Learning features of optimal CAR T cells for LBCL from patient data

PROJECT SUMMARY/ABSTRACT Chimeric antigen receptor (CAR) T cells have emerged as breakthrough treatments for patients with hematologic malignancies, earning 12 approvals from the U.S. Food and Drug Administration (FDA) since 2017. Experimental CAR T cell therapies have also demonstrated complete remissions in solid tumors, and the FDA is projecting to grant 10-15 approvals per year by 2025, highlighting the potential of these ‘living therapies’. Despite this, current CAR T cell designs have not yet mediated sustained efficacy in solid tumors, and only 30-50% of B cell leukemia and lymphoma patients experience long-term disease control. To develop safe and potent next-generation CAR T cell therapies, it is critical to understand why existing CAR T cells succeed or fail in patients. As a scientist trained in both experimental and computational immuno-oncology, I have chosen to focus my career on using a systems biology approach to uncover the molecular mechanisms governing efficacy of engineered T cell immunotherapies. This proposal outlines a structured 2-year training plan and a comprehensive 5-year career development program to complete my training and launch an independent research career. My specific research goals are: (1) to define the most therapeutically relevant CAR T cell subsets in patients with large B cell lymphoma (LBCL), and (2) to overcome an immune suppression mechanism of resistance to CAR T cell therapy for LBCL. First, I will follow individual CAR T cell clones through time in patients treated for LBCL using matched single-cell sequencing of transcriptome, a panel of surface proteins, and endogenous T cell receptors (Aim 1). This approach, termed reverse fate mapping, will pinpoint T cell clones in the pre-manufacture apheresis and infusion products with sought-after properties, including abilities to expand, persist, and home to the tumor. In Aim 2, I will apply reverse fate mapping and methylation analyses to identify the origin of circulating CAR T regulatory (Treg) cells that I recently linked to limited CAR T cell efficacy in LBCL. In Aim 3, I will mechanistically dissect the interplay between Treg and non-Treg CAR T cells to design a potent ‘Treg-free’ CAR T cell therapy for clinical evaluation. My work will generate a comprehensive CAR T cell atlas and insights, leading to promising avenues for engineering the next-generation CAR T cell therapies. The results of my proposed research will positively impact public health, as they will gather sufficient preliminary data for testing a ‘Treg-free’ CD19-CAR T cell therapy for LBCL in a clinical trial and will deliver fundamental insights into CAR Treg biology that may generalize to other diseases, including solid tumors, where engineered T cell therapies have not manifested similarly potent effects as in LBCL. To build upon my skills, I have assembled a mentorship team, including my primary mentor, Dr. Crystal Mackall, a pioneer in CAR T cell immunotherapies; co-mentor, Dr. Sylvia Plevritis, a leader in cancer systems biology; and an advisory committee with extensive expertise relevant to all aspects of this proposal. The completion of this K99/R00 program will prepare me to compete for R01 funding and to launch an independent research career focused on improving immunotherapies for patient with cancer.