Comprehensive Analysis of mA Regulators Characterized by the Immune Cell Infiltration in Head and Neck Squamous Cell Carcinoma to Aid Immunotherapy and Chemotherapy.

Background: N6-Methyladenosine (mA), which is a prevalent regulator of mRNA expression, has gathered increasing study interests. Though the role of mA as being important in many biological processes (such as growth and proliferation of cancers) has been well documented, its potential role in tumor immune microenvironment (TIME) has rarely been analyzed.

Methods: We downloaded RNA expression, single nucleotide polymorphism (SNP), and copy number variation (CNV) data from The Cancer Genome Atlas (TCGA). We then curated 21 mA regulators and clustered patients into three mA subtypes and mA-related gene subtypes and compared them based on overall survival (OS). The combination of CIBERSORT as well as ssGSEA quantified the infiltration levels of immune cells and immune-related functions. The mA scores were determined by using principal component analysis (PCA) algorithm. Furthermore, we evaluate the correlation of mA regulators with immune and response to therapy.

Results: Three mA clusters were identified based on the TCGA-HNSCC cohort, and there were significant associations among them in overall outcomes and caner-related pathways. We found that three mA clusters were consistent with three phenotypes: immune-inflamed, immune-dessert, and immune-excluded. HNSCC patients were divided into high- and low-mA score groups based on the cutoff of mA score. Patients with lower mA score had better overall survival outcome. Further analysis indicated that patients with higher mA score presented higher tumor mutation burden (TMB). In addition, patients in low-mA score subgroup had high chemotherapeutics sensitivity. GEO cohort confirmed patients with low mA score demonstrated significant overall survival advantages and clinical benefits. Low mA score carry an increased neoantigen load, eliciting a response to immunotherapy, and its value in predicting survival outcomes of immunotherapy was also confirmed in three anti-PD-1 cohorts.

Conclusions: Our study demonstrated that mA regulators are closely related to TIME and the mA score was an effective prognostic biomarker and predictive indicator for immunotherapy and chemotherapeutics. Comprehensive evaluation of mA regulators in tumors will extend our understanding of TIME and effectively guide increasing study investigations on immunotherapy and chemotherapy strategies for HNSCC.