부산대학교 도서관

Simple Summary: Lung cancer is a leading cause of cancer-related deaths worldwide, characterized as a disease usually diagnosed in the advanced stages with limited therapeutic options. Significant progress in the treatment of lung cancer has been achieved by the application of targeted therapy and immunotherapy based on the identification of molecular abnormalities of the tumor tissue. However, only a small proportion of patients is carrying genetic alterations and will benefit from targeted therapy. Here, we conducted transcriptomic profiling and a comprehensive biostatistics analysis of the squamous-cell lung carcinoma (SqCLC), a histological subtype of the non-small cell lung carcinoma (NSCLC), aiming to identify the specific transcriptomic signature of SqCLC and evaluate the functional relevance of identified genes. This study sheds light on individual SqCLC tumors' transcriptomic landscape and discusses the therapeutic and prognostic potential of identified biomarkers. Squamous cell lung carcinoma (SqCLC) is associated with high mortality and limited treatment options. Identification of therapeutic targets and prognostic biomarkers is still lacking. This research aims to analyze the transcriptomic profile of SqCLC samples and identify the key genes associated with tumorigenesis, overall survival (OS), and a profile of the tumor-infiltrating immune cells. Differential gene expression analysis, pathway enrichment analysis, and Gene Ontology analysis on RNA-seq data obtained from FFPE tumor samples (N = 23) and healthy tissues (N = 3) were performed (experimental cohort). Validation of the results was conducted on publicly available gene expression data using TCGA LUSC (N = 225) and GTEx healthy donors' cohorts (N = 288). We identified 1133 upregulated and 644 downregulated genes, common for both cohorts. The most prominent upregulated genes were involved in cell cycle and proliferation regulation pathways (MAGEA9B, MAGED4, KRT, MMT11/13), while downregulated genes predominately belonged to immune-related pathways (DEFA1B, DEFA1, DEFA3). Results of the survival analysis, conducted on the validation cohort and commonly deregulated genes, indicated that overexpression of HOXC4 (p < 0.001), LLGL1 (p = 0.0015), and SLC4A3 (p = 0.0034) is associated with worse OS in early-stage SqCLC patients. In contrast, overexpression of GSTZ1 (p = 0.0029) and LILRA5 (p = 0.0086) was protective, i.e., associated with better OS. By applying a single-sample gene-set enrichment analysis (ssGSEA), we identified four distinct immune subtypes. Immune cell distribution suggests that the memory T cells (central and effector) and follicular helper T cells could serve as important stratification parameters. [ABSTRACT FROM AUTHOR]