Evaluation and in vitro verification of the prognostic value of palmitoylation-related genes in ovarian cancer

Background Ovarian cancer (OC) remains the most lethal malignancy within the spectrum of gynecological cancers globally. While protein S-palmitoylation has been extensively implicated in tumor progression, its specific functional contributions and molecular mechanisms in the context of OC pathogenesis remain to be fully elucidated. This article aims to explore the prognostic effect associated with palmitoylation in OC. Methods To begin with, we obtained transcriptomic data for ovarian cancer (OC) from publicly available genomic repositories. Using comparative analysis, we pinpointed two distinct sets of differentially expressed genes (DEGs): DEGs1, which are associated with OC, and DEGs2, which are linked to palmitoylation. Consequently, a prognostic risk model was constructed and validated. Following this, an independent survival analysis was executed, a nomogram was subsequently developed to establish a predictive model. Multiple analytical approaches were applied to stratified risk groups, including pathway enrichment assessment, immune microenvironment infiltration evaluation, immune checkpoint examination, potential drug screening, and genomic mutation profiling. The expression patterns of identified prognostic markers were subsequently validated by means of reverse transcription quantitative PCR (RT-qPCR). Results Through intersecting DEGs1 and DEGs2, we obtained 24 candidate biomarkers. Our investigation revealed that HSPG2, BRD4, RARRES1, and SCGB1D2 served as prognostic markers, which were utilized to develop a risk assessment model demonstrating excellent capability in evaluating OC patient prognosis via comprehensive analytical procedures. Risk scoring, ethnicity, and tumor staging emerged as independent predictive determinants for OC. The constructed prognostic nomogram exhibited robust predictive capacity for patient clinical outcomes. There were four variables, including age (> 45), race (white), stage 3, and histologic G3, with survival distinctions between two risk cohorts. Relevant pathways contained distinct ribosome-related and translation initiation activities. The prognostic genes were linked to seven immune cells, like Eosinophils, and notable distinctions were found in seven immune checkpoints, like CTLA4 and CD274, between the two risk cohorts. Finally, there was a notable distinction in IC ₅₀ for all 131 drugs, like BMS.536924 and CGP.60474, and the TP53 gene showed a notable mutation rate in risk cohorts. Relative to the control cohort, the expression levels of HSPG2, SCGB1D2, and BRD4 showed a significant up-regulation in the OC cohort, while the expression of RARRES1 was notably up-regulated in the control cohort, consistent with its expression in GSE26712. Conclusion This study identified HSPG2, BRD4, RARRES1, and SCGB1D2, which were prognostic genes associated with palmitoylation, providing valuable insights that could lay the foundation for innovative therapeutic strategies.