TCGA Database-Based Screening of Tumor Microenvironment Immunomodulators Related to Bladder Cancer Prognosis

Bladder cancer (BC), as the most common malignant tumor of the urinary tract, has a complex biological behavior. Currently, there are still some limitations in the diagnosis and treatment of BC. Despite the great progress made in immunotherapy, there is still a lack of key genes for the diagnosis of BC. Therefore, it is particularly important to explore the differentially expressed genes (DEGs) and their effectiveness on prognosis of BC with different tumor microenvironment scores.

The gene expression dataset of BC was downloaded from the Cancer Genome Atlas (TCGA) database. The correlation between clinicopathological characteristics of patients and scores of immune and stromal components was analyzed. Patients were divided into high and low score groups according to their tumor microenvironment score (Immune score, Stromal score, ESTIMATE score). DEGs between high and low score groups were identified using R software and then subjected to enrichment analyses to assess their potential biological functions and signaling pathways. The protein-protein interaction (PPI) network was constructed using the STRING database to further identify hub genes. The expression levels of hub genes in BC were verified by TCGA database. Subsequently, the hub genes were evaluated for overall survival (OS), disease-free survival (DFS), progression-free survival (PFS), and disease-specific survival (DSS), and corresponding forest plots were created.

A total of 2346 DEGs were obtained, including 1120 up-regulated genes and 1226 down-regulated genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses found DEGs were mainly enriched in cell migration and immune-related pathways. Meanwhile, The PPI network finally yielded top 10 hub genes with predictive value, which included actin beta (ACTB), interleukin 6 (IL-6), Jun proto-oncogene (JUN), CD4 molecule (CD4), heat shock protein 90 alpha family class A member 1 (HSP90AA1), protein tyrosine phosphatase receptor type C (PTPRC), tumor protein p53 (TP53), SRC proto-oncogene (SRC), fibronectin 1 (FN1), and tumor necrosis factor (TNF). Among them, CD4, PTPRC, and SRC were potential protective factors for BC.

The top 10 hub genes (ACTB, IL-6, JUN, CD4, HSP90AA1, PTPRC, TP53, SRC, FN1, TNF) obtained based on tumor microenvironment scores all had potential predictive value. Elevated expression of protective factors (CD4, PTPRC, and SRC) indicates better survival outcome of BC subjects. Further exploration of the molecular developmental mechanisms of these hub genes will help to develop novel personalized therapies and improve BC prognosis.