Identifying Tumor Maintenance Genes

We are also using RNAi to systematically identify genotype-specific drug targets. While many investigators focus on human-derived cancer cell lines for these studies, our efforts heavily use murine model systems, owing to the defined nature of the driving genetic events and our ability to rapidly extend results to in vivo systems. By combining inducible RNAi systems and linked fluorescent reporters, many candidate tumor maintenance genes can be identified and rapidly triaged to focus on those that show the most promise. Although our efforts to combine technologies for target discovery focus on a variety of cancers, our initial successes have come largely from the study of hematopoietic malignancies.

One area of investigation focuses on the identification of tumor maintenance genes in mouse models of refractory acute myeloid leukemia (AML). For example, by characterizing how MLL fusion proteins promote self-renewal, we identified the Myb transcription factor as specifically required for the maintenance of AMLs that are refractory to conventional chemotherapy, such that transient suppression of Myb eradicates these leukemias  (1). With Christopher Vakoc (CSHL), we screened an shRNA library targeting “epigenetic” regulators and have identified several histone-modifying activities whose suppression causes the selective arrest or death of leukemic cells. These approaches identified Brd4 as a therapeutic target for acute myeloid leukemia  (2). More recently, we showed that IDH2 mutant genes found in human AML cooperate with oncogenic ras or altered Flt3 to drive aggressive leukemia in mice, and that IDH2 could have anti-leukemic effects (3). Interestingly, these IDH2 mutant leukemias were also sensitive to Brd4 inhibition, which worked rapidly to eliminate the leukemic cells.

Recent efforts have expanded our target discovery efforts to solid tumors. As one example that illustrates our overall approach, we developed and used a mouse model that recapitulates the genetics and pathology of human cholangiocarcinoma (bile duct cancer) to validate the FIG-ROS fusion protein as a therapeutic target in this disease (Figure 4). Specifically, our studies produced a rapid “mosaic” model of cholangiocarcinoma and tested the impact of constitutive and conditional FIG-ROS expression in this system  (5). We showed that FIG-ROS could dramatically accelerate disease onset and that subsequent inhibition of the fusion protein in vivo could have anticancer effects. With Brian Druker (OHSU), we then used these models to demonstrate efficacy of a new ROS inhibitor that is now in clinical trails against FIG-ROS mutant cancers  (4). We are continuing to perform similar screening and modeling approaches to discover and validate new therapeutic targets in several tumor types.

Figure 4.  A mouse model of intrahepatic cholangiocarcinoma used to validate FIG-ROS as a therapeutic target. -- