Transcriptomic evaluation of immune-infiltrated patient-derived tumor organoids as preclinical models in renal cell carcinoma

Patient-derived tumor organoids (PDTOs) have emerged as valuable preclinical models for studying tumor biology and therapeutic responses. However, despite the development of protocols for tumor dissociation and immune cell infiltration, their fidelity in representing clear cell renal cell carcinoma (ccRCC) tumors remains poorly characterized. To address this, we established matched samples, including tumor tissue, enzymatically dissociated tumor, formed PDTOs, and immune-infiltrated PDTOs from three ccRCC patients, and performed bulk RNA sequencing to capture dynamic molecular changes across the experimental workflow. Our analyses revealed that tumor dissociation triggered stress-related transcriptional changes, marked by the upregulation of heat shock genes (e.g., HSPA1A) and the downregulation of the hypoxia pathway, while PDTOs recapitulated hypoxic signaling. Immune-infiltrated PDTOs retained critical immune signatures including T-effector, and exhibited an enhanced pro-inflammatory phenotype (CXCL10, JAK-STAT). Furthermore, predictive gene signatures and immunotherapy response scores further underscored the clinical relevance of immune-infiltrated PDTOs consistent with the original tumor tissue. Collectively, these findings validate immune-infiltrated PDTOs as robust, patient-specific models for personalized therapeutic exploration, offering a platform to optimize immunotherapy strategies in ccRCC.