Employing cancer driver genes for the identification of immunological features in two esophageal cancer subtypes to facilitate immunotherapy.

Background: Esophageal cancer (ESCA) is a pervasive health threat, and cancer driver genes (CDGs) are under investigation as potential biomarkers for its treatment.

Methods: This study applied univariate regression to identify CDGs affecting survival and performed clustering analysis in TCGA-ESCA samples based on CDG expression. It explored differentially expressed genes (DEGs) and immune landscapes between the subtypes, analyzed tumor mutations, and further predicted the potential small-molecule drugs. In addition, we collected ESCA-related cell lines and investigated the expression levels of CDGs that were most significantly differentially expressed and related to survival.

Results: Our research pinpointed 18 survival-associated CDGs and split TCGA-ESCA patients into cluster 1 and cluster 2 via consensus clustering. The subtypes exhibited different levels of immune cell infiltration, with lower Tumor Immune Dysfunction and Exclusion scores in cluster 1. Enrichment analysis revealed that DEGs between the two subtypes were primarily linked to the humoral immune response, receptor ligand activity, and neuroactive ligand-receptor interaction. Mutation analysis did not find significant differences in mutation rates between the subtypes. Additionally, potential small-molecule drugs targeting DEGs in ESCA were investigated, such as 3,3'-diindolylmethane, SJ-172550, aminoglutethimide, nitrazepam, actarit, and epigallocatechin. The results of qRT-PCR showed that RUNX1, NONO, and TSC2 were not only significantly associated with the survival of esophageal squamous cell carcinoma (ESCC) but also significantly overexpressed in the ESCC cell lines (KYSE150 and KYSE450).

Conclusion: This study is valuable for elucidating CDG functions in ESCA and for biomarker identification.