Modifying the Gut Microbiome to Improve CAR-T, HSCT, and Other Therapeutic Responses

The human gut microbiome is known to influence many important physiological functions, and dysbiosis of the microbiome has been implicated in a considerable range of disease indications. More recently, dysbiosis of the microbiome has been shown to impact the effectiveness of cancer treatments, including chemotherapy, radiotherapy, and immunotherapy approaches. Modification of the microbiome in conjunction with cancer treatment shows promise for improving therapeutic responses to many emerging modalities, particularly for adoptive cell therapies. Experience with the development and manufacturing of live biotherapeutics will play a pivotal role in tailoring their immunomodulatory effects so that they can be harnessed to enable specific therapeutic objectives.

The Evolving Understanding of the Central Role of the Microbiome in Health and Disease

The human microbiome a vast community of trillions of microorganisms, including bacteria, fungi, and viruses, inhabiting the body and comprising a “second genome” plays an intricate network of roles in the maintenance of health and well-being. Approximately 80% of these microbes are believed to be beneficial, making in many cases significant contributions to physiological functions. In support of metabolism, the microbiome aids in the digestion of complex carbohydrates and the synthesis of short-chain fatty acids (SCFAs) and essential vitamins like B and K, often contributing metabolic enzymes that are not encoded in the human genome. Owing to the ability of microbial organisms to interact with receptors on epithelial cells and subepithelial cells, the microbiota also release a number of cellular factors that influence human metabolism, presenting potential roles in suppressing the pathogenesis of metabolic syndrome, diabetes, non-alcoholic fatty liver disease, and cognition.  Even more extensive is the role that these symbiotic microorganisms play in regulation of the immune system, including defending against pathogenic invaders by competing for resources and space and preventing them from establishing a foothold and promoting the development of a robust immune response to pathogens while preventing inappropriate immune reactions, such as allergies and autoimmune diseases. 

Dysbiosis a disruption of the delicate homeostatic balance within the microbiome can have severe consequences for human health. Dysbiosis can result from factors ranging from the indiscriminate use of antibiotics, viral infections, or chronic stress and can lead to malfunctions in the systems in which the microbiome is implicated. While gastrointestinal disorders and food allergies are the most obvious consequences of microbiome dysbiosis, a growing body of research has linked imbalances in the microbiome to conditions as diverse as cardiovascular diseases, autoimmune disorders, neurological conditions like Parkinson's disease, diabetes, and cancer. Since gut microbiota are crucial for the proper development of the immune system, imbalances in the microbiome have been associated with an increased risk of various cancers that evade immune detection. The microbiome's influence on the immune system also extends to enhancing responses to therapies like anti-PD-1 immunotherapy for cancer treatment. Dysbiosis of the microbiome has also been implicated in metabolic diseases, such as obesity, insulin resistance, and type 1 and type 2 diabetes, owing to its ability to affect glucose tolerance, which impacts the absorption and efficacy of drugs used to treat diabetes. For example, the effectiveness of the widely used diabetes drug metformin varies among individuals due in part to differences in their microbiomes. 

The Role of the Gut Microbiota in Cancer Development

The gut microbiota plays many diverse functions in the health of the host. In fact, it is estimated that pathogenic microorganisms rather than the symbiotic and commensal microbiota associated with homeostasis are implicated in the origins of more than 20% of cancers.1 Certain viral and bacterial infections are known to lead to the development of some cancers,2 and gut microbiota have been shown to influence the immune response to tumors, with some having positive and others having negative effects.3 They also systemically alter metabolic pathways and homeostasis.1

The mechanisms by which a disturbed (dysbiotic) microbial community affects tumor development are classified as direct and indirect.3 An example of the former is bacterial toxins that interact with cancer-related signaling pathways, while chronic inflammation caused by microbiota is an example of the latter.

Next-generation sequencing technologies have made it possible to identify many of the thousands of bacteria, yeast, and fungi that comprise the human microbiome.3 Bacterial pathogens in the dysbiotic gut microbiota thought to be connected to different cancer types include Propionibacterium acnes, which is associated with prostate cancer; Helicobacter hepaticus and H. pylori, implicated in breast and prostate cancers and gastric cancer, respectively; and Fusobacterium nucleatum, which is involved in the transformation of epithelial cells into tumor cells.1

