Integrated transcriptomic analysis and RT-qPCR validation using FFPE patient tissues reveal the role of FOXQ1 and MCM10 in ovarian cancer

Abstract

Introduction: Ovarian cancer has a high mortality rate due to late diagnosis and limited availability of reliable molecular biomarkers. Integrated transcriptomic analysis may facilitate the identification of key regulatory genes involved in tumor progression. Objective: To identify and validate key regulatory genes associated with ovarian cancer progression through integrated transcriptomic analysis and experimental validation. Methods: Differential gene expression analysis was conducted using the GSE18520 microarray dataset to compare ovarian cancer tissues with normal ovarian epithelium. Genes with log2 fold change ≥ 1, and adjusted p-value < 0.05 were considered significant. Functional enrichment and protein–protein interaction (PPI) network analyses were performed to prioritize hub genes. FOXQ1 and MCM10 were selected for experimental validation using quantitative real-time polymerase chain reaction (RT-qPCR) in formalin-fixed paraffin-embedded (FFPE) ovarian cancer tissues. Relative expression levels were calculated using the 2⁻ΔΔCt method and normalized to GAPDH. Results: Transcriptomic analysis identified multiple differentially expressed genes associated with cell cycle regulation, DNA replication, and transcriptional control. FOXQ1 (log2 fold change = +5.00) and MCM10 (log2 fold change  = +2.74) were significantly upregulated and occupied central hub positions in the PPI network. RT-qPCR validation confirmed marked overexpression of FOXQ1 (45.3×) and MCM10 (11.3×) in FFPE ovarian cancer tissues. Conclusion: This integrated transcriptomic and experimental validation study identifies FOXQ1 and MCM10 as key regulators in ovarian cancer, highlighting their potential as biomarkers for disease progression.