Fig. 3: CAR33- and CAR33-KLRC1^ko-NK cell pools contain an increased fraction of cells with activated, mature NK cell phenotype.

a t-SNE representation of NK cells at single-cell level according to their combined RNA and protein expression profile. Cells are colored and faceted according to the different conditions (NT-NK, KLRC1^ko-NK, CAR33-NK and CAR33-KLRC1^ko-NK cells). b Principal component analysis of differently modified NK cell expression profiles following CITE-seq of two different donors. c Pooled subclustering of NK cell expression profiles from all conditions (t-SNE representation as in (a)). Louvain clustering on PCA results. d Relative abundance of cells belonging to the six clusters as percentage of all sequenced single cells. e Relative abundance of cells belonging to the 6 subclusters as fraction of the NK cell pools. For each NK cell pool (NT-NK, KLRC1^ko-NK, CAR33-NK and CAR33-KLRC1^ko-NK), the relative abundances over all clusters sum up to one. f Differential expression score of selected gene or protein features per cluster. The gene and protein features are grouped according to function (Checkpoint & Suppressive Regulators, Downstream TCR signaling, Lymphocyte Activation, Mature NK Cells). Each dot represents one gene or protein feature. The differential expression score of feature X in cluster Y is the mean expression of feature X over all cells in cluster Y divided by its mean over all cells in all other clusters (excluding cluster Y, displayed as log10). A score above zero indicates upregulation of a particular feature in a given cluster compared to the other clusters. Black squares indicate median differential expression score of its features (statistics are medians over genes). g Grouping of genes and proteins according to their function. A description of each group and their associated features is shown. a, c–f Representative analysis of cells from donor D1.