Naïve and central memory-derived exhausted T cells share common dysfunctional attributes while maintaining distinct transcriptional profiles related to cell of origin
Rachel C. Lynn1*, Evan W. Weber1, Robert C. Jones1,2, Charles de Bourcy3, & Crystal L. Mackall1
1Stanford Cancer Institute, Stanford University School of Medicine. Stanford, CA; 2Fluidigm Corporation, South San Francisco, CA; 3Stanford Bioengineering Department, Stanford University, Stanford, CA
Chimeric antigen receptor (CAR) T cell therapy has mediated remarkable clinical success in acute lymphoblastic leukemia, but has not yet proven effective for solid tumors, due in part to the development of T cell exhaustion upon chronic antigen exposure within a suppressive tumor microenvironment. We previously described a GD2-specific CAR that self-aggregates on the T cell surface, leading to tonic CAR signaling and development of an exhausted phenotype in bulk T cells (Long et al. Nat Med, 2015). Here we sought to test the hypothesis that the T cell developmental state impacts susceptibility to exhaustion by interrogating the relative “exhaustability” of naïve (N) and central memory (CM)-derived GD2-28z CAR T cells. Sorted N and CM T cells were activated and transduced with GD2-28z and/or control CD19-28z CAR. On d10 both N and CM-derived GD2-28z CAR T cells displayed striking increases in surface expression of PD-1, TIM-3, LAG-3, CD39, and 2B4 compared with CD19-28z control T cells, consistent with the development of exhaustion in both N and CM-derived subsets. However, IL2 production was substantially higher in N vs CM-derived GD2-28Z CAR T cells, indicating N cells may be more resistant to exhaustion-induced dysfunction. Total RNAseq was performed on N or CM-derived CD4 or CD8 CAR+ T cells. Interestingly, hierarchical clustering revealed that the gene signatures of subset-derived GD2-28z and CD19-28z CAR T cells grouped most closely based on their originating developmental state regardless of exposure to a constant activation signal. We conclude that T cell developmental state plays a major role in modulating susceptibility to exhaustion in the presence of chronic T cell activation.