Fig. 4: Co-culture of expanded NK cells with CML cell lines show upregulated IFN-γ response in CML cells and active phenotype of NK cells.
a UMAP representation of K562 and LAMA84 cells cultured with and without expanded NK cells, colored by the presence of expanded NK cells. b Differentially expressed genes (Padj < 0.05, Bonferroni corrected t-test) between K562 and LAMA84 cells cultured with and without expanded NK cells. The genes related to IFN-γ response HALLMARK-category are highlighted in teal color. c Expression of selected co-inhibitory genes and IFN-γ response score in K562 and LAMA84 cells, calculated with the HALLMARK-category genes and shown in five equal quantiles. d UMAP representation of expanded NK cells cultured with and without K562 or LAMA84 cells, colored by the presence of tumor cells. e Differentially expressed genes (Padj < 0.05, Bonferroni corrected t-test) between expanded NK cells cultured with and without K562 or LAMA84 cells. f Expression of selected co-stimulatory genes in NK cells with and without co-culture of CML cells. g Expression of IFN-γ response score in primary CML LSCs. h Scaled average expressions (avg exp) and proportion of active NK cells expressing (pct.exp) some genes induced in the co-culture of NK cells, in patient samples. Encircled dots are differentially expressed (Padj < 0.05, Bonferroni corrected t-test) in a given patient group in comparison to other groups. i Proportion of expanded NK cells expressing IFN-γ after co-culture with CML cell lines LAMA84 or K562 with or without TIM3 blocking antibody in different concentrations. P-values were calculated with a paired t-test. *=P < 0.05, **=P < 0.01, ***=P < 0.001, ****=P < 0.0001.
