Identification of m(6)A Regulator-Associated Methylation Modification Clusters and Immune Profiles in Melanoma

RNA N6-methyladenosine (m(6)A) modification in tumorigenesis and progression has been highlighted and discovered in recent years. However, the molecular and clinical implications of m(6)A modification in melanoma tumor microenvironment (TME) and immune infiltration remain largely unknown. Here, we utilized consensus molecular clustering with nonnegative matrix factorization based on the melanoma transcriptomic profiles of 23 m(6)A regulators to determine the m(6)A modification clusters and m(6)A-related gene signature. Three distinct m(6)A modification patterns (m(6)A-C1, C2, and C3), which are characterized by specific m(6)A regulator expression, survival outcomes, and biological pathways, were identified in more than 1,000 melanoma samples. The immune profile analyses showed that these three m(6)A modification subtypes were highly consistent with the three known immune phenotypes: immune-desert (C1), immune-excluded (C2), and immune-inflamed (C3). Tumor digital cytometry (CIBERSORT, ssGSEA) algorithm revealed an upregulated infiltration of CD8(+) T cell and NK cell in m(6)A-C3 subtype. An m(6)A scoring scheme calculated by principal component of m(6)A signatures stratified melanoma patients into high- and low-m(6)sig score subgroups; a high score was significantly associated with prolonged survival and enhanced immune infiltration. Furthermore, fewer somatic copy number alternations (SCNA) and PD-L1 expression were found in patients with high m(6)Sig score. In addition, patients with high m(6)Sig score demonstrated marked immune responses and durable clinical benefits in two independent immunotherapy cohorts. Overall, this study indicated that m(6)A modification is involved in melanoma tumor microenvironment immune regulation and contributes to formation of tumor immunogenicity. Comprehensive evaluation of the m(6)A modification pattern of individual tumors will provide more insights into molecular mechanisms of TME characterization and promote more effective personalized biotherapy strategies.