Identification of METTL3 and PRMT5 as an oncogenic pair for the prognosis and therapeutic targets of colorectal cancer subtype

BACKGROUND: METTL3 is a pivotal N6-methyladenosine (m⁶A) regulator that is linked to a worse prognosis of colorectal cancer (CRC). However, METTL3's oncogenic molecular networks in CRC remain unclear. This study aims to establish a co-expression network of METTL3 and identify novel diagnostic and therapeutic targets for CRC. METHODS: We integrated transcriptomic datasets with clinical cohorts and patient-derived organoids (PDOs) to evaluate the expression profiles of METTL3 and PRMT5. Mechanistic insights were gained through co-immunoprecipitation (Co-IP), m⁶A-methylated RNA immunoprecipitation (MeRIP), and Quantitative real-time PCR (qRT-PCR) assays. Single-cell and spatial transcriptomics were employed to resolve their spatial co-localization and cellular architecture. Furthermore, we performed patient stratification based on the METTL3/PRMT5 axis to characterize tumor microenvironment (TME) remodeling. The functional roles of these proteins in cell proliferation, mitochondrial fission, and mitophagy were validated in CRC cells and PDOs. Finally, the synergistic efficacy of the METTL3 inhibitor STM2457 and the PRMT5 inhibitor GSK591 was evaluated. RESULTS: We identified a reciprocal positive feedback loop between METTL3 and PRMT5 that drives CRC malignancy: PRMT5 enhances METTL3 stability via symmetric dimethylarginine modification, while METTL3 facilitates PRMT5 expression in an m⁶A-dependent manner. Spatial and single-cell analysis revealed that their co-expression is spatially restricted and strongly correlates with an immunosuppressive TME. High METTL3/PRMT5 expression defines a specific molecular subtype characterized by accelerated cell cycle progression, DNA replication, and aberrant organelle fission. Critically, these phenotypes were functionally validated, showing that the METTL3/PRMT5 axis governs mitochondrial homeostasis. From a clinical perspective, CRC cell lines and PDOs with high METTL3/PRMT5 expression exhibited heightened sensitivity to combined inhibition with STM2457 and GSK591, revealing a potent therapeutic vulnerability. CONCLUSION: Our findings establish METTL3 and PRMT5 as a pair of robust biomarkers for patient stratification and highlight the synergistic targeting of m⁶A and protein methylation as a promising precision oncology strategy for CRC.