Abstract 798: Clonal analysis and clinical translation of pancreatic adenocarcinoma genomes.

A fundamental challenge for the study and translation of pancreatic ductal adenocarcinoma (PDA) genomes in patients in vivo is the presence of varied admixtures of reactive stroma, inflammatory cells, and necrosis within the tumor. Furthermore biopsies frequently contain multiple clonal populations of neoplastic cells that cannot be distinguished on the basis of morphology alone. To overcome the limitations of histopathology based methods we are using DNA content based flow cytometry to identify and purify distinct clonal PDA populations from over 60 surgical samples from a Stand up to Cancer (SU2C) sponsored clinical trial. Sorted tumor populations from each patient have been interrogated with CGH arrays and whole exome sequencing. In addition we have interrogated the genomes of sorted PDA populations from a SU2C phase II trial of liver metastases from 35 patients with advanced previously treated disease, as well as those from a series of rapid autopsy samples. The genes targeted by the somatic aberrations in each tumor genome are overlaid onto a collection of 33 PDA specific maps, containing 763 genes of interest, developed as part of the Metaminer Oncology initiative. An example of the translational potential of these data includes the detection of a homozygous deletion of STAG2 in an aneuploid tumor population present in the primary and in each metastatic site of a rapid autopsy case. Targeted resequencing identified somatic mutations in a small number of additional sorted samples from our patient cohorts. Strikingly genetic and histopathologic analysis of tumors induced by transposon insertion in a KrasG12D genetically engineered mouse model showed that disruption of STAG2 promotes the development of PDA and its progression to metastatic disease. To assess the clinically significance of STAG2 expression in human tumors we screened a TMA containing a collection of 344 specimens obtained from resected patients. In normal tissue nearly all ductal cells stained with a high intensity. There was a statistically significant loss of STAG2 expression in the tumor tissue (Wilcoxon-Rank test). In univariate Kaplan Meier analysis nearly complete STAG2 positive staining (> 95% of nuclei positive) was associated with a survival benefit of median survival of 6.41 months (p = 0.031). Interestingly, the survival benefit of adjuvant chemotherapy was only identified in the group of patients with a STAG2 staining of less than 95% (median survival benefit 7.65 months; p = 0.028). Multivariate Cox Regression analysis showed that STAG2 is an independent prognostic factor for survival in PDA patients. We propose that our unbiased clonal profiling of PDA genomes provides a unique and highly efficient framework to identify clinically relevant genomic events in PDA Citation Format: Michael T. Barrett, Elizabeth Lenkiewicz, Evers Lisa, Pedro Perez-Mancera, David Tuveson, Daniela Aust, Christian Pilarsky, Meraj Aziz, Richard Posner, Ramesh Ramanathan, Victor Velculescu, Amy Kramer, Jeffrey Drebin, Daniel D. Von Hoff. Clonal analysis and clinical translation of pancreatic adenocarcinoma genomes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 798. doi:10.1158/1538-7445.AM2013-798