Mining TCGA database for prognostic genes in head and neck squamous cell carcinoma microenvironment

Abstract Background Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignant tumors. Many previous reports have already shown that the extent of infiltrating immune and stromal cells in tumor tissues and the tumor microenvironment (TME) cells play a significant role in the overall prognosis. Methods The convenient access to The Cancer Genome Atlas (TCGA) database facilitates global gene expression profiling and database mining in a large‐scale for potential correlation between genes and overall survival of a variety of malignancies including HNSCC. The quantification of the immune and stromal components in tumor tissues could be facilitated by calculating mmune scores and stromal scores on the basis of Estimation of stromal and Immune cells in Malignant Tumor tissues using Expression data (ESTIMATE) algorithm could facilitate the quantification of the immune and stromal components in tumor tissues. The effects of genes involved in immune and stromal cells on prognosis were categorized. Prognosis associated genes of HNSCC patients were further identified. Result This study showed that GIMAP6, SELL, TIFAB, KCNA3, P2RY8 and CCR4 may mediate immune response, extracellular matrix, and immunoglobulin binding via neutrophil activation in HNSCC. Conclusion Depicting a comprehensive landscape of the TME characteristics of HNSCC may therefore help to interpret the responses of HNSCC to immunotherapies and provide new strategies for the treatment of cancers.