs to provide specific functions and benefits that are unique to that CAR.  

(09:18): CAR T-cell therapy has led to significant advances for patients with hematologic malignancies, especially those with relapsed or refractory disease. There are seven CARs that are now FDA approved; five for CD19 malignancies and two for B-cell maturation antigen (BCMA) targets for multiple myeloma – all with really encouraging data.

(09:45): This is an older photo of Emily Whitehead, who was the first pediatric B-cell acute lymphoblastic leukemia recipient of CAR in 2022. This is a photo from when she was 11 years post-therapy; she's now in college and still cancer-free. Similarly, there are reports of patients –pediatric and adult patients – who have been in remission after CAR T-cell therapy for more than a decade. So, a very promising therapy leading to better outcomes.

(10:32): However, there are still some limitations. This data is from a publication in 2021 looking at patients with non-Hodgkin's lymphoma who received CAR T-cell therapy. Up to 60% of patients with this therapy may still relapse, and most commonly relapse within the first year after CAR T-cell therapy.

(10:57): CAR-related toxicity is another limitation. Cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS) are the most common neurotoxicities that occur following CAR T-cell therapy. They most frequently present within the first two weeks, but can occur anytime during the first 30 days after CAR T-cell therapy, and is an area that we need to continue to address and improve upon.

(11:31): Due to the various limitations that still present after an allo-HCT or CAR T-cell therapy for hematologic malignancies, we continue to investigate ways to improve patient outcomes. One approach that we're focusing on, particularly in my research, is whether endogenous factors – or factors that are within the individual – can alter patient response. One of those endogenous factors that we're investigating is the impact of the intestinal microbiome.

(12:02): The intestinal microbiome are the microorganisms that live in the human body, including bacteria, viruses, and fungi. There are 1014 microbes per person, and microbes make up about 3% of the human body mass. The majority of these microbes reside in the gastrointestinal (GI) tract from the oropharynx all the way through the gut.

(12:52): There is a growing body of literature looking at the relationship between the microbiome and cancer treatments and therapies.  

(13:20): So, in summary, cancer immunotherapies are a class of cancer treatments that enable the immune system to target cancer that may have otherwise gone undetected by the immune system. Allo-HCT and CAR-T are cancer immunotherapies that offer key therapeutic options for patients with blood cancers. And the intestinal microbiome, which consists of the bacteria, viruses, and fungi in the host, are being investigated in its role in the patient's response to these therapies.

(13:49): Now, let’s talk about the impact of allo-HCT and CAR T-cell therapy on the intestinal microbiome. So again, as a broad overview, we wrote this review earlier this year that really highlights the intestinal microbiome and CAR T-cell therapy.

(14:05): Treatment with antibiotics can induce dysbiosis – or alterations in the microbiome – which can impair outcomes for transplant and CAR T. Patients with exposure to certain antibiotics prior to an allo-transplant, have increased antibiotic resistance, and increased mortality due to graft-versus-host disease of the gut. Within CAR T-cell therapy, specific antibiotics have been associated with decreased survival and increased neurotoxicity.

(14:51): We hypothesize that these antibiotic exposures lead to a loss of some of the normal constituents – what we call commensals – within the gut. They alter some of the substances that those bacteria produce into the microenvironment, and therefore decrease the diversity.

(15:18): Potential implications from these findings are that antibiotic stewardship – or really being thoughtful about the type of antibiotics that we give patients – as well as eventually giving back a specific consortia of healthy bacteria, could be beneficial. More research is needed before we begin recommending these.

(15:43): The microbiome is very diverse – there are many different types of bacteria with distinct roles – and the more diverse that bacteria is, the healthier your microbiome. A microbiome with less diversity is not a healthy microbiome.  

(16:21): We found that when we look at overall survival in allo-transplant patients, around the time of engraftment, patients with a low to intermediate-diversity microbiome, compared to those with a high-diversity microbiome had poorer outcomes. There are a lot of different things that can impact the diversity of the microbiome as well, including diet and various exposures to medications and antibiotics. Similarly, when we look at lethal graft-versus-host disease, a less diverse microbiome was associated with a higher risk of mortality compared to those patients with a higher diversity.

