Pancreatic Adenocarcinoma Therapeutic Targets Revealed by Tumor-Stroma Cross-Talk Analyses in Patient-Derived Xenografts

Preclinical models based on patient-derived xenografts have remarkable specificity in distinguishing transformed human tumor cells from non-transformed murine stromal cells computationally. We obtained 29 pancreatic ductal adenocarcinoma (PDAC) xenografts from either resectable or non-resectable patients (surgery and endoscopic ultrasound-guided fine-needle aspirate, respectively). Extensive multiomic profiling revealed two subtypes with distinct clinical outcomes. These subtypes uncovered specific alterations in DNA methylation and transcription as well as in signaling pathways involved in tumor-stromal cross-talk. The analysis of these pathways indicates therapeutic opportunities for targeting both compartments and their interactions. In particular, we show that inhibiting NPC1L1 with Ezetimibe, a clinically available drug, might be an efficient approach for treating pancreatic cancers. These findings uncover the complex and diverse interplay between PDAC tumors and the stroma and demonstrate the pivotal role of xenografts for drug discovery and relevance to PDAC.

Abstract 4396: Multiomics assessment of the cancer and stromal compartments of patient-derived pancreatic xenografts reveals clinically-relevant subtypes and novel targeted therapies

Patient-derived xenografts (PDX) are appearing as a prime approach for preclinical studies despite being insufficiently characterized as a model of the human disease and its diversity. In this work, 29 PDX were obtained from either surgery or endoscopic ultrasound-guided fine needle aspirate of pancreatic adenocarcinoma. The extensive genomic profiling of these pancreatic PDX, revealed two clinically-relevant subtypes having broad similarities with human primary tumors. These subtypes are defined by highly specific DNA methylation and transcriptomic profiles (mRNA, miRNA or lncRNA) but are not distinguishable by exonic mutations or copy number aberrations. Moreover, by specifically analyzing the stroma transcriptome, as defined by the expression of murine transcripts, we found that it is able to stratify the patients with the same efficiency than the analysis of grafted human tumor cells. This finding suggest that transformed pancreatic cells drive the composition of their own stroma. Finally, the multiomics analysis pinpoints novel therapeutic targets, one of which we demonstrate to be an efficient method for treating pancreatic cancer. Overall, we show that PDX are trustworthy pre-clinical models of pancreatic adenocarcinoma including of unresectable tumors. Their multiomics profiling allow the independent analysis of the uncontaminated cancer or stromal compartments and discloses several original therapeutics targets.

Citation Format: Remy Nicolle, Yuna Blum, Laetitia Marisa, Celine Loncle, Odile Gayet, Vincent Moutardier, Olivier Turrini, Marc Giovannini, Benjamin Bian, Martin Bigonnet, Marion Rubis, Nabila Elarouci, Lucile Armenoult, Mira Ayadi, Pauline Duconseil, Mohamed Gasmi, Mehdi Ouaissi, Aurélie Maignan, Gwen Lomberk, Jean-Marie Boher, Jacques Ewald, Erwan Bories, Jonathan Garnier, Anthony Goncalves, Flora Poizat, Jean-Luc Raoul, Veronique Secq, Stephane Garcia, Philippe Grandval, Marine Barraud-Blanc, Emmanuelle Norguet, Marine Gilabert, Jean-Robert Delpero, Julie Roques, Ezequiel Calvo, Fabienne Guillaumond, Sophie Vasseur, Raul Urrutia, Aurélien de Reyniès, Nelson Dusetti, Juan Iovanna. Multiomics assessment of the cancer and stromal compartments of patient-derived pancreatic xenografts reveals clinically-relevant subtypes and novel targeted therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4396. doi:10.1158/1538-7445.AM2017-4396

Abstract A48: Multi-omics characterization of PDAC subtypes using PDX reveals that epigenetic but not genetic analysis permit a clinically relevant classification

Genome-wide molecular profiles have been proven to be beneficial for the identification of clinically relevant tumor subtypes in many neoplastic diseases. While pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-related death, very few genomic and transcriptomic studies have been conducted. This is mainly due to the difficulty to obtain a suitable cohort of PDAC tumor samples. The major obstacle is the usually high proportion of non-transformed stromal cells, which can greatly hinder the analysis of carcinogenic-specific processes. Moreover, tumor cohorts requiring resection samples can be biased by the exclusion of inoperable patients, representing 85% of all patients presenting PDAC.

