Marcel van den Brink Lab Research
The van den Brink lab focuses on understanding the intestinal microbiome as an immune modulator, the role of thymic regeneration in immune response and clinical outcomes, and the mechanisms of chimeric antigen receptor (CAR) T cells in hematologic malignancies. Our investigations are performed via perpetual dialogue between work with mice and humans: human studies enable us to observe correlations, develop hypotheses, and test therapeutic strategies; animal studies enable us to establish or refute causal relationships and to obtain mechanistic insights. Our data then inform the development of clinical trials testing therapeutic strategies to enhance the efficacy and decrease the toxicity of cancer immunotherapies.
The gut microbiota consists of a community of diverse microbes and has many effects on human (patho) physiology. Microbiome composition has been associated with many diseases, but causal inference is often lacking. Preclinical and clinical studies have demonstrated that the intestinal microbiota can regulate innate and adaptive immunity, including T cell and antitumor immunity after allogeneic hematopoietic cell transplantation (allo-HCT) and checkpoint blockade. We have demonstrated that microbiota composition undergoes significant and frequent changes during allo-HCT. We have found that lower intestinal microbiota diversity is associated with increased mortality; that dominance by certain species, most frequently Enterococci, is associated with lethal graft-versus-host disease (GVHD); that exposure to certain antibiotics is associated with worse outcomes following allo-HCT and immunotherapy; and that the presence of beneficial flora is associated with hematopoietic reconstitution. These studies have been translated into clinical trials using autologous fecal microbiota transplant, administration of defined bacterial consortia, and antibiotic stewardship to spare and/or restore the commensal flora.
While robust thymic function and T cell production are essential for a competent immune response during cancer therapies, thymic injury decreases thymic output of T cells and increases the risk of malignancies, morbidity, and all-cause mortality. We have demonstrated that thymic regeneration is critical for the renewal of immune competence following thymic injury and that we can harness pathways driving thymic regeneration to promote immune reconstitution and improve outcomes, especially following allo-HCT. We are studying various pathways of thymic regeneration in both preclinical models and human cohorts. The resulting clinical approaches could benefit patients undergoing cytoreductive therapies, as well as individuals suffering from T cell deficiencies due to age-related lymphoid atrophy, autoimmune diseases, infectious diseases, and shock.
T cells modified to express chimeric antigen receptors (CARs) against markers found on cancer cells are a newer therapeutic option for patients with hematologic malignancies. While immunotherapies are curative in some recipients, improving their efficacy and abating toxicities are unmet needs in oncology. We have investigated allogeneic donor CD19 CAR T cells as a therapeutic strategy in mouse models and have demonstrated potent graft-versus-lymphoma (GVL) activity and reduced GVHD activity using these cells. Similar results have also been found for patients receiving allogeneic donor CAR T cells. We are currently investigating methods to overcome mechanisms of resistance to CAR T cell therapies including T cell dysfunction and exhaustion, which limit the effectiveness of CAR T cells, and antigen heterogeneity, which enables cancer cells to escape detection and elimination by CAR T cells. We are also developing novel CARs and CAR platforms targeting human antigens associated with hematologic malignancies for human therapeutics.
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a curative-intent therapy for hematologic and some other malignancies. However, patients can experience life-threatening complications including graft-versus-host disease (GVHD), relapse, and infections. Allogeneic donor T cells attack not only residual tumor cells but also the recipient’s tissues and organs during GVHD.
The gut is a primary target of GVHD and plays a role in its development, as allo-HSCT conditioning disrupts host–microbiota equilibrium. The healthy gut is characterized by a diverse, mostly anaerobic community of bacteria, while gut dysbiosis involves expansion of facultative anaerobes such as Enterococci. Microbiota dysbiosis—including decreased bacterial diversity and lower abundance of anaerobic commensal species—is associated with increased mortality rates and other poor outcomes in patients with cancer.
The gut microbiota interacts with immune system function and immune reconstitution to affect clinical outcomes (Nat Rev Cancer 2018). Gut bacterial (alpha) diversity decreases, sometimes rapidly, during allo-HSCT, owing to cancer treatments, antibiotics, and other medications as well as inflammation and dietary changes. We have found that certain antibiotics increase the risk of domination by pathobionts (e.g., Enterococcus species), which are associated with worse outcomes, or infection by intestinal pathogens (e.g., Clostridium difficile). In one study, we found similar patterns of microbiota disruption among patients receiving allo-HSCT at four U.S. transplant centers, including loss of diversity and domination by single taxa (NEJM 2020). Patients with more diverse gut microbiota during neutrophil engraftment had lower mortality rates two years after treatment. Similarly, in an international study of microbiota diversity after allo-HSCT, we found that patients with gut domination by Enterococcus species had higher risk of GVHD and mortality (Science 2019).
