Abstract PR3: Development of a transcriptomic T-cell atlas highlights the differential role of T-cell subpopulations in CAR T-cell therapy resistance
Authors: Chen Gregory M. , Chen Changya , Das Rajat K. , Ding Yang-Yang , He Bing , Kim Hannah , Barrett David M. , Tan Kai 
Published: March 2020

Chimeric antigen receptor (CAR) T-cell therapy has been a major breakthrough in B-cell acute lymphoblastic leukemia (B-ALL), yet therapeutic resistance remains an important clinical challenge. Given that approximately 20% of patients do not respond to therapy and 40% of initial responders relapse within a year, there is a pressing need to understand the basis of therapy resistance in order to identify prognostic biomarkers and improve the therapeutic modality. We hypothesize that intrinsic T-cell factors are a major contributor to early therapeutic failure to CAR T-cell therapy. Most protocols do not select for specific T-cell subtypes, leading to the use of heterogeneous T-cell populations for CAR T-cell engineering. In order to characterize the molecular phenotypes of T cells underlying therapeutic response, we performed subtype-specific transcriptomic profiling of clinical T-cell populations in patients subsequently treated with anti-CD19 CAR T-cell therapy. We identified 71 patients with B-ALL treated with CAR T-cell therapy at the Children’s Hospital of Philadelphia, and obtained T cells via clinical leukapheresis prior to CAR T-cell engineering. We used FACS to separate T cells into five subtypes per patient (Naive, Stem Cell Memory, Central Memory, Effector Memory, and Effector), and performed bulk RNA-sequencing on all 355 samples. To our knowledge, this is the largest and most comprehensive transcriptomic profiling of clinical T cells in CAR T-cell therapy to date. We find that a higher proportion of CCR7+CD62L+ naive and early memory T-cell phenotypes associates with longer clinical T-cell persistence (HR=3.25 [1.37-7.89], p=0.006), and that combining proportions of these populations with CCR7−CD62L−CD45RO+CD95+ effector memory T cells has the greatest prognostic value (HR: 4.82 [1.89-12.32]; p&lt;0.001). We identified global transcriptomic markers of early and differentiated T-cell populations and identified differentially expressed genes that discriminated between clinical responders and nonresponders. Single-sample gene set enrichment analysis identified an enrichment of T-cell exhaustion pathways among the clinical nonresponders, which was predominant in the early lineage T-cell phenotypes (p=0.018-0.095) but not in the effector T-cell phenotypes (p=0.15-0.37). Together, these data shed light on the critical role of preinfusion T-cell populations in CAR T-cell therapy, and may inform clinical prognosis and the development of improved CAR T-cell therapies.

This abstract is also being presented as Poster A65.

Citation Format: Gregory M. Chen, Changya Chen, Rajat K. Das, Yang-Yang Ding, Bing He, Hannah Kim, David M. Barrett, Kai Tan. Development of a transcriptomic T-cell atlas highlights the differential role of T-cell subpopulations in CAR T-cell therapy resistance [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr PR3.