Abstract B18: Transcriptional profiling of tumor stroma using ovarian cancer PDX models with induced platinum-resistance
Authors: Valentina Zanfagnin, Yuanhang Liu, Pritha Chanana, Xiaonan Pritha, Beverly Long, Joe Pathoulas, Brad Evans, Jaime Davila, Chen Wang, Saravut John Weroha
Journal: Clinical Cancer Research (2020)

Abstract Introduction: Acquired resistance to platinum remains a major clinical problem in ovarian cancer since systemic therapies have limited efficacy in this setting. There is growing evidence that the tumor microenvironment (TME) contributes to such resistance, as well as the pathogenesis of the disease. The study of the TME is limited by technical challenges of separating the epithelial from the stromal component. To overcome this limitation, we performed RNA sequencing (RNA-Seq) for three pairs of sensitive and induced resistant patient-derived xenograft models since the epithelial transcripts originate from human tissue and the stroma component is murine. Methods: To determine which TME genes might be contributing to chemotherapy resistance, three platinum-sensitive ovarian cancer PDX lines were treated repeatedly with carboplatin/paclitaxel until resistance occurred. Primary platinum-sensitive and induced platinum resistant tumors were characterized histologically by H&amp;E and Masson Trichrome staining. The three pairs of sensitive and resistant PDX models were then subjected to RNA-Seq. Raw sequencing data were processed through Xenome to classify the reads into epithelial carcinoma (human) or TME (mouse) through Mayo Clinic’s internal RNA-Seq pipeline for transcriptome quantification. Differential expression analysis between induced resistant and sensitive models was carried out for both carcinoma and TME components using edgeR paired analysis. Gene set enrichment analysis was used to identify overrepresented biologic functions for differentially expressed genes between the pairs. Top significantly varied, differentially expressed genes between the pairs were validated using species-specific qPCR. Results: Histologic analysis of the matched sensitive/resistant pairs revealed a marked increase of the stromal component in the resistant tumors evident by H&amp;E and Masson trichrome staining. A total number of 95 and 312 genes were differentially expressed in the epithelial and TME component, respectively (FDR&amp;lt;0.05; absolute log2 fold-change &amp;gt;1.5). The stemness marker SOX2 was significantly upregulated in the human component of the resistant tumors as confirmed by qPCR. Genes involved in stroma remodeling were upregulated in the “murine” component of the resistant tumors, and upregulation was confirmed by qPCR (normalized to a murine housekeeper gene). Gene set enrichment analysis showed that the upregulated genes in TME of resistant models were enriched for cytoskeleton related functions, while the downregulated genes were enriched for extracellular matrix-related functions. Conclusion: A bioinformatics strategy able to map human and murine reads separately may identify resistance mechanisms attributed to the two tumor subcompartments and could lead to strategies to potentially target each separately or concurrently. Citation Format: Valentina Zanfagnin, Yuanhang Liu, Pritha Chanana, Xiaonan Pritha, Beverly Long, Joe Pathoulas, Brad Evans, Jaime Davila, Chen Wang, Saravut John Weroha. Transcriptional profiling of tumor stroma using ovarian cancer PDX models with induced platinum-resistance [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B18.