Tumoral switch in NUMB splicing changes essential transcription pathways and induces malignant properties in tumour cells.

Abstract

BACKGROUND: Emerging evidence indicates that cancer is associated with widespread splicing alterations that generate tumour-specific isoforms. One example is NUMB, an evolutionarily conserved adaptor protein, which produces four isoforms (p72, p71, p66, and p65) through alternative splicing of exons 3 and 9. Although traditionally considered as a tumour suppressor, NUMB has also been reported as an oncogene. We propose that this dual role reflects isoform-specific expression. RESULTS: Using public databases, we identify a tumour-associated switch in NUMB isoform expression: p72 and p71 are upregulated in tumours, whereas p66 and p65 are more highly expressed in non-tumour tissues. These isoforms show distinct associations with key cellular processes. NUMBL, a NUMB homolog, displays expression patterns similar to p65. We further identify two transcriptional clusters: one characterised by high expression of p72 and p71, and the other by enhanced p66/p65/NUMBL expression. These clusters exhibit differential associations with Notch, WNT/β-catenin, Hedgehog, and Hippo signalling pathways, suggesting isoform-specific regulatory roles. In breast cancer cell lines, we develop a NUMB-score based on isoform expression, which classifies cell lines into biologically distinct groups. The p72/p71-enriched group shows distinct signatures, pathway activity, and drug sensitivity. Application of this score to TCGA-BRCA samples reveals a significant link between high NUMB-score and poor survival, as confirmed by Kaplan-Meier analysis. CONCLUSIONS: We find that NUMB emerges as a potential oncogenic contributor and biomarker in the context of splicing-based precision oncology, highlighting Isoform-specific expression as a clinical determinant of tumour behaviour, pathway activity, and therapeutic response.