Investigating Epigenetic Mechanisms of Response to Allogenic CAR T Cell Therapy
St. Jude Children’s Research Hospital
Caitlin Zebley, MD/PhD
Young Investigator Grants
Type of Childhood Cancer:
General Pediatric Cancer
While autologous chimeric antigen receptor (CAR) T cell therapy has proven efficacious for many patients with acute lymphoblastic leukemia, CD19-positive relapse often occurs after CD19-CAR T cell therapy indicating that the CAR T cells either lack persistence or functionality. Based on our longitudinal assessment of patient samples, we have now shown that autologous CD19 CAR T cells undergo exhaustion-associated epigenetic programming during an in vivo tumor response. We hypothesize that acquisition of the exhaustion-associated epigenetic programs is hastened in autologous-derived CAR T cells due to underlying leukemia-induced T cell dysfunction. Therefore, I will explore whether CAR T cell therapy can be improved by the use of allogeneic CAR T cells generated from healthy donors. In this application, I propose 1) To determine if leukemia-induced T cell dysfunction promotes acquisition of exhaustion-associated epigenetic programs. 2) To determine the kinetics of exhaustion-associated epigenetic programs in allogeneic CAR T cells during a clinical response. Identifying mechanisms that contribute to the decline in CAR T cell survival and effector function (defining features of T cell exhaustion) is critical for addressing this challenge of limited therapeutic response. We have previously reported that DNA methyltransferase 3A (DNMT3A) programming is causal in establishing T cell exhaustion in murine systems and have confirmed this mechanism in humans using a variety of CAR T cell models. Building upon our insights into the epigenetic basis of T cell exhaustion, we have recently generated a bioinformatic tool termed the Multipotency Index (MPI) which is based on the DNA methylation programs of T cells and can predict the T cell’s differentiation potential. To determine the impact of leukemia-induced T cell dysfunction on the efficacy of CAR T cell therapy, I will compare autologous- (leukemia patient) and allogeneic- (healthy donor) derived CAR T cells by performing whole genome bisulfite sequencing methylation profiling to apply our MPI as well using our established ex vivo chronic antigen stimulation assays to examine proliferation and anti-tumor function. Furthermore, having identified the epigenetic signature of T cell exhaustion acquired in autologous CAR T cells, we will determine the kinetics of allogeneic CAR T cell dysfunction and highlight epigenetic differences between autologous and allogeneic CAR T cells during an in vivo tumor response.
The research proposed here will identify DNA methylation programs that limit expansion and persistence of CAR T cells generated from a healthy donor. In pediatrics, a parent can serve as a T cell donor and our study will provide further insight into the epigenetic programs that restrict allogeneic CAR T cell survival after infusion into patients. Furthermore, our study will provide insight into leukemia-associated dysfunction of autologous T cells used for CAR T cell therapy in pediatric patients. Lastly, these studies will identify targetable molecular mechanisms that can be exploited to prolong CAR T cell anti-tumor responses.