Alterations in NF-Y splicing enable the metabolic plasticity of colon cancer cells and foster dynamic interactions within the tumor niche

Altered splicing events play a significant role in tumor progression, in part by contributing to metabolic reprogramming that enable cancer cells to adapt and survive in a constantly evolving tumor microenvironment (TME). Additionally, splicing alterations may influence the interaction between cancer cells and their surrounding stroma and immune cells, further promoting tumor growth and resistance to therapy. Transcriptomic data from colorectal adenocarcinoma (COAD) highlighted altered expression of NF-YAs and NF-YAl transcripts produced by alternative splicing of the gene encoding the DNA-binding subunit of the transcription factor NF-Y. High NF-YAl levels predict lower patients’ survival and distinguish the mesenchymal molecular subtype CMS4, which is characterized by stromal infiltration and an extracellular matrix (ECM)-related signature associated with a poor prognosis. In vitro 3D cellular models and in vivo zebrafish xenografts point at a transcriptional role of the NF-YAl isoform in sustaining enhanced migratory and invasive behavior of COAD cells. High NF-YAl expression sustains a metabolic rewiring enabling metastasizing cancer cells to survive in the circulation. Finally, we demonstrate that increased NF-YAl levels in COAD cells transform stromal fibroblasts into CAFs (Cancer Associated Fibroblasts) and trigger the polarization of Tumor-Associated Macrophages (TAMs) from M1 to M2, with CAFs and M2-like TAMs facilitating tumor invasiveness. Our results suggest that targeting NF-YA with antisense oligonucleotides may represent a new therapeutic splice switching correction to effectively stop tumor metastasis.