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Published on: January 12, 2020
A Molecular Test for Quantifying Functional Notch Signaling Pathway Activity in Human Cancer
Kirsten Canté-Barrett1, Laurent Holtzer2, Henk van Ooijen3
1Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands.
Background:
The Notch signal transduction pathway is pivotal for various physiological processes, including immune responses, and has been implicated in the pathogenesis of many diseases. The effectiveness of various targeted Notch pathway inhibitors may vary due to variabilities in Notch pathway activity among individual patients. The quantitative measurement of Notch pathway activity is therefore essential to identify patients who could benefit from targeted treatment.
Methods:
We here describe a new assay that infers a quantitative Notch pathway activity score from the mRNA levels of generally conserved direct NOTCH target genes. Following the calibration and biological validation of our Notch pathway activity model over a wide spectrum of human cancer types, we assessed Notch pathway activity in a cohort of T-ALL patient samples and related it to biological and clinical parameters, including outcome.
Results:
We developed an assay using 18 select direct target genes and high-grade serous ovarian cancer for calibration. For validation, seven independent human datasets (mostly cancer series) were used to quantify Notch activity in agreement with expectations. For T-ALL, the median Notch pathway activity was highest for samples with strong NOTCH1-activating mutations, and T-ALL patients of the TLX subtype generally had the highest levels of Notch pathway activity. We observed a significant relationship between ICN1 levels and the absence/presence of NOTCH1-activating mutations with Notch pathway activity scores. Patients with the lowest Notch activity scores had the shortest event-free survival compared to other patients.
Conclusions:
High Notch pathway activity was not limited to T-ALL samples harboring strong NOTCH1 mutations, including juxtamembrane domain mutations or hetero-dimerization combined with PEST-domain or FBXW7 mutations, indicating that additional mechanisms may activate Notch signaling. The measured Notch pathway activity was related to intracellular NOTCH levels, indicating that the pathway activity score more accurately reflects Notch pathway activity than when it is predicted on the basis of NOTCH1 mutations. Importantly, patients with low Notch pathway activity had a significantly shorter event-free survival compared to patients showing higher activity.
Insights
Quantifying Notch pathway activity with a new mRNA assay is crucial for personalized cancer treatment. Low Notch activity predicts poorer event-free survival in T-ALL patients, highlighting its clinical significance.
Area of Science:
- Biochemistry
- Molecular Biology
- Oncology
Background:
- The Notch signaling pathway regulates critical physiological processes, including immune responses.
- Dysregulation of Notch signaling is implicated in various diseases, necessitating accurate activity measurement for targeted therapies.
- Individual variability in Notch pathway activity impacts the efficacy of targeted inhibitors.
Purpose of the Study:
- To develop and validate a novel assay for quantifying Notch pathway activity.
- To assess Notch pathway activity in T-ALL patient samples and correlate it with clinical parameters.
- To identify potential biomarkers for predicting treatment response and patient outcomes.
Main Methods:
- Developed a quantitative assay using mRNA levels of 18 conserved direct NOTCH target genes.
- Calibrated the Notch pathway activity model using high-grade serous ovarian cancer data.
- Validated the model across seven independent human cancer datasets and assessed T-ALL patient samples.
Main Results:
- The assay accurately quantified Notch activity, correlating with expectations across diverse cancer types.
- T-ALL samples with strong NOTCH1-activating mutations and the TLX subtype showed the highest Notch pathway activity.
- Lower Notch pathway activity scores were significantly associated with shorter event-free survival in T-ALL patients.
Conclusions:
- Notch pathway activation in T-ALL extends beyond strong NOTCH1 mutations, suggesting additional regulatory mechanisms.
- The developed assay provides a more accurate reflection of Notch pathway activity than prediction based solely on NOTCH1 mutations.
- Quantified Notch pathway activity serves as a significant prognostic indicator for event-free survival in T-ALL.
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