RNA-seq data of nasopharyngeal carcinoma (NPC) in non-endemic areas

Epstein-Barr virus (EBV) related nasopharyngeal carcinoma (NPC) is an epithelial malignancy with higher incidence in Asian endemic area (EA) than in non-endemic area (NEA), where frequency is below 1/105/year. The causes of such difference are unclear and might be related to viral, environmental (e.g. diet) and genomic factors. We aimed at dissecting the gene expression (GE) and microenvironment landscape in NPC leading to the identification of molecular subtypes explaining the differences between EA and NEA. FFPE tumor tissue of 50 Italian EBV related NPC patients were collected at initial diagnosis. RNASeq was carried out by QuantSeq 3' mRNA-Seq (Lexogen). Tumor microenvironment and biological characteristics of EA and NEA cases were evaluated by xCell, and Gene Set Enrichment analyses, while the association with radiosensitivity was assessed with a specific signature. By unsupervised clustering analysis, four molecular clusters (cl 1,2,3,4) were disclosed in EA. All clusters were predicted in NEA with the exclusion of cl4. Cl4 and cl3 exhibited a high RadioSensitivity Index (RSI) suggesting that patients classified in these clusters are more resistant than patients included in cl2 and cl1 (p=5.9e-05). To our knowledge this is the first in-deep molecular comparison between EA and NEA NPC.