Multi-omics analyses uncover METTL1-mediated tRNA m7G modification–TRADD axis driving breast cancer brain metastasis

Patients with breast cancer (BC) brain metastases (BCBrM) have poor survival rate. N(7)-methylguanosine (m7G) modification has emerged as a vital regulator of tumor metastases. This research sought to probe into potential role of m7G in BCBrM. Single-cell RNA sequencing (scRNA-seq) and RNA-seq datasets were available from the GEO database. The tumor immune regulation, survival analysis, and function of METTL1 were performed. The m7G tRNA reduction and cleavage sequencing (Trac-seq) was used to explore the levels of m7G tRNA modification. Translational efficiency analysis and integrative codon-usage analyses were conducted to identify downstream translational targets, followed by rescue experiments in vivo. scRNA-seq results indicated heterogeneity in m7G score and expression of m7G-related genes across 9 cell types in BC and BCBrM samples. The m7G high-score group was associated with immunosuppression characteristics. m7G score was higher in BCBrM samples compared to BC samples, accompanied by a distinct immune-related transcriptomic features. Among m7G-related genes, METTL1 was significantly correlated with immune cell abundance, immune score, and immune checkpoints. Survival curve showed that low-m7G score, low expression of METTL1, NUDT1, and NCBP2, and high IFIT5 expression were associated with improved brain metastasis–free survival. Among these, only METTL1 expression was consistently upregulated in BCBrM, differentially expressed between tumor and paracancerous tissues, and prognostically significant in TCGA cohorts. GSVA and GSEA unraveled that enrichment of immune-related pathways in the METTL1_Low expression group in BCBrM samples. Cellular experiments confirmed that METTL1 promotes invasion of BCBrM cells in vitro. Trac-seq profiled METTL1-mediated m7G tRNA methylome in BC cells. Integrative translation efficiency analysis revealed that METTL1-mediated tRNA m7G modification reprograms translation of MAPK pathway–related genes. Among these, TRADD exhibited the most significant increase in translation efficiency. Codon-mutation and knockdown experiments confirmed that METTL1 enhances TRADD expression through m7G-dependent translational regulation. In vivo rescue experiments demonstrated that pharmacological inhibition of METTL1 suppressed brain metastasis, while enforced TRADD overexpression partially reversed this effect. Mechanistically, METTL1 promotes TRADD translation through tRNA m7G-dependent translational regulation, thereby facilitating BCBrM. m7G modification is closely related to BCBrM and immune-related molecular characteristics, and METTL1 promotes BCBrM by reprogramming tRNA m7G modification and enhancing TRADD translation, which provides novel insights for target therapy of BCBrM.