In this study, we generated Patient Derived Xenografts (PDX) with samples collected from 29 patients using either Endoscopic Ultrasound-Guided Fine-Needle Aspirates or, for operable patients, resections. The transcriptomic profiles, of both mRNA and miRNA, and the epigenetic landscape of early PDX passages consistently identified two tumor-specific molecular subtypes: a well differentiated group often referred to as classical, and an undifferentiated group previously recognized as Basal, Quasi-Mesenchymal or Squamous. Of all the genetic alterations determined by Copy Number analysis and exome sequencing, none were specific to any of the two subtypes, which therefore could not be discriminated solely on genetic basis.

These two PDAC subtypes are characterized by distinct epigenetic and transcriptomic profiles of which the analysis revealed the deregulation of several pathways previously imputed in PDAC development and carcinogenesis in general. In particular, we showed that the Wnt pathway as well as several metabolic pathways, including cytochrome P450 genes recently implicated in drug resistance, are both epigenetically and transcriptionally deregulated. Altogether, our results provide new insights on pancreatic carcinogenesis and suggest that PDAC phenotypical heterogeneity is mainly driven by epigenetic rather than genetic events.

Citation Format: Remy Nicolle, Yuna Blum, Laetitia Marisa, Jonathan Garnier, Benjamin Bian, Celine Loncle, Martin Bigonnet, Odile Gayet, Vincent Moutardier, Pauline Duconseil, Mohamed Gasmi, Mehdi Ouaissi, Olivier Turrini, Marc Giovannini, Aurélie Maignan, Jean-Marie Boher, Jacques Ewald, Erwan Bories, Marc Barthet, Anthony Goncalves, Flora Poizat, Jean-Luc Raoul, Veronique Secq, Stephane Garcia, Philippe Grandval, Marine Barraud-Blanc, Emmanuelle Norguet, Marine Gilabert, Jean-Robert Delpero, Ezequiel Calvo, Aurélien de Reyniès, Nelson Dusetti, Juan Iovanna.{Authors}. Multi-omics characterization of PDAC subtypes using PDX reveals that epigenetic but not genetic analysis permit a clinically relevant classification. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr A48.

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 shows an upregulation of complementary genes associated with several metabolic pathways.

Taken together, our transcriptomic analysis reveals that human transformed pancreatic cells determine the composition, quantitatively and qualitatively, of stroma mouse cells in a PDX model. This model also reveals a broad variability of PDAC stromas and highlights potential cross-talks between them through known and novel pathways.

Citation Format: Rémy Nicolle, Yuna Blum, Laetitia Marisa, Jonathan Garnier, Benjamin Bian, Celine Loncle, Martin Bigonnet, Odile Gayet, Vincent Moutardier, Pauline Duconseil, Mohamed Gasmi, Mehdi Ouaissi, Olivier Turrini, Marc Giovannini, Aurélie Maignan, Jean-Marie Boher, Jacques Ewald, Erwan Bories, Marc Barthet, Anthony Goncalves, Flora Poizat, Jean-Luc Raoul, Veronique Secq, Stephane Garcia, Philippe Grandval, Marine Barraud-Blanc, Emmanuelle Norguet, Marine Gilabert, Jean-Robert Delpero, Ezequiel Calvo, Aurélien de Reyniès, Juan Iovanna, Nelson Dusetti.{Authors}. Pancreatic cancer cell drives stroma composition. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr B72.