RNA methylation patterns of tumor microenvironment cells regulate prognosis and immunotherapeutic responsiveness in patients with triple-negative breast cancer

Abstract

Abstract Immunotherapy research focuses on reshaping the tumor microenvironment (TME) to enhance its antitumor immune responses, with an emphasis on understanding the impact of RNA methylation in triple-negative breast cancer (TNBC) TME regulation. This study explored the influence of various RNA methyltransferases on TME cells in TNBC and their correlation with prognosis and immunotherapy response. Using non-negative matrix factorization on single-cell RNA-sequencing data, distinct TME cell clusters were identified based on the expression of 30 RNA methyltransferases. Various analyses, including pseudotime, cell communication, transcription factor regulatory network, and gene enrichment, were conducted on these clusters. The roles of RNA methyltransferase-mediated TME clusters in prognosis and immunotherapy response were determined using TNBC bulk RNA-Seq data, and the findings were validated through immunofluorescence analysis of a tissue microarray comprising 87 samples. Spatial transcriptomic analysis further revealed the distribution of TME cell clusters. Different methyltransferase-mediated cell clusters exhibited unique metabolic, immune, transcriptional, and intercellular communication patterns. Survival analysis indicated prognostic significance in specific TME cell clusters, and immunofluorescence analysis confirmed the prognostic value of m6A_WTAP + CD8T + cells. In conclusion, our study illustrated the involvement of these cell subgroups in tumor growth and antitumor immunity modulation, providing insights into the enhancement of TNBC immunotherapy.

Keywords

• Triple-negative breast cancer
• RNA methyltransferase
• Tumor microenvironment
• Immunotherapy
• Prognosis
• Multiomics