Single-cell N(6)-methyladenosine regulator patterns guide intercellular communication of tumor microenvironment that contribute to colorectal cancer progression and immunotherapy

BACKGROUND: N6-methyladenosine (m(6)A) RNA methylation plays a critical role in key genetic events for various cancers; yet, how m(6)A functions within the tumor microenvironment (TME) remains to be elucidated. METHODS: A total of 65,362 single cells from single-cell RNA-seq data derived from 33 CRC tumor samples were analyzed by nonnegative matrix factorization (NMF) for 23 m(6)A RNA methylation regulators. CRC and Immunotherapy cohorts from public repository were used to determine the prognosis and immune response of TME clusters. RESULTS: The fibroblasts, macrophages, T and B cells were respectively grouped into 4 to 5 subclusters and then classified according to various biological processes and different marker genes. Furthermore, it revealed that the m(6)A RNA methylation regulators might be significantly related to the clinical and biological features of CRC, as well as the pseudotime trajectories of main TME cell types. Bulk-seq analysis suggested that these m(6)A-mediated TME cell subclusters had significant prognostic value for CRC patients and distinguished immune response for patients who underwent ICB therapy, especially for the CAFs and macrophages. Notably, CellChat analysis revealed that RNA m(6)A methylation-associated cell subtypes of TME cells manifested diverse and extensive interaction with tumor epithelial cells. Further analysis showed that ligand-receptor pairs, including MIF − (CD74 + CXCR4), MIF − (CD74 + CD44), MDK–NCL and LGALS9 − CD45, etc. mediated the communication between m(6)A associated subtypes of TME cells and tumor epithelial cells. CONCLUSIONS: Taken together, our study firstly revealed the m(6)A methylation mediated intercellular communication of the tumor microenvironment in the regulation of tumor growth and antitumor immunomodulatory processes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-022-03395-7.