Integrative functional experiments and single-cell transcriptomics reveal the METTL1/NSUN1 axis drives malignant progression in kidney renal clear cell carcinoma

Abstract

N7-methylguanosine (m7G) mediated by methyltransferase-like 1 (METTL1) orchestrates tumor progression across multiple malignancies, while its functions and mechanisms in kidney renal clear cell carcinoma (KIRC) remain elusive. In this study, we integrated multifaceted bioinformatics data, functional experiments, and single-cell transcriptomics to uncover the role of the METTL1/NSUN1 axis in KIRC. Clinically, both mRNA and protein levels of METTL1 were significantly elevated in KIRC tumors and correlated with advanced progression and poor prognosis. Gene effect scores based on CRISPR screening data demonstrated that METTL1 knockout inhibited cell growth across multiple tumor cell lines, including renal, esophageal, gastric, and colorectal cancers. METTL1 was significantly co-expressed with NSUN1, which was also increased and correlated with unfavorable prognosis in KIRC. Mechanistically, METTL1 installed m7G modifications on NSUN1 mRNA and upregulated its expression, whereas NSUN1 knockdown partially rescued the oncogenic effects induced by METTL1 overexpression. Single-cell sequencing data further revealed progressive upregulation of METTL1 and NSUN1 during epithelial-to-malignant transformation, accompanied by coordinated activation of RNA modification genes and EMT-related transcription factors (ZEB1, KLF4, TBX3, etc.). Intensive crosstalk between cancer cells and basal cells was identified in the tumor microenvironment. Moreover, high METTL1 expression correlated with increased infiltration of pro-tumor M0 macrophages and neutrophils, shaping an immunosuppressive microenvironment. Collectively, our study demonstrates that the METTL1/NSUN1 axis drives malignant progression and immune microenvironment remodeling, providing novel epigenetic biomarkers and therapeutic targets for KIRC.