(17:25): Medications also have an impact on the intestinal microbiome. Antibiotics impact cellular therapy, but there is also a publication that showed exposure to other medications that patients receive, not just antibiotics, has a differential impact on the intestinal microbiome. This was an analysis from a cohort of transplant patients looking at everything from high blood pressure medications to diabetes medications and scoring the medications based on those that impacted the microbiome most. If you're really interested in delving into all the specific medications, this paper analyzes that. The main take away is that all medications impact the microbiome, but antibiotics are the most damaging because they can cause dysbiosis.

(18:23): Antibiotics, especially those aimed at obligate anaerobes – which are microorganisms that live in the gut and survive in the presence of oxygen – have a negative impact on this healthy gut bacteria that plays a crucial role in maintaining gut health.

(18:37): Obligate anaerobes are really important for the immune system, and anaerobe-targeting antibiotics have been linked to the poorer responses in transplant and CAR T-cell therapy.

(19:12):  First, these obligate anaerobe-targeting antibiotics – such as imipenem and piperacillin – are specifically designed to target obligate anaerobes. It's been found that in allo-transplant settings, exposure to these obligate anaerobe-targeting antibiotics did not impact overall survival, but was associated with a higher risk of graft-versus-host disease compared to exposure to other antibiotics or no antibiotics. So, obligate anaerobe antibiotics do have an association with increased graft-versus-host disease mortality.

(19:44): Likewise, we also analyzed similar obligate anaerobe-targeting antibiotics in the CAR T-cell therapy setting, including piperacillin/tazobactam, imipenem, and meropenem. And again, exposure to these antibiotics four weeks prior to their CAR T-cell therapy, was associated with decreased overall survival.  

(20:15): Many of these obligate anaerobe antibiotics are very important and very necessary to consider administering to patients who are neutropenic – or don't have immune cells. If patients have a fever and they’re neutropenic, you need to give them antibiotics because their immune system can't fight infections. So, that's why these obligate anaerobe antibiotics are important and often used.

(20:41): Cefepime is an antibiotic that can also be used to treat neutropenic fever. It's a great option as it fights against a large spectrum of bacteria, but does not disrupt those obligate anaerobes to the same extent.  

(20:55): When comparing exposure to cefepime to either receiving no antibiotics, or receiving anaerobic-targeting antibiotics, we discovered cefepime was not associated with decreased survival, in the same way obligate anaerobic antibiotics were.

(21:11): And I think this is a really important piece of information because it helps prove that these poorer outcomes we saw weren't just due to the fact we were looking at sicker patients receiving antibiotics who then did worse, but the antibiotics themselves and what bacteria they were targeting. This cefepime data on overall survival suggests that it's not just antibiotic exposure in general, but what the antibiotics were targeting.

(21:54): Two separate publications have also reaffirmed this data, in addition to our initial finding from 2022. A study looking at an international cohort of patients who got CAR T-cell therapy, compared outcomes after receiving no antibiotics, low-risk antibiotics, or high-risk antibiotics – many of those being obligate anaerobes targeting antibiotics. Patients exposed to the high-risk antibiotics had the lowest survival and worst outcomes than the two other groups.

(22:25): Another analysis looked at no antibiotics, cephalosporins – such as cefepime, – or anaerobic-targeting antibiotics, and again found that anaerobic-targeting antibiotic recipients did worse compared to the two other groups. So again, anaerobic antibiotic exposure before CAR T-cell infusion has been associated with decreased overall survival.

(22:52): Anaerobic antibiotic exposure before CAR T-cell infusion was also associated with increased neurotoxicity. We looked at both cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS). We didn't see any association with CRS and the use of anaerobic-targeting antibiotics. However, when we looked at ICANS and neurotoxicity, we did see that patients who were exposed to these antibiotics, had worse survival compared to those patients who did not receive one of the obligate anaerobe-targeting antibiotics.

(23:35): A separate publication did a similar analysis looking at the cytokine release syndrome versus neurotoxicity, and they also concluded that exposure to the high-risk antibiotics was associated with increased neurotoxicity.

(23:50): Finally, we looked at specific bacteria, what they secrete into their environment, and the metabolic pathways that the bacteria utilize, and found that both the specific bacteria and their metabolites – these compounds that the bacteria produce – have been linked to how well patients respond to CAR T-cell therapy.

(24:15): In summary, anaerobic-targeting antibiotic exposure during allo-HCT is associated with decreased survival and increased graft-versus-host disease mortality. Exposure to anaerobic-targeting antibiotics in the weeks preceding CAR T-cell therapy is linked to decreased survival and increased neurotoxicity. This data provides potential insights regarding antibiotic stewardship for clinicians caring for CAR T-cell and allo-HCT patients.

