Fig. 2: CAR33 expression and KLRC1 knockout induce changes in NK cell gene and but not in surface marker expression profiles.

a Scheme of the sorting strategy for NK single-cell analysis of the four different NK cells preparations. CAR-NK cells were sorted on CAR+, KLRC1^ko-NK cells on NKG2A- and CAR33-KLRC1^ko-NK cells on CD33+/NKG2A− NK cells prior to CITE-Seq analysis. b-d Overall transcriptional (RNA) changes in NK cells upon introduction of CAR33 (b), knockout of KLRC1 (c) and synergistic effects of CAR33 and knockout of KLRC1 (d). Statistical test: quasi-likelihood (QL) F-test against threshold (b–d). Volcano plots show combined analysis of NK cells from donors D1 and D2 and indicate adjusted p-value (y-axis) and inferred logFC (x-axis) for each gene feature and for each genetic modification (CAR33 (b), KLRC1^ko (c), synergistic effect of CAR33 and KLRC1^ko (d)). Up- and down-regulated features are highlighted in color. The horizontal line indicated an FDR of 5% and the vertical lines delimit the range of logFC between −log2 (1.2) and log2 (1.2). Selected genes of interest are labeled. Statistical test: quasi-likelihood (QL) F-test against threshold. e Distribution of surface marker expression from CITE-seq data for the four cell preparations. Distributions are displayed as density, with an area under the curve normalized to 1. f Surface expression of different receptors of NK cells measured by flow cytometry. Representative histograms are shown.