FigureĀ 4.
Identification of CD8+ CARneg bystander T cells in patients after tisagenlecleucel infusion. (A) UMAP of scRNA-seq data from 6 pediatric patients after tisagenlecleucel, colored by patient ID. (B) UMAP with shared nearest-neighbor clustering across all patients, colored by 15 transcriptional clusters. (C) UMAP colored by cell source, as well as normalized expression of genes from bystander signature 4 (CD8, CD160, CCL5, KLRK1 [NKG2D], and KLRD1 [CD94]). The product was not cytometrically sorted into CARpos and CARneg T cells and therefore contained a mixed population of CARpos and CARneg T cells. (D) Composition of clusters by cell source, with an arrow highlighting clusters 0 and 12, which were enriched for bystander signature 1. (E) Bystander score determined by applying bystander signature 1 to each CD8+ CARneg cluster using decoupleR. (F) Composition of clusters by patient ID, with arrows highlighting clusters 0 and 12, which were enriched for bystander signature 1. (G) Shannon diversity of T-cell clones in bystander clusters 12 and 0 vs all CD8+ CAR T cells in each patient.

Identification of CD8+ CARneg bystander T cells in patients after tisagenlecleucel infusion. (A) UMAP of scRNA-seq data from 6 pediatric patients after tisagenlecleucel, colored by patient ID. (B) UMAP with shared nearest-neighbor clustering across all patients, colored by 15 transcriptional clusters. (C) UMAP colored by cell source, as well as normalized expression of genes from bystander signature 4 (CD8, CD160, CCL5, KLRK1 [NKG2D], and KLRD1 [CD94]). The product was not cytometrically sorted into CARpos and CARneg T cells and therefore contained a mixed population of CARpos and CARneg T cells. (D) Composition of clusters by cell source, with an arrow highlighting clusters 0 and 12, which were enriched for bystander signature 1. (E) Bystander score determined by applying bystander signature 1 to each CD8+ CARneg cluster using decoupleR. (F) Composition of clusters by patient ID, with arrows highlighting clusters 0 and 12, which were enriched for bystander signature 1. (G) Shannon diversity of T-cell clones in bystander clusters 12 and 0 vs all CD8+ CAR T cells in each patient.

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