Comparative transcriptomic analysis of chemotherapy-naive and post-chemotherapy germ cell tumors.

5026 Background: Cisplatin-based chemotherapy is highly effective in testicular germ cell tumors (GCTs); however, the presence of viable tumor after first-line chemotherapy is associated with chemoresistance and poor clinical outcome. The transcriptional programs distinguishing chemotherapy-naïve and post-chemotherapy viable GCTs remain incompletely characterized. Methods: Tumor samples from 50 GCT patients treated between 2010 and 2022 were analyzed, including 30 chemotherapy-naïve tumors and 20 post-chemotherapy viable GCTs resected from the retroperitoneum. Five normal testicular tissue samples served as controls. Formalin-fixed paraffin-embedded samples were profiled using the HTG EdgeSeq Oncology Biomarker Panel. Differential gene expression analysis was performed using DESeq2, adjusted for histology, with significance defined as adjusted p-value < 0.1 and |log2 fold change| > 1. Functional enrichment analysis was conducted to identify deregulated biological pathways. Results: Compared with normal testicular tissue, chemotherapy-naïve GCTs and post-chemotherapy viable GCTs exhibited 1,010 and 720 differentially expressed genes, respectively. Direct comparison between chemotherapy-naïve and post-chemotherapy tumors identified 424 differentially expressed genes. Post-chemotherapy viable GCTs demonstrated marked downregulation of genes associated with pluripotency and embryonal stem cell identity, including POU5F1 , UTF1 , DPPA4 , and PRDM14 . In contrast, post-chemotherapy tumors showed upregulation of immediate early stress response genes, inflammatory and cytokine signaling pathways, EGFR-related growth factor signaling, and metabolic stress adaptation. Conclusions: Post-chemotherapy viable GCTs are characterized by loss of pluripotent transcriptional programs and acquisition of stress-responsive, inflammatory, and adaptive signaling pathways. These transcriptional changes provide insight into the biology of chemotherapy resistance in GCTs and may have prognostic and therapeutic implications.