Bioinformatic analysis identifies HPV-related tumor microenvironment remodeling prognostic biomarkers in head and neck squamous cell carcinoma

作者：Qimin Zhou, Ouyang Yuan, Hongtu Cui, Tao Hu, Gary Guishan Xiao, Jiao Wei, Honglei Zhang, Chengjun Wu · 发表于：Frontiers in Cellular and Infection Microbiology · 年份：2022 · DOI：10.3389/fcimb.2022.1007950 · 被引用次数：15 · 研究领域：Ferroptosis and cancer prognosis、Epigenetics and DNA Methylation、RNA modifications and cancer

Head and neck squamous cell carcinomas (HNSCCs) are highly aggressive tumors with rapid progression and poor prognosis. Human papillomavirus (HPV) infection has been identified as one of the most important carcinogens for HNSCC. As an early event in HNSCC, infection with HPV leads to altered immune profiles in the tumor microenvironment (TME). The TME plays a key role in the progression and transformation of HNSCC. However, the TME in HNSCC is a complex and heterogeneous mix of tumor cells, fibroblasts, different types of infiltrating immune cells, and extracellular matrix. Biomarkers relevant to the TME, and the biological role of these biomarkers, remain poorly understood. To this end, we performed comprehensive analysis of the RNA sequencing (RNA-Seq) data from tumor tissue of 502 patients with HNSCC and healthy tissue of 44 control samples. In total, we identified 4,237 differentially expressed genes, including 2,062 upregulated and 2,175 downregulated genes. Further in-depth bioinformatic analysis suggested 19 HNSCC tumor tissue-specific genes. In the subsequent analysis, we focused on the biomarker candidates shown to be significantly associated with unfavorable patient survival: ITGA5 , PLAU , PLAUR , SERPINE1 , TGFB1 , and VEGFC . We found that the expression of these genes was negatively regulated by DNA methylation. Strikingly, all of these potential biomarkers are profoundly involved in the activation of the epithelial–mesenchymal transition (EMT) pathway in HNSCCs...