Identification of prognostic biomarkers in early stage squamous cell lung cancer (LUSC) by transcriptomic and miRNA profiling [sRNA-Seq]
Squamous cell lung cancer (LUSC) is a frequently diagnosed histological subtype of lung malignancy associated with high mortality due to limited number of treatment options. Identification of potential targets suitable for drug development using high-throughput methods is still lacking. Therefore, the purpose of this research is to analyze expression profiles of mRNA and miRNA in LUSC, aiming to identify the key molecules associated with tumorigenesis and prognosis (overall survival; OS). We performed differential gene expression analysis, pathway enrichment analysis and gene ontology analysis on RNA-seq data obtained from 23 FFPE tumor samples and 3 FFPE healthy individuals. TCGA LUSC and GTEx healthy donors' cohorts were used for validation. We identified 1133 up-regulated and 644 down-regulated genes, common for both cohorts. The most significant up-regulated genes were involved in cell-cycle regulation pathways, while down-regulated genes predominately belonged to immune-related pathways. Survival analysis performed on selected genes, commonly dysregulated in both cohorts and performed only on non-metastatic patients, identified novel prognostic biomarkers associated with OS in early-stage LUSC patients (HOXC4-worse OS, p=0.0001; LILRA5-better OS, p=0.0086). In total, 50 differentially expressed genes are correlated with patients' OS. Aiming to get better insight into the profile of the tumor microenvironment, we estimated levels of immune-cells infiltration in LUSC and identified 4 subtypes based on immune-cell infiltration levels. Protein-protein interaction (PPI) network was built based on differentially expressed genes, and PPI modules and hub-genes were identified. Weighted gene co-expression network analysis was conducted to identify significant modules and hub-genes in correlation to clinical traits. Differential analysis on miRNA-Seq data, obtained from 16 tumor and 4 healthy tissue samples, was conducted as well. 75 up-regulated and 47 down-regulated miRNAs were identified. Further, targets of differentially expressed miRNA were identified, following gene ontology analysis and miRNA-mRNA networks construction. Overall design: Expression profiling of miRNA from 14 patients diagnosed with squamous cell lung cancer (LUSC), and 4 healthy controls. Profiling was done on FFPE tissue samples, for both LUSC and control samples.