Glutamine-driven upregulation of NPDC1 promotes colorectal cancer progression through PI3K/AKT signaling.

BACKGROUND: Colorectal cancer (CRC) ranks as one of the leading causes of cancer-related mortality globally. NPDC1 is a novel regulator involved in cell proliferation and is upregulated in CRC. However, the biological function and mechanism of NPDC1 driving CRC progression have not been investigated. METHODS: We integrated single-cell RNA-seq data and bulk RNA-seq cohorts to identify prognostic epithelial gene clusters. The R package “ClusterGVis” was employed to categorize six distinct gene clusters within epithelial cells, following Cox regression identifying poor prognosis genes (HR > 1) in the C1 cluster showing progressive upregulation across the four stages. NPDC1 expression was validated by quantitative real-time polymerase chain reaction (qRT-PCR), immunohistochemistry (IHC) and immunofluorescence (IF). Functional impacts on proliferation, metastasis, and immune microenvironment were assessed using CCK8 assays, EdU staining, colony formation, transwell assays and flow cytometry. Additionally, gene set enrichment analysis (GSEA) based on KEGG terms was performed to investigate the potential signaling pathways and biological functions associated with NPDC1 in CRC. The regulatory role of NPDC1 in tumor progression was assessed establishing subcutaneous xenograft tumor model and lung metastasis model of mouse CRC. RESULTS: NPDC1 is significantly upregulated in KRAS mutant CRC and correlates with poor prognosis. Functional experiments demonstrated that NPDC1 drives CRC proliferation in vitro and in vivo but does not affect apoptosis, migration, or invasion. Mechanistically, KRAS mutation-induced glutamine metabolism elevates NPDC1 expression via JUND, activating the PI3K-AKT pathway to promote tumor growth independently of immune modulation. CONCLUSION: Collectively, our results reveal NPDC1 as a KRAS-glutamine axis effector that specifically regulates CRC proliferation via PI3K/AKT signaling, suggesting that NPDC1 could serve as a potential therapeutic target for CRC treatment, particularly in KRAS mutant CRC. GRAPHICAL ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07733-x.