Abstract B72: Pancreatic cancer cell drives stroma composition

The extensive desmoplasia in pancreatic ductal adenocarcinoma (PDAC) has raised major interrogations on its role and function in the carcinogenic process. Patient-derived xenograft (PDX) offers an ideal setting to distinguish and to study the interactions between the cancerous epithelial cells and its stroma. Indeed, sequencing profiles of a mix of cancerous/Human and stroma/Mouse cells can be analyzed separately in silico by unambiguously assigning each sequence to the human or mouse genome. Using RNA sequencing, we profiled 30 pancreatic tumor PDXs and extracted the transcriptome profiles of epithelial cancerous cells as well as their corresponding stroma. On average, 70% of RNA sequencing reads were specifically attributed to a human origin, and therefore an epithelial origin, while 22% of RNA sequencing reads were mouse-specific. Using the rate of mouse sequences as a surrogate of the proportion of non-transformed cells, we observe a high variability in the infiltration level from 7% to 60%. The estimation was also consistent in whole exome sequencing (using the same sequencing process) and with the histological quantification of fibrotic tissue. By specifically analyzing the gene expression in mouse-stromal cells, we show that their transcriptomic profile is consistent with the recent description of human PDAC in situ tumors with high levels of genes of the reported activated-stroma and normal-stroma signatures. We also show that stromal cells over-express genes involved in the SLIT/ROBO axon guidance signalling pathway, in angiogenesis as well as a large number of collagens, cytokines and ligands associated with growth and developmental pathways. Recent studies identified two major subtypes of PDAC from transcriptomic analysis: a well differentiated, often referred as classical, and an undifferentiated, previously recognized as Basal, Quasi-Mesenchymal or Squamous. The stroma characterized in this work broadly reflects this heterogeneity with stromal gene expression signatures predictive of each subtype. For instance, collagens are significantly over-expressed in the stroma of squamous tumors. The concomitant analysis of transcriptomic profiles of both subtypes shows potential cross-talks between cancerous and stromal cells. Particularly in Squamous tumors, genes implicated in the axon-guidance and Wnt pathways are significantly upregulated in both, stroma and transformed cells. On the other hand, the stroma and transformed cells of Classical tumors