Gene set enrichment analysis of oral cavity carcinoma to identify pathways associated with lymph node metastasis.

Abstract

e18108 Background: Oral cavity cancers (OCC) have a high propensity for lymph node metastasis (LNM), and level one evidence supports disease-free and overall survival benefits from elective neck dissection (END) in even early stage clinically node-negative (cN0) patients. Given that ENDs are often bilateral and come along with significant toxicities, new trials like HN006 are exploring sentinel lymph node biopsies as an alternative to upfront END. Identifying gene sets associated with LNM could help identify the highest risk patients, enabling more targeted treatment strategies. Methods: This study analyzed primary tumor transcriptome data of oral tongue and floor of mouth OCC patients from the TCGA dataset. Gene set enrichment analysis (GSEA) was performed with curated gene sets from the MSigDB Hallmark 2020 collection to evaluate pathways significantly enriched in patients with pathologically node-positive (pN+). Pathways were ranked by normalized enrichment scores (NES), and statistical significance was assessed using nominal p-values and false discovery rate q-values (FDR-q) at level <0.05. All statistical analyses were conducted using Python 3.7, with the following packages: scipy.stats, gseapy, and sklearn. Results: Among 162 patients, 69 were pathologically node-negative and 93 were pN+. GSEA revealed eight pathways significantly associated with pN+ OCC: Epithelial Mesenchymal Transition (NES = 1.70, FDR-q <0.001), Myogenesis (NES = 1.54, FDR-q = 0.002), Coagulation (NES = 1.39, FDR-q = 0.028), Angiogenesis (NES = 1.38, FDR-q = 0.043), Hedgehog Signaling (NES = 1.33, FDR-q = 0.043), Apical Surface (NES = 1.31, FDR-q = 0.049), Complement (NES = 1.31, FDR-q = 0.045), and Wnt-beta Catenin (NES = 1.29, FDR-q = 0.050). Mean expression scores of lead genes from each respective pathway were evaluated, identifying 149 genes associated with LNM (Table 1). Conclusions: This study identifies several key molecular pathways and their respective lead genes associated with LNM in OCC. These findings have potentially valuable clinical implications for risk-stratification, informing therapeutic decision-making (patient selection for END), and facilitating precision medicine initiatives. Future work could investigate if these molecular markers may also have implications in the response to adjuvant treatments like radiation therapy or chemotherapy. Top 5 lead genes for each pathway. Pathway Top Lead Genes Epithelial Mesenchymal Transition TPM1, MYL9, SERPINE1, PCOLCE, THY1 Coagulation ANXA1, SERPINE1, C9, FN1, DUSP6 Angiogenesis KCNJ8, VCAN, TIMP1 Hedgehog Signaling ADGRG1, THY1, AMOT, LDB1, PLG Apical Surface SLC34A3, SRPX, THY1, EFNA5, PKHD1 Complement PRSS3, RCE1, SERPINE1, PLA2G4A, C9 Wnt-beta Catenin FZD8, CSNK1E, WNT5B, WNT6, HDAC11