Characterization of autologous T cells engineered to express NY-ESO-1 TCR with multiplexed CRISPR/Cas9 editing (NYCE T Cells)

Abstract

Background & Aim NY-ESO-1 is a cancer testis antigen with ectopic expression on multiple myeloma (MM), melanoma and sarcoma but restricted expression on normal tissues, rendering it a good candidate target for cancer immunotherapy. We recently reported a phase 1 pilot trial of multiplex CRISPR/Cas9 genome-edited NY-ESO-1 TCR cells (NYCE T cells; NCT03399448) for patients (pts) with advanced MM, synovial sarcoma and myxoid/round cell liposarcoma (MRCL) demonstrated safety and feasibility as well as persistence of T cells. Here, we characterize the phenotype and function of the ex vivo manufactured NYCE T cells from the 3 pts that were infused in the trial. Methods, Results & Conclusion The 3 infusion products (2 MM – pt #35 and Pt #7, and 1 MRCL – pt #39) were used to compare expanded T cells with either CRISPR/Cas9 editing without TCR transduction or with Mock-editing and TCR transduction from the same pt. We examined the phenotypic markers of T cell differentiation and checkpoint inhibitors by multicolor flow cytometry and assessed in vitro anti-tumor efficacy via a luciferase-based killing assay. We found heterogeneity in the composition of T cell subsets from all 3 infusion products with various CD4 and CD8 ratios, ranging from 0.12-1.1. Transduction efficiencies (determined by Vbeta8.1+ staining) varied between 1-11% and different levels of knockout efficiency in TRAC, TRBC and PDCD1 genes were observed by digital PCR. Three NYCE T cell infusion products displayed a terminally differentiated T cell phenotype similar to CRISPR/Cas9 edited counterpart. In contrast to Mock-edited T cells from the same pt, NYCE T cells exhibited lower levels of differing combinations of exhaustion-associated markers (PD1, TIM3, LAG3, EOMES and CTLA4) in both CD4+ and CD8+ T cell compartments. All 3 infusion products elicited antigen-specific killing of NY-ESO-1 expressing target cells. We demonstrate that NYCE T cells are heterogeneous in composition. Furthermore, we showed that CRISPR/Cas9 editing does not affect T cell differentiation and anti-tumor efficacy, but does reduce levels of exhaustion-associated markers expressed by the final products. This work provides an in-depth characterization of the heterogeneous product composition and function of the first multiplex CRISPR/Cas9-edited T cells tested in humans.