Single-cell analysis reveal cell-type-specific RNA methylation patterns in breast cancer

ObjectiveThis study aimed to investigate cell-type-specific RNA methylation patterns in primary breast cancers and metastatic lymph nodes and explore their roles in cancer progression and immune regulation.MethodsUsing single-cell RNA sequencing data from five breast cancer patients (primary cancers and matched metastatic lymph nodes), we calculated RNA methylation scores per cell using the AUCell method. Cell types were annotated using Seurat. Differentially expressed gene analysis, pseudotime trajectory assessment, copy number variation analysis, and cell-cell communication analyses were performed between high- and low-methylation groups. Validation was conducted using bulk RNA sequencing data from The Cancer Genome Atlas.ResultsMetastatic lymph nodes showed significantly lower RNA methylation scores than primary cancers, particularly in T cells and B cells. Low methylation was correlated with enhanced cell differentiation, increased malignancy in epithelial cells, and reduced immune cell communication. Monocytes exhibited opposite trends. Differentially expressed genes from methylation groups stratified The Cancer Genome Atlas patients into two clusters with distinct survival and immune infiltration profiles.ConclusionsRNA methylation is suppressed during breast cancer metastasis, affecting cell differentiation, immune communication, and patient outcomes.