SMAD4 loss induces c-MYC-mediated NLE1 upregulation to support protein biosynthesis, colorectal cancer growth and metastasis

Abstract Growth and metastasis of colorectal cancer (CRC) is closely connected to the biosynthetic capacity of tumor cells, and CRC stem cells that reside at the top of the intratumoral hierarchy are especially dependent on this feature. By performing disease modeling on patient-derived tumor organoids, we found that elevated expression of the ribosome biogenesis factor NLE1 occurs upon SMAD4 loss in TGF-β1-exposed CRC organoids. TGF-β signaling-mediated downregulation of NLE1 was prevented by ectopic expression of c-MYC, which occupied an E-box-containing region within the NLE1 promoter. Elevated levels of NLE1 were found in CRC cohorts compared to normal tissues and in CRC subtypes characterized by Wnt/MYC and intestinal stem cell gene expression. In CRC cells and organoids, NLE1 was limiting for de novo protein biosynthesis. Upon NLE1 ablation, CRC cell lines activated p38/MAPK signaling, accumulated p62 and LC3-positive structures indicative of impaired autophagy, and displayed more reactive oxygen species. Phenotypically, knockout of NLE1 inhibited proliferation, migration and invasion, clonogenicity, and anchorage-independent growth. NLE1 loss also increased the fraction of apoptotic tumor cells, and deletion of TP53 further sensitized NLE1-deficient CRC cells to apoptosis. In an endoscopy-guided orthotopic mouse transplantation model, ablation of NLE1 impaired tumor growth in the colon and reduced primary tumor-derived liver metastasis. In CRC patients, NLE1 mRNA levels predicted overall and relapse-free survival. Taken together, these data reveal a critical role of NLE1 in CRC growth and progression and suggest that NLE1 represents a potential therapeutic target in CRC patients.