(24:46): One important point I want to highlight is when patients have a fever and they're neutropenic, they need antibiotics; that's not a question.  

(24:55): What this data suggests, is that we may be able to select antibiotics that are less damaging to the gut, and associated with less harmful outcomes during treatment. Antibiotics are lifesaving and critical when patients don't have immune cells to fight an infection. Ongoing studies are investigating the mechanisms behind these antibiotic associations, and we're currently doing some of this work in my lab – trying to understand the mechanics behind what the bacteria and their metabolites are doing the CAR T-cells, and how they are modulating the immune system.

(25:33): There are interventions, including diet and lifestyle changes, that patients can do to help promote a healthy microbiome.

(25:45): A common question I get is, "What can I do to enhance my microbiome? What about probiotics?”

(26:02): I want to show you some data from a study that was performed at MD Anderson Cancer Center by Dr. Jen Wargo. This specifically looked at a cohort of patients who received immune checkpoint blockade therapies, giving a probiotic supplement to half the group, and nothing to the other.  

(26:38): Patients who were taking probiotics had poorer outcomes and decreased survival probability. These findings were not statistically significant, because the P value is 0.29, but there was a clear trend.

(27:03): These findings highlight the fact that many of the probiotics are just a different consortia of bacteria, but not necessarily the bacteria that the microbiome may need, or are most important for the improvement of outcomes. And so just a word of caution. Probiotic supplementation has not been studied in the setting of CAR T or allo-HCT, so we can only extrapolate what we know from this setting.

(27:41): A study looking at fiber intake found that patients who had a sufficient fiber intake, compared to those who didn’t, had improved survival. I can't remember what the exact threshold was, but promoting a high-fiber diet, and having a serving of fiber at each meal was considered sufficient versus insufficient.

(28:22): So, prioritize fiber, as opposed to a probiotic. Fiber is a prebiotic because bacteria feeds on this fiber, and it helps to promote a healthy microbiome. Fiber basically gives the bacteria the sustenance it needs to help to promote a healthier consortia of bacteria.

(28:54): A group of my colleagues here at Stanford also really wanted to understand the impact or potential benefit of fiber versus fermented foods. They did a 10-week diet randomization study for 36 healthy adults, who were randomly assigned to a high in fiber diet versus a high in fermented food diet.

(29:23): On this slide you can see the apple versus kimchi, but the food could be anything. With high-fiber foods, we think of fruit, vegetables, whole grains, things like that. Fermented foods would be like kimchi, sauerkraut, yogurt, kefir, kombucha, those types of things. Within the study, they controlled to make sure that those who were on the high-fiber diet were not eating a lot of kimchi and vice versa, to ensure they’d get a clean assessment.

(30:04): What they found was that the high-fiber diet certainly did have some benefits; it increased some microbiome function, short-chain fatty acids, and changes in inflammation over time. But the high-fermented-food diet increased the diversity of the microbiome and decreased inflammatory signals and activity. So it was more anti-inflammatory for the gut.  

(30:37): While both diets did show some functional benefits, they found that the high-fermented-food diet had some increased immune benefits compared to the high-fiber diet that they thought were significant.

(30:55): There's still limited data on dietary interventions and cancer immunotherapy, and much has to be extrapolated from other studies. But the data does suggest that both a diet high in fermented and high-fiber foods promotes a healthy microbiome. I think a diet really enriched in both would help to promote a healthy microbiome.

(31:17): And there's really no evidence to support the use of probiotics to improve the microbiome or clinical outcomes in this setting. The data that we have shows that probiotics for cancer immunotherapy – although not statistically significant – did show a trend for worse outcomes in those patients taking probiotics.

(31:38): With that, I'd like to conclude and thank our patients and fecal microbiome donors who helped to contribute to our research, my microbiome colleagues both at Stanford, UNC, and Duke, my lab, and funding sources. 

[Susan Stewart]: Closing. With that, we will wrap up this session. I want to thank Dr. Smith for a very interesting presentation and great responses to the questions. And, I want to thank the audience for asking some excellent questions. Please contact BMT Infonet if we can help you in any way. And I hope that you enjoy the rest of the symposium. Thank you.