The Microbiome Modulates Cancer Treatments

Although an imbalance of the gut microbiome may lead to cancer, evidence suggests that a well-balanced microbiome can influence the effectiveness of cancer therapies. Gut microbes affect metabolic pathways via particular metabolites that modulate the side effects and/or metabolism of the chemotherapeutic agents themselves. They also influence the immune response by causing inflammation or interfering with immune cells in peripheral blood and/or within the tumor microenvironment (TME).2 Translocation of gut microbiome constituents (migration across the intestinal epithelial barrier to induce systemic effects) also occurs, as does enzymatic degradation.1

Disruption of the normal microbiome state, whether through the use of antibiotics, changes in diet, or other environmental factors, can thus impact the performance of cancer therapies.3 Specific mechanisms of drug inactivation include suppression of programmed cell death, altered expression of transporter proteins, epigenetic changes, altered gene amplification, and interruption of DNA repair.4 General negative impacts include reduced immune surveillance activities, inhibition of tumor-killing activity, and initiation of pro-inflammatory responses.3

Meanwhile, some bacteria help cancer therapies fight tumors by directly or indirectly (through metabolite production) activating immune cells. Examples include species of Akkermansia, Bacteroides, Burkholderiales, and Bifidobacterium.5

Evidence of Immune Checkpoint Inhibitor Modulation

The introduction of immune checkpoint inhibitors (ICIs) was a tremendous advance in cancer therapy, but it remains an ineffective solution for too many patients. Evidence is mounting that for both ICIs that target PD-1 and CTLA-4 pathways the gut microbiome plays a significant role in determining the outcome of these anticancer treatments.6 The gut microbiome is also believed to mediate or exacerbate the toxic side effects that are often observed with immunotherapies.

Patients found to have “favorable” gut microbiomes generally have better responses, potentially due to increased activation of their immune cells.2 Similarly, patients with dysbiotic gut microbiomes often exhibit resistance to ICIs. Pretreatment with certain antibiotics was found to have a negative impact, which researchers link to disruption of the microbiome.1 The specific bacterial species found to suppress and promote positive patient responses differ for different types of cancer and often from patient to patient, with the latter diversity attributed to genetic and environmental factors.3

Both preclinical and clinical studies have been pursued to explore the role that the gut microbiome plays in suppressing and promoting ICI therapy.7 For instance, Bifidobacterium species in mouse models of melanoma enhanced CD8+ T cell priming and accumulation in the TME. A clinical study in melanoma, non–small cell lung cancer, and sarcoma, meanwhile, found that B cell activity and the level of Ruminococcus species were lower in nonresponders.

The Microbiome’s Influence on Adoptive Cell Therapy

Allogeneic hematopoietic stem cell transplantation (allo HSCT) is an adoptive cell therapy and precursor to more advanced genetically modified chimeric antigen receptor (CAR)-T cell therapies. HSCT has been applied for half a century and is used to treat hematologic malignancies. The therapy involves infusion of HSCs to establish blood cell production in patients whose bone marrow or immune system is damaged or defective. CAR-T cell therapy involves the removal of a patient’s immune cells, genetic modification of those cells to target specific tumor antigens, and reintroduction of the modified cells to the patient’s body. Approved CAR-T cell therapies target CD19, but many are in development against other tumor antigens.

As with ICI therapy, many patients who receive adoptive cell therapies do not respond. A high percentage also experience relapse.8 Not surprisingly, treatment with certain antibiotics before allo HSCT and CAR-T cell therapy is associated with poor responses.8–11 Incidence of graft-versus-host disease (GVHD), poor treatment efficacy, and relapse after allo HSCT are also associated with the presence of unfavorable gut microbes.

Different bacterial species have been found to be associated with successful and unsuccessful CAR-T treatments as well.9,10 In one study, patients with higher levels of Lachnospiraceae and Ruminococcaceae species were more likely to achieve complete remission, while those with an abundance of Peptostreptococcaceae and Clostridiales species often did not respond.9

CAR-T cell therapies are also associated with toxic side effects, most notably cytokine release syndrome (CRS), immune effector cell–associated neurotoxicity syndrome (ICANS), and high-grade infections. Gut microbiota have been proposed to modulate pathogen-induced immune cytokine responses and treatment efficacy.9 A recent study found that patients with higher levels of Bifidobacteria experienced severe CRS.

