Fig. 4: NOTCH1ΔPEST represses MHC class II genes in CLL.
a H3K27ac ChIP-seq profile of the entire MHC class II locus following NOTCH1ΔPEST overexpression. The peaks represent the mean of the ratio of values obtained from CLL cells transduced with NOTCH1ΔPEST or with an empty vector control (n = 5). Each gene and loci locations are shown. b HLA-DR expression quantified by flow cytometry of transduced CLL cells (n = 12). HLA-DR expression was analyzed on GFP-positive cells 5 days post transduction. Each symbol refers to an individual patient sample (p = 0.002). c Quantification of HLA-DR expression on NOTCH1-mutated CLL cells treated for 48 h with a γ-secretase inhibitor (10 µM) or DMSO as control. Relative expression compared to empty vector control is shown (n = 4). Each symbol refers to an individual patient sample. (p = 0.017). d CIITA mRNA expression analyzed by RNAseq of n = 13 CLL patients. e H3K27ac ChIP-seq profile at CIITA locus. The peaks represent the mean of the ratio of values obtained from CLL cells transduced with NOTCH1ΔPEST compared to an empty vector control (n = 5). Chromatin states are color-coded, corresponding to the legend in panel a. f Time to treatment (TTT) curve of a cohort of patients classified as expressing high (red line, CIITA > 14.9, n = 156) or low (blue line < 14.9, n = 110) CIITA level. g Relative percentage of distribution of NOTCH1-mutated patients in the two sub-groups. Statistical significance was assessed by a Fisher t-test. h Survival of a cohort of patients with a high NOTCH1 gene signature identified by high expression of (HES1/2, HEY1/2) and further classified by high or low CIITA expression (upper panel). i Relative percentage of distribution of NOTCH1 mutated patients in the 4 sub-groups. Statistical analysis was done by a Mann–Whitney test. Error bars are shown as mean ± SEM. Statistical analysis was done by two-tailed paired t-tests or log-rank tests (f, h). *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001 and not significant (ns) P > 0.05.
