Fig. 6: Kinase signature associated with resistance to NOTCHi reveals PKC activation in resistant cells.

a Kinase-Substrate Enrichment Analysis (KSEA) output is represented in a heatmap. Columns are the different comparisons and rows are the kinases whose activity is significantly regulated (q: Benjamini–Hochberg FDR < 0.05) in at least three out of five comparisons. Kinases with less than four substrates were excluded. The three clusters have been generated through k-means row clustering (n = 3). KSEA significance derives from n = 3 biologically independent experiments per comparison, and it is indicated as *q < 0.05; **q < 0.01; ***q < 0.001. b P-S6 S235-S236 Log2 fold-change for the five different comparisons used in a. “*/**/***” represent p values resulting from unpaired two-sided t test. *** = 0.001; ** = 0.01; * = 0.05. c, e–f. Immunoblot analysis of lysates from T-ALL cell lines (C; n = 1 for left blot; right blot is representative of n = 2 independent experiments), DND-41 cells (E; n = 1 for upper blot; lower blot is representative of n = 5 independent experiments) and PDTALL11 cells FACS-sorted from the spleen (F; n = 1). β-Actin in c was run of a different gel. Protein expression was quantified in ImageJ. Mouse n° 5 in e (red): outlier in the proteomics data. d PKCδ gene expression (RNAseq) in a T-ALL cell line panel. The black line indicates the mean and the dashed line is the SEM (n = 4–13 biologically independent cell lines). An unpaired two-sided t test was used to assess the differences in mean log2 Transcripts Per Million (TPM) between the GSI resistant and sensitive T-ALLs. Data (RNAseq) were taken from the CCLE database (Expression Public 19Q3 dataset). g Quantification of the immunoblot in Fig. 6f. The values shown are mean ± SEM (n = 5–6 biologically independent mice). An unpaired two-sided t test was used to assess the differences in protein expression and phosphorylation. Outliers values are marked in white. RTX Rituximab. Source data are provided as Source Data file.