Gut microbial metabolites and microbial ligands also have been shown to have significant effects on the activity of T cells, including genetically modified T cells administered as part of adoptive cell therapies.9,10,12 Microbiome-derived SCFAs, such as butyrate and pentanoate, are receiving significant interest. These compounds are termed postbiotics.10 Other important metabolites include indoles and 5-hydroxytryptophan.9

Modulating the Microbiome to Enhance Cancer Therapy

Given that some gut microbiota help enhance the safety and efficacy of cancer therapies, while others have the opposite effect, researchers have begun exploring a number of different approaches for modifying the gut microbiome in conjunction with anticancer treatments.3,7 Use of targeted (rather than broad-spectrum) antibiotics could potentially eliminate or decrease the presence of undesirable bacteria without harming favorable species.

Fecal microbiota transplantation (FMT) to re-establish healthy intestinal flora has been investigated in clinical trials with various types of cancer therapies. Oral administration of prebiotic food components that are digestible by beneficial bacteria but not harmful bacteria might lead to larger populations of the desired bacterial species. Finally, oral administration of probiotics or live biotherapeutic products (LBPs) is intended to populate the gut with beneficial bacteria.

In vitro and in vivo studies have shown that probiotics and LBPs can affect cell proliferation, apoptosis, and cell cycle arrest through direct and indirect interactions. Lactobacillus and Bifidobacterium are two common gut-based bacteria that have been targeted. Clinical studies are underway involving a variety of LBPs administered in combination with cancer therapies, including ICIs, such as the following examples:

  • Genome & Co.’s GEN-001, a single-strain LBP being studied in combination with Merck's anti-PD1 mAb therapy pembrolizumab (Keytruda) as a treatment for biliary tract cancer, a challenging malignancy with limited treatment options;
  • BMC128, a rationally designed consortium of four bacterial strains under investigation by Biomica, also in combination with Keytruda as a treatment for biliary tract cancer;
  • CBM588 from Osel Inc., an orally administered Clostridium butyricum strain with a long history of use in diarrheal disorders now being studied as a potential treatment for metastatic kidney cancer in combination with nivolumab (Opdivo), an ICI marketed by Ono Pharmaceutical and Bristol Myers Squibb;
  • CJRB-101, acquired by CJ Bioscience, a single strain of Enterococcus gallinarum developed for unresectable locally advanced or metastatic urothelial carcinoma that was used in combination with Pfizer’s and Merck’s avelumab (Bavencio), and for solid tumors (non-small cell lung cancer, renal cell carcinoma, bladder cancer, and melanoma) in combination with Keytruda; and
  • MB097, a consortium of nine bacterial strains developed by Microbiotica that is entering clinical trials in combination with Keytruda for the treatment of melanoma.

LBP Candidates Targeting Cell Therapy Improvement

Development of LBP candidates designed to enhance anticancer treatments is underway for applications in traditional chemotherapy, immunotherapy with ICIs, and immunotherapy leveraging cell-based drugs. In early 2023, South Korean company CJ Bioscience, which is developing microbiome-based biomarker technology, acquired the LBP platform technology of UK firm 4D Pharma, including its anticancer candidates,13 namely both MRx0518 (now CJRB-101, see above) and a novel LBP based on Megasphaera massiliensis that enhances the performance of CAR-T cell therapies against solid tumors.13, 14

Also in early 2023, Seres Therapeutics announced initiation of enrollment for a phase Ib study investigating SER-155, its LBP candidate designed to reduce the incidence of gastrointestinal (GI) and bloodstream infections and GVHD in patients undergoing allo HSCT.15 SER-155 is a consortium of bacterial species selected using Seres’ reverse translation discovery and development platform technologies. The design incorporates microbiome biomarker data from human clinical data and nonclinical human cell–based assays and in vivo disease models.

Additionally, in February, the University of Texas MD Anderson Cancer Center announced a collaboration with microbiome company Federation Bio to leverage the latter’s ACTTM bacterial cell therapy platform to design and manufacture a microbial consortium derived from a donor fecal sample shown in a clinical trial to improve responses to ICIs in cancer patients via FMT,16 could potentially be used with cell-based immunotherapies as well. While the status of that program is unclear in the wake of Federation Bio’s uncertain future, it is an indication of the ongoing priorities of MD Anderson’s Platform for Innovative Microbiome and Translational Research (PRIME-TR), which aims to support microbiome-based profiling and interventional trials to accelerate of the understanding of microbe–host interactions in the context of cancer onset, progression, and response to treatment.

Microbial Mediation of Cancer Therapies

One of the remarkable features of LBPs in oncology is the precision by which they can selectively target tumor sites. Bacteria including Salmonella, Escherichia coli (E. coli), Listeria, and Clostridium have a natural affinity for the hypoxic and nutrient-deprived tumor microenvironments surrounding solid tumors, with their anaerobic metabolism allowing them to thrive in these hostile environments while sparing healthy tissues.16 This inherent tumor-tropic behavior addresses a significant challenge faced by traditional cancer treatments, which often struggle to discriminate between cancerous and healthy cells.

