Mutations in NOTCH1 PEST Domain Orchestrate CCL19-Driven Homing of Chronic Lymphocytic Leukemia (CLL) Cells By Modulating the Tumor Suppressor Gene DUSP22

BACKGROUND.NOTCH1 PEST domain mutations were among the first to be identified using whole exome sequencing and their prevalence and prognostic power for CLL patients has since been extensively studied. Nevertheless, the functional contribution of NOTCH1 and the impact of its mutations in CLL remain poorly understood. This is mainly due to the intrinsic limits in using primary CLL cells and to the rapid inactivation of the NOTCH1 pathway in vitro.

AIM. The aim of the study was to highlight the NOTCH1-dependent mechanisms contributing to CLL pathogenesis and progression and the effects of PEST mutations in this disease context.

RESULTS. By using the CRISPR/Cas9 technology, we first generated a cellular model either lacking NOTCH1 (Mec-1/KO) or expressing it in its wild-type or mutated forms. RNA-seq analysis of the transcriptome of Mec-1/WT and /KO cells, highlighted signaling and migration as the most prominently down-regulated pathways in KO cells. These findings were confirmed by showing that Mec-1/KO cells migrated significantly less towards CCL19 than their WT counterparts, as the result of the down-modulation of CCR7, the CCL19 receptor. Mechanistically, Mec-1/KO were characterized by increased expression of the tumor suppressor gene DUSP22, a phosphatase that negatively regulates MAPK and STAT3 signaling, in turn responsible for CCR7 gene transcription. Up-regulation of DUSP22 in Mec-1/KO was caused by decreased methylation of the gene promoter, as shown using a methylation specific PCR. Re-expression of the NOTCH1 Intracellular Domain (NICD) rescued the phenotype, increasing methylation of the DUSP22 promoter, which in turn led to decreased gene and protein expression. Mec-1 cells with reconstituted NICD expression showed increased STAT3 phosphorylation, CCR7 expression and, ultimately, migrated more actively in response to CCL19. Importantly, reconstitution with an NICD carrying the PEST domain mutation most commonly found in patients (ΔCT_7541-7542), significantly enhanced all these events, including DUSP22methylation, STAT3 phosphorylation, CCR7 expression, generating cells with the highest chemotactic responses to CCL19.

NOTCH1 directly participates to the epigenetic regulation of DUSP22, by conditioning the activity of the DNA methyltransferase 3A (DNMT3A) on the gene promoter. By binding RBPJk, the NICD displaces HDAC1 from the repressor complex and initiates NOTCH1-dependent signaling. Consequently, free HDAC1 binds to and stabilizes DNMT3A, promoting its activity on DUSP22promoter.

These results were first corroborated in a large cohort of CLL (n=113) carrying mutations in NOTCH1 PEST domain (ΔCT_7541-7542)at the clonal (>12%) or subclonal (≤12%) level. The clonally mutated subset showed significant downregulation of DUSP22expression and gene promoter hypermethylation compared to subclonal samples. Consistently, the clonal subset displayed higher constitutive STAT3 phosphorylation, expressed higher levels of CCR7 and migrated more efficiently to CCL19 than subclonally mutated CLL.

The second confirmation was obtained by studying a Mec-1 variant with PEST domain mutation (Mec-1/PEST), generated using the CRISPR/Cas9 system. Like primary cells, Mec-1/PEST needed the ligand to initiate signaling. As predicted, the mutant NICD was more stable and more transcriptionally active. Consistently, these cells had the lowest DUSP22 levels and the highest CCR7 expression. When Mec-1/PEST were xenografted in immunocompromised mice, activation of the NOTCH1 pathway was more pronounced than that of Mec-1/WT cells. In keeping with their minimal expression of DUSP22, Mec-1/PEST cells were characterized by markedly increased metastatic properties, with extensive colonization of the liver, the spleen, and the brain, at variance with the other cell variants.

CONCLUSIONS. Considered together, these results show that PEST mutations increase NICD stability, in turn affecting a complex nuclear balance. The final outcome for the CLL cell is decreased expression of the tumor suppressor gene DUSP22 and increased chemotaxis towards CCL19. As this chemokine regulates homing to secondary organs, conceivably NOTCH1 mutations might favor CLL recirculation to lymph node and spleen, where the local environment triggers proliferation and protects from apoptosis, two conditions that are associated with a more aggressive disease and an unfavorable prognosis.