Metabolic reprogramming controlled by NF-YA alternative splicing creates therapeutic opportunities in colorectal cancer

Authors

Belluti, S., Mularoni, V., Iseppato, N., Campani, V., Ronzio, M., Righi, V., Cuoghi, L., Rinaldi, A., Martinelli, T., Cani, O., Salsi, V., Alessandrini, A., Miserocchi, G., Dolfini, D., Zappavigna, V., Imbriano, C.

Abstract

Metabolic reprogramming is a fundamental strategy that allows colorectal cancer (CRC) cells to endure microenvironmental constraints and sustain malignant progression. Here, we identify the transcription factor NF-Y as a master regulator of glutamine metabolism in CRC, with particular relevance to the aggressive CMS4 subtype. Loss of function experiments, integrated with metabolomic and transcriptomic analyses, reveal a critical role for NF-YA in regulating glutamine metabolism in CRC cells. Complementary gain of function studies pinpoint NF-YAl as the isoform specifically driving glutamine-centered rewiring. Mechanistically, NF-YAl directly binds the Glul promoter, inducing transcriptional upregulation of glutamine synthetase and increasing intracellular glutamine availability. This metabolic reprogramming enhances resistance to mechanical shear and oxidative stress under glutamine-limiting conditions, thereby promoting migratory and metastatic traits. Importantly, pharmacological inhibition of glutamine synthesis, but not uptake or downstream catabolism, selectively abrogates the survival and migratory advantage of NF-YAlhigh cells both in vitro and in vivo, highlighting a targetable vulnerability in aggressive CRC. Beyond CRC cell-autonomous advantage, NF-YAl-dependent glutamine biosynthesis reshapes the tumor microenvironment by promoting M2 macrophage polarization. Conditioned medium from NF-YAlhigh CRC cells is sufficient to induce human monocytes to adopt an M2-like phenotype. This effect is dependent on NF-YAlhigh tumor-derived glutamine, as inhibition of glutamine uptake by monocytes fully blocks their conversion to M2. In line with this, integrative analyses of patient-derived datasets underscore the predictive relevance of the NF-YAl-Glul-M2 axis in driving CRC aggressiveness. These findings define glutamine synthetase as a pivotal mediator of NF-YAl activity and a promising druggable metabolic Achilles' heel in NF-YAlhigh CRC tumors.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 06 Mar 2026.

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