Alternative splicing of the transcription factor NF-Y promotes cell migration and invasion in colon cancer

The heterotrimeric transcription factor NF-Y directly controls the expression of genes involved in cellular pathways commonly altered in cancer cells, such as cell cycle, apoptosis and metabolism. Consistently, the binding site for NF-Y is highly enriched in the regulatory regions of genes overexpressed in tumors, and mRNA levels of NF-Y subunits are altered in cancer tissues and cells. In particular, the DNA binding subunit NF-YA is up-regulated in various tumors, among which gastric, lung, breast, ovarian, osteosarcoma and prostate cancers. Moreover, a switch between the two alternatively NF-YA spliced transcripts, NF-YAs and NF-YAl, occurs in tumor tissues compared to normal ones. Colorectal cancer (CRC) is the third most common malignancy worldwide. Four internationally approved consensus molecular subtypes (CMS) represent the best current description of CRC heterogeneity at the gene-expression level: the CMS1 group is characterized by the immune infiltration signature, CMS2 is the canonical epithelial subtype, CMS3 represents the metabolic group, and CMS4 is the mesenchymal one, associated with a worse prognosis and poor response to therapies compared to other subtypes. Here we show that increased levels of NF-YA characterize CRC versus healthy tissues. We identified a significant association between NF-YA isoforms and CRC subtypes: NF-YAs is up-regulated in all CMSs in opposition to NF-YAl, which is down-regulated in all subtypes with the exception of aggressive and metastatic CMS4 group. By using in vitro cell models, we confirmed that NF-YAs is the predominant isoform in CRC cell lines, while NF-YAl levels proportionally increase from epithelial to hybrid and mesenchymal cells. The modulation of NF-YA isoforms in CRC cells significantly affects cancer cell behavior by modulating differently, even oppositely, the transcription of genes associated to extracellular-matrix (ECM) and epithelial-to-mesenchymal transition (EMT). We described different modes of migration and invasion properties for NF-YAs and NF-YAl overexpressing cells by using 2D and 3D culture conditions, time-lapse imaging of CRC cells and intravascular distribution of NF-YAs/l transduced CRC cells in the embryonic zebrafish xenograft model. Altogether, our data highlight the direct role of the longer NF-YA isoform in CRC cell dissemination and suggest its possible use as biomarker for molecular stratification predictive of progressive disease in CRC patients.