Abstract
BackgroundEsophageal squamous cell carcinoma (ESCC) is one of the most common cancer types and represents a threat to global public health. N6-Methyladenosine (m6A) methylation plays a key role in the occurrence and development of many tumors, but there are still few studies investigating ESCC. This study attempts to construct a prognostic signature of ESCC based on m6A RNA methylation regulators and to explore the potential association of these regulators with the tumor immune microenvironment (TIME).MethodsThe transcriptome sequencing data and clinical information of 20 m6A RNA methylation regulators in 453 patients with ESCC (The Cancer Genome Atlas [TCGA] cohort, n = 95; Gene Expression Omnibus [GEO] cohort, n = 358) were obtained. The differing expression levels of m6A regulators between ESCC and normal tissue were evaluated. Based on the expression of these regulators, consensus clustering was performed to investigate different ESCC clusters. PD-L1 expression, immune score, immune cell infiltration and potential mechanisms among different clusters were examined. LASSO Cox regression analysis was utilized to obtain a prognostic signature based on m6A RNA methylation modulators. The relationship between the risk score based on the prognostic signature and the TIME of ESCC patients was studied in detail.ResultsSix m6A regulators (METTL3, WTAP, IGF2BP3, YTHDF1, HNRNPA2B1 and HNRNPC) were observed to be significantly highly expressed in ESCC tissues. Two molecular subtypes (clusters 1/2) were determined by consensus clustering of 20 m6A modulators. The expression level of PD-L1 in ESCC tissues increased significantly and was significantly negatively correlated with the expression levels of YTHDF2, METL14 and KIAA1429. The immune score, CD8 T cells, resting mast cells, and regulatory T cells (Tregs) in cluster 2 were significantly increased. Gene set enrichment analysis (GSEA) shows that this cluster involves multiple hallmark pathways. We constructed a five-gene prognostic signature based on m6A RNA methylation, and the risk score based on the prognostic signature was determined to be an independent prognostic indicator of ESCC. More importantly, the prognostic value of the prognostic signature was verified using another independent cohort. m6A regulators are related to TIME, and their copy-number alterations will dynamically affect the number of tumor-infiltrating immune cells.ConclusionOur study established a strong prognostic signature based on m6A RNA methylation regulators; this signature was able to accurately predict the prognosis of ESCC patients. The m6A methylation regulator may be a key mediator of PD-L1 expression and immune cell infiltration and may strongly affect the TIME of ESCC.
Highlights
Esophageal cancer (EC) is a highly aggressive malignancy and is the eighth most common malignant tumor in the world; the mortality rate of EC ranks sixth worldwide and is still rising [1,2,3]
We entered 20 m6A RNA methylation regulators into STRING to understand their interactions and performed functional annotation analysis to initially explore the biological process (BP), cell composition (CC), molecular function (MF) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways involved in these regulators
To understand the expression pattern of m6A RNA methylation regulators between esophageal squamous cell carcinoma (ESCC) tumors and normal tissues, we drew a heatmap based on 20 m6A methylation genes in the The Cancer Genome Atlas (TCGA) database
Summary
Esophageal cancer (EC) is a highly aggressive malignancy and is the eighth most common malignant tumor in the world; the mortality rate of EC ranks sixth worldwide and is still rising [1,2,3]. Among the two main histopathological subtypes of EC, esophageal squamous cell carcinoma (ESCC) is more common than esophageal adenocarcinoma [5]. The identification of novel and reliable prognostic molecular signatures from multiple dimensions is very important for selecting the most appropriate treatment strategy and improving the poor prognosis of ESCC patients. Esophageal squamous cell carcinoma (ESCC) is one of the most common cancer types and represents a threat to global public health. N6-Methyladenosine (m6A) methylation plays a key role in the occurrence and development of many tumors, but there are still few studies investigating ESCC. This study attempts to construct a prognostic signature of ESCC based on m6A RNA methylation regulators and to explore the potential association of these regulators with the tumor immune microenvironment (TIME)
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