Clonal Abundance Determines The Prognostic Relevance Of a NOTCH1 Mutation In Chronic Lymphocytic Leukemia

The transmembrane receptor NOTCH1 operates as a ligand-activated transcription factor controlling developmental processes, proliferation and apoptosis. In the context of cancer, activating NOTCH1 mutations are the most frequent oncogenic events in T-cell acute lymphoblastic leukemia and have been implicated in chronic lymphocytic leukemia (CLL) as well. The most prevalent CLL NOTCH1 mutation (N1ΔCT) leads to a truncation of the protein (p.P2515Rfs*4) and has been associated with impaired overall survival (OS). Here, we applied three different methods to study the N1ΔCT prevalence and subclone size in a cohort of n=275 CLL patients.

Presence of the N1ΔCT mutation was analyzed using newly established restriction fragment length polymorphism (RFLP) and allele-specific PCR (AS-PCR) methodologies. A novel real-time PCR (qRT-PCR) assay was used to precisely quantify the N1ΔCT allele frequency. Presence of the N1ΔCT mutation was confirmed by conventional Sanger sequencing.

Using RFLP analysis we detected the N1ΔCT mutation in n=17 CLL patients. In parallel, we used a more sensitive AS-PCR and identified n=12 additional N1ΔCT-mutated cases resulting in a total N1ΔCT mutation rate of 10.5% (n=29/275) in our cohort. The OS of RFLP-positive patients (RFLP+) was significantly shorter than the OS of N1ΔCT-unmutated patients (wt) (mean OS; RFLP+, 87 months vs. wt, 218 months; p=0.017). In contrast, OS of AS-PCR-positive cases (AS-PCR+) did not differ significantly from the OS of wt patients (mean OS; AS-PCR+, 175 months vs. wt, 218 months; p=0.42). These data prompted us to design a quantitative real-time PCR (qRT-PCR) assay, which is capable of precisely quantifying the size of the N1ΔCT-mutated subclones (allele frequency, %) in our CLL cohort. As expected, significantly different allele frequencies between RFLP+ (mean±SEM 27.1±3.4%), AS-PCR+ (3.7±0.6%) and wt patients (0.6±0.04%) were revealed by qRT-PCR (p<0.0001). In order to determine a methodology-independent cut-off which correlates with the clinical significance of the N1ΔCT mutation, we employed Receiver Operating Characteristics (ROC) analysis based on survival status and calculated a N1ΔCT allele frequency cut-off of 15.2% (AUC=0.71). Next, we determined N1ΔCT allele frequencies over time to investigate clone dynamics within individual patients (n=15 patients, mean observation period 87.4 months; range 5-186 months). Unexpectedly, the N1ΔCT allele frequencies remained relatively constant and none of the patients with N1ΔCT allele frequencies below 15.2% rose above this cut-off over time.

Our data demonstrate that high abundance of a N1ΔCT-mutated CLL clone correlates with an aggressive disease course. In our CLL cohort a N1ΔCT allele frequency below 15% was of negligible clinical relevance. Thus, mere qualitative detection of a N1ΔCT mutation by PCR is not inevitably associated with shortened survival. Surprisingly, we did not observe that a minor N1ΔCT clone became dominant over time.

No relevant conflicts of interest to declare.