Tumoral switch in NUMB splicing changes essential transcription pathways and induces malignant properties in tumour cells
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Background
Recent evidence suggests that cancer can exhibit splicing alterations that give rise to tumour-specific isoforms. One example is NUMB, which produces four isoforms (p72, p71, p66, and p65) through alternative splicing of exons 3 and 9. Traditionally considered a tumour suppressor, it also has been considered an oncogene. We propose that this duality is due to isoform-specific expression.
Results
Using public databases, we identified a tumour-associated switch in NUMB isoform expression: p72/p71 are upregulated in tumours, whereas p66/p65 are more expressed in non-tumour tissues. These isoforms correlate differently with cellular processes. NUMBL, a NUMB homolog, behaves similarly to p65. We identified two transcriptional clusters: one characterized by high expression of p72/p71, and another by p66/p65/NUMBL. Each group was associated differently with the Notch, WNT/β-catenin, Hedgehog, and Hippo signalling pathways, suggesting isoform-specific regulatory roles. Analysis of breast cancer cell lines (CCLE) led to a NUMB score based on isoform expression, which classified cell lines into biologically distinct groups. The p72/p71-enriched group showed distinct signatures, pathway activity, and drug sensitivity. Applying this score to TCGA-BRCA samples revealed a significant link between high NUMB-score and poor survival, confirmed by Kaplan–Meier analysis.
Conclusions
NUMB emerges as a potential oncogenic contributor and biomarker in splicing-based personalised medicine, highlighting isoform-specific expression as a clinically relevant determinant of tumour behaviour, pathway activity, and therapeutic response.