As such, LBPs offer a panoply of mechanisms for combating cancer. Beyond their ability to target tumors, these bacteria can elicit robust immune responses against the tumors. Bacteria like Salmonella and Listeria have been engineered to express specific antigens or immunomodulatory molecules.17 When introduced into the tumor microenvironment, these bacteria stimulate the host immune system, leading to the activation of cytotoxic T cells and natural killer (NK) cells. This immune activation creates a potent anti-tumor response, effectively turning the body's own defenses against the malignancy.

Another approach involves leveraging LBPs to deliver therapeutic proteins directly to the tumor microenvironment.18 Bacterial strains engineered to express therapeutic proteins can release therapeutic cargos locally inside the tumor, maximizing their efficacy while minimizing systemic side effects. This targeted protein delivery can include various anticancer agents, such as immunomodulators, toxins, or enzymes that disrupt the tumor's microenvironment.19,20

Challenges to Developing Microbiome Modulators for Cancer Therapy

As with any approach to cancer therapy, there are numerous challenges that must be overcome to make microbiome modulation a practical and widespread component of anticancer treatment protocols. One of the biggest issues is the fact that the gut microbial species that exhibit positive effects vary greatly with the type of cancer.2 These microbial shifts vary with the progression of each tumor phase as well. Often, there are also inter-patient differences due to variations in intestinal flora related to genetics, diet, and other environmental factors.3 Still, cancer bacteriotherapy3 appears poised to be another example of truly personalized medicine.7

Partnering to Navigate Complexities and Drive the Innovation Ahead

The complex bidirectional nature of interactions between the gut microbiota and tumors, along with the high level of variation in gut ecology from one person to another, is driving the need for microbiome modulators comprising large consortia that can compensate for both this complexity and diversity. Developers of LBPs intending to modulate the microbiome with the goal of enhancing the performance of cellular and other types of cancer therapies will benefit from partnering with a contract development and manufacturing organization (CDMO) with extensive experience and expertise in strain development and the efficient, cost-effective manufacturing of multi-strain LBPs.

At List Labs, we are very excited about the challenges that lie ahead in successfully harnessing the power of the microbiome to increase the therapeutic success of CAR-T and other cutting-edge immunotherapies. Our extensive strain and process experience position us well to be an effective, supportive partner to innovators working in this space. List Labs has decades of experience developing and manufacturing bacterial-derived products, including GMP therapeutics. We have expertise with over 60 different species of microorganisms and hundreds of different strains, including anaerobes, aerobes, and spore formers from key LBP candidates representing Lachnospiracea, Ruminococcaceae, Akkermansia, and Bacteroides species. List Labs was also one of the first companies to manufacture an LBP that progressed into clinical trials. We have experience in aseptic processing and fills required for live bacteria-based therapy injectables and the production of unique dosage forms, such as vaginal applicators and other delivery vehicles. We are focused on developing and scaling LBP manufacturing processes and providing GMP material for early- to late-phase trials and commercial sale.

By early 2025, our Campbell, California, clinical-scale facility will be complemented by a new large-scale GMP manufacturing facility located in Indiana that will support customer products as they advance to phase III studies and eventually commercial launch. With the construction of the List Bio large-scale LBP production facility, List Labs is already taking action to solidify its position as a leading CDMO in the field of microbiome-based therapies.

Combined with our ability to provide end-to-end solutions for not just LBPs but many types of microbiome-based therapeutics, List Labs is very well positioned to facilitate the tremendous growth trajectory of microbiome-based therapeutics across a wide range of applications, including microbiome modulation, to enhance the safety and effectiveness of cancer immunotherapies.



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Stacy Burns-Guydish, Ph.D.

With over 25 years’ experience in transformative biotechnology applications for microbes, Dr. Burns-Guydish has developed breakthrough technologies for bacterial production of a biochemical resulting in intellectual property and patents and scaled up a strict anaerobic fermentation to 100,000 L. Joining List Labs in 2016, she has directed the development and manufacturing of many different live biotherapeutic drug products for phase I and II clinical trials. Dr. Burns-Guydish earned her Ph.D. in microbiology and immunology from Baylor College of Medicine and completed her postdoctoral training at Stanford University School of Medicine.