RNA-seq Identifies Nuclear ErbB-2-Induced Transcriptome as a Key Driver for Triple Negative Breast Cancer Growth

María Florencia Chervo¹, Micaela Parra², Nicolás Bellora², Ezequiel Petrillo³, Santiago Madera¹, Agustina Roldán Deamicis¹, Kohzoh Mitsuya⁴, Violeta Alicia Chiauzzi¹, Cecilia Jazmín Proietti¹, Roxana Schillaci¹, Tim H-M Huang4, Rosalía Inés Cordo Russo1, Patricia Virginia Elizalde1


Triple negative breast cancer (TNBC) does not express estrogen and progesterone receptors, and lack membrane overexpression/gene amplification of ErbB-2, a tyrosine kinase receptor. TNBC is a heterogeneous disease presenting four molecular subtypes. Up to 78% of TN tumors in the clinic belong to the basal-like (BL) subtype. We found ErbB-2 in an unanticipated scenario: the nucleus of TNBC (NErbB-2). Our study on ERBB2 alternative splicing, using a PCR-sequencing approach combined with RNA interference, revealed that BL cells express the canonical ErbB-2, encoded by transcript 1, and the non-canonical isoform c, encoded by alternative transcript  3. Evicting both from the nucleus or silencing isoform c only, blocks TNBC growth. To explore whether isoform c growth-promoting effect is due to its functions as a transcriptional regulator, we performed RNA-seq in BL cells expressing only this isoform. We identified a set of genes differentially regulated in BL cells where we evicted isoform c from the nucleus, as compared to control cells. In the up-regulated group, we found enrichment of pro-apoptotic and tumor suppressor genes and in the down-regulated one, genes involved in proliferation and stemness. Furthermore, our clinical studies identified NErbB-2 as an independent predictor of shorter overall and disease-free survival in 99 TN primary tumors. Collectively, our findings reveal the potential of NErbB-2 isoforms as novel therapeutic targets and clinical biomarkers in TNBC.