Impact of Subcutaneous versus Orthotopic Implantations on Transcriptomic Profiles of Patient-derived Xenografts

Patient-derived xenografts (PDXs) are essential preclinical models, capturing the histological and molecular features of human tumors. Subcutaneous (s.c.) and orthotopic (ortho) PDXs are widely used, but their comparative utility remains unclear, especially regarding tumor and stromal gene expression. This study analyzed 45 matched s.c. and ortho PDX models spanning five cancer types using bulk RNA sequencing. Tumor (human) gene expression was highly conserved between s.c. and ortho PDXs, with similar epithelial-mesenchymal transition (EMT), angiogenesis, and stemness scores. In contrast, stromal (mouse) gene expression varied by implantation site, with orthotopic models better reflecting native tissue environments. A conserved subset of stromal genes, consisting of histone and ribosomal protein genes and driven by tumor-intrinsic factors, exhibited stable expression patterns across implantation sites, indicating that tumor characteristics shape stromal responses. Differential expression analysis identified metastasis-related stromal genes in both PDX types, although no direct links to metastatic pathways were found. These findings highlight the stability of tumor-driven gene expression across implantation sites and reveal the impact of implantation location on stromal profiles, guiding model selection for future cancer research.