Abstract B17: A prioritization pipeline for the identification of somatic driver aberrations in pancreatic cancer.

Abstract

Pancreatic cancer is a notoriously lethal disease that remains one of the most challenging malignancies to treat successfully. The development of improved therapeutics will require a better understanding of the molecular pathways driving tumor progression. Recognizing this, groups such as the International Cancer Genome Consortium (ICGC) are cataloging genomic aberrations across major tumor lineages that include pancreatic cancer. These efforts are revealing an extraordinary level of genome complexity made up of not only key “driver” events critical to pathogenesis, but also numerous biologically neutral “passengers” inherent to unstable tumor genomes. The challenge now is to find ways to identify functional driver aberrations, as targeting such events or their activated molecular pathways has the greatest hope of improving patient outcomes. Efficient driver identification requires robust pipelines to prioritize the thousands of putative targets emerging from genomics studies. Unfortunately, little progress has been made toward developing gain-of-function systems for validating overexpressed or activated oncogenes, which are especially attractive given the efficacy of antibody and small molecule inhibitor therapies. To identify such factors in melanoma, we recently reported high-throughput strategies used to functionally prioritize 18 of 230 genes whose overexpression promotes oncogenicity, metastasis and prognosticates clinical outcome across several cancer types (Scott et al., Cancer Cell , 2011, 20: p. 92-103). This study demonstrates that our function-based approach is a powerful means to identify drivers of tumor progression with both prognostic and therapeutic potential. The success of this study motivated us to expand our screening platform to ~35,000 sequence-verified open reading frames (ORFs, hereafter termed “genes”). We have developed key protocols permitting high-throughput gene processing and virus production for infecting screenable “target” cells for entry into screen-based assays. We are using these tools to implement a screening infrastructure permitting high-content genetic screens to accelerate validation of functional somatic aberrations driving pancreatic cancer. This work is made possible through several recent advances made in our laboratory that include (1) high-throughput, highly accurate modeling of somatic mutations into our gene collection and (2) a novel molecular barcoding approach that facilitates cost-effective detection of driver events followingin vitro and in vivo functional screens. We are collaborating with the Baylor College of Medicine Human Genome Sequencing Center to select up to 500 somatic events for modeling into our gene collection. An important feature of our system is that target cells, once infected with a particular gene library, can be simultaneously entered into parallel screens to maximize discovery potential (e.g., screens for drivers of cell invasion, anchorage-independent growth, gemcitabine resistance, etc.). While cell-based screening systems like these are tractable, in vitro models do not fully recapitulate all hallmarks of tumorigenesis and metastasis. Therefore, we have also developed an in vivo positive selection screen using a pooled virus approach permitting detection of single and combinatorial drivers of pancreatic tumor progression. In summary, our goal is to employ a novel screening platform to discover functionally important cancer genes identified by pancreatic cancer sequencing efforts. Our “prioritization pipeline” will provide the cancer research community information on the most promising somatic aberrations for drug development, which is critical for pancreatic cancer given its devastating clinical course and abysmal response to standard therapies. Citation Format: Turgut Dogruluk, Armel Gifford, Marie-Calude Gingras, Kenneth L. Scott. A prioritization pipeline for the identification of somatic driver aberrations in pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Progress and Challenges; Jun 18-21, 2012; Lake Tahoe, NV. Philadelphia (PA): AACR; Cancer Res 2012;72(12 Suppl):Abstract nr B17.