To better understand the influence of drug exposure on the microbiota, we developed a computational method called PARADIGM (parameters associated with dynamics of gut microbiota) to identify medication-microbiome associations and their role in patient outcomes (Cell 2023). In this longitudinal analysis, several nonantibiotic drugs were associated with reduced alpha diversity and expansion of Enterococcus species. We are now exploring how medical record data on pharmacologic exposures can be used to predict changes in microbiota composition and indicate opportunities to intervene to preserve or increase diversity. Given the role of the gut microbiota in modulating systemic immune responses, we have also investigated the potential use of the microbiota as a biomarker of therapeutic response and resistance. Our data support the development of microbiome-derived biomarkers and prophylactic interventions for acute GVHD.
Some commensal species are protective against GVHD and other treatment complications. We reported that patients with higher abundance of Blautia species in class Clostridia during the peri-engraftment period had reduced GVHD-related mortality and longer survival after allo-HSCT. Clostridia and other commensals produce short-chain fatty acid (SCFA) metabolites, such as butyrate, propionate, and acetate, as a byproduct of carbohydrate fermentation (Blood 2022). These bacterial metabolites are important for intestinal gut health and immune regulation. We aim to determine how to increase SCFAs during allo-HSCT, given that acute and chronic GVHD are associated with lower concentrations of butyrate and other SCFAs.
In addition, to further understand how bacterial metabolism affects the immune system, we have studied how the gut microbiota shapes the intestinal bile acid (BA) pool (Nat Microbiol 2024). Our analyses suggest that dysbiosis and loss of microbe-derived BAs during inflammation may be an important mechanism exacerbating T cell-mediated diseases. However, microbiota-targeted strategies could support therapeutic responses. For instance, some patients receive prophylaxis with ursodeoxycholic acid (UDCA), which is also a microbe-derived BA. While patients with GVHD after allo-HSCT had an altered BA pool in our study, those who received UDCA had better responses, supporting the use of this supplement in the peri-transplant setting.
Our recent findings suggest that changes in the intestinal microbiome can also affect clinical outcomes after chimeric antigen receptor (CAR) T cell therapy (Nat Med 2022). This newer cell therapy has led to unprecedented responses in patients with high-risk hematologic malignancies despite persistently high rates of relapse and toxicity. In the first study describing the associations between the microbiome and CAR T cell therapy responses, we found that patients exposed to anaerobe-targeting, broad-spectrum antibiotics before CAR T cell therapy had higher rates of mortality and neurotoxicity. Our metagenomic analyses revealed specific bacterial taxa (especially in the class Clostridia) and metabolic pathways associated with clinical benefit, mirroring our findings in the allo-HSCT setting.
We have investigated several strategies to promote intestinal diversity after allo-HSCT, including by limiting the use of broad-spectrum antibiotics, administering dietary interventions, or restoring diversity through fecal microbiota transplantation. Lastly, we are exploring the administration of live biotherapeutic products, which deliver a tailored consortium of beneficial bacteria, to improve the efficacy of CAR T cell therapy. Our overall goal is to further characterize how the microbiome and its related metabolites influence patient outcomes after allo-HSCT and CAR T cell therapies.
T cells are a major component of adaptive immunity and immune reactions against malignant cells, as well as essential to immune reconstitution after cancer therapies. T cells are produced in the thymus, an organ that produces a wide diversity of T cells enabling normal vaccine responses, protection against pathogens, and anti-cancer immunity. Unfortunately, the thymus is highly sensitive to acute injury and thymic involution is associated with aging.
We have demonstrated that cytoreductive conditioning and graft-versus host disease (GVHD) impair thymic function in patients with cancer. Furthermore, decreased thymic regeneration prolongs T cell deficiency, leading to higher rates of morbidity and mortality from infections and malignant relapse, a phenomenon affecting T cell reconstitution post-transplantation (Sci Transl Med 2022, Sci Transl Med 2023, Blood 2022).
Although the thymus is acutely sensitive to injury, it has incredible capacity to regenerate itself. Our research aims to find solutions to lymphopenia in cancer patients by harnessing the endogenous capacity of the thymus to regenerate itself and stem cells to develop into T cells.
We have identified several pathways regulating endogenous thymic regeneration, involving interleukin (IL-) 7 and IL-22 (Blood 2012), endothelial cells secreting bone morphogenetic protein 4 (Sci Immunol 2018), and sex steroid inhibition (J Exp Med 2014; Nat Med 2018), as well as elucidated the role of stem cells in this mechanism (Nat Cell Biol 2013; Nat Med 2006). We demonstrated that some pathways driving endogenous thymic regeneration, such as pathways involving innate lymphoid cells (Blood 2017) and IL-22 (Science 2012), can be harnessed to promote immune reconstitution after allogeneic hematopoietic cell transplantation (allo-HCT).
We have described how thymic epithelial cell (TEC) regeneration is central to thymic recovery and demonstrated that the master TEC transcription factor forkhead box N1 (FOXN1) is induced by the products of injury-resistant thymic cells. Changes in this cell population with aging lead to the emergence of atypical thymic epithelial cell states (Nat Immunol 2024).
We are investigating how to enhance thymic function and T cell reconstitution through different approaches in mice and human studies, using adoptive Treg cell therapies, CRISPR screens to identify upstream regulators of thymic epithelial cell regeneration, multiome analyses, and investigation of the mechanisms driving sex- and age-associated thymic involution.
For patients with hematologic malignancies, allogeneic hematopoietic cell transplantation (allo-HCT) therapy is potentially curative. However, common complications of allo-HCT, including graft-versus-host disease (GVHD) and relapse, remain major causes of morbidity and mortality following transplant. T cells modified to express chimeric antigen receptors (CARs) against markers found on cancer cells are a newer therapeutic option for patients with hematologic malignancies. These non-MHC-restricted T cell receptor-like constructs confer T cells with novel antigen recognition capabilities such that they can proliferate and mediate anti-tumor activity.
We have investigated the use of universal third-party T cell precursors expressing CARs that promote recovery of thymic function, stimulate immune reconstitution, and reduce risk of disease relapse following allo-HCT (Nat Biotechnol 2008). We have also investigated allogeneic donor CD19 CAR T cells as a strategy to reduce disease relapse. Using preclinical models of allo-HCT and lymphoma, we studied mouse allogeneic CD19-specific CAR T cells. In mice receiving donor CD19 CAR T cells, we observed potent graft-versus-lymphoma (GVL) activity, yet with reduced GVHD activity. Our results suggest that this strategy could prevent relapse of CD19+ malignancies after allo-HCT without increasing the risk for GVHD (Nat Med 2017). We are interested in better understanding the mechanisms of the reduced GVHD potential of these allogeneic cells, as well as generating novel receptor constructs that could inhibit GVHD while retaining GVL.
Despite the successes of CAR T cells, including several cellular therapies now approved for clinical use, many therapeutic challenges remain. Cancer cells can develop resistance to CAR T cells through multiple mechanisms, including downregulation or loss of the target antigen, induction of T cell exhaustion, and expression of immune suppressive factors. We have developed a novel approach to engineer T cells with the ability to overcome multiple resistance mechanisms simultaneously. This technology, called “Zip-sort”, enables researchers to positively select cells incorporating two retroviral vectors in a single immunomagnetic sorting step to increase the number of incorporated transgenes so that T cells simultaneously express multiple CARs and switch receptors, and we observed enhanced anti-tumor activity in vitro and in vivo (Nat Biomed Eng 2024). Because these cells simultaneously target multiple tumor-associated antigens and can receive stimulation from multiple inhibitory ligands, we expect they will be better able to overcome tumor escape associated with loss and reduction of antigens and inhibitory receptor signaling. To enhance the safety of these CAR T cells, we have also integrated multiple safety switches and have designed drug-regulated CAR molecules. In another study using Zip-sort technology, we engineered T cells with co-expression of two CARs targeting multiple myeloma and engineered IL-18 secretion, which promoted elimination of multiple myeloma weakly expressing CAR target antigens (Blood 2024). We are developing methods to tune CAR signal strength to reduce toxicity, tonic signaling, and antigen-dependent T cell dysfunction and to further enhance T cell activity.
To test these novel approaches, we are using syngeneic mouse models of hematologic malignancies. These analyses help us better understand mechanisms of CAR T cell dysfunction, CAR T cell-mediated on-target, off-tumor toxicity, and toxicity from cytokine release syndrome. We are also developing novel CARs targeting human antigens associated with hematologic malignancies, with the goal of translating human therapeutics.