Single-cell expression and TCR data from CD19-specific CAR T cells in a phase I/II clinical trial

By leveraging single-cell transcriptome and T cell receptor (TCR)
sequencing, we aimed to track the transcriptional signatures of CAR T cell
clonotypes throughout the course of treatment and furthermore identify
molecular patterns leading to potent CAR T cell cytotoxicity. The data
presented in this study encompass blood and bone marrow samples from
patients ≤ 21 years of age with relapsed or refractory B-cell acute
lymphoblastic leukemia (B-ALL) participating in the SJCAR19 phase I/II
clinical trial (NCT03573700). In brief, patients enrolled in the clinical
trial received either 1 x 10^6 (dose level 1) or 3 x 10^6 (dose level 2)
per kilogram of body weight following successful generation of autologous
CAR T cell products and lymphodepleting chemotherapy. Peripheral blood was
drawn from each participant every week until week 4 post-infusion, at week
6 or 8, and month 3 or 6 if feasible. At week 4 post-infusion, blood
marrow was also collected from participants. Total T cells (CD3+) were
sorted from each post-infusion sample, as well as the pre-infusion CAR T
cell products, and processed through 10x Genomics’ single-cell gene
expression and V(D)J sequencing platform using the standard protocol. We
identified a unique and unexpected transcriptional signature in a subset
of pre-infusion CAR T cells that shared TCRs with post-infusion cytotoxic
effector CAR T cells. Functional validation of cells with even a subset of
these pre-effector markers demonstrated their immediate cytotoxic
potential and resistance to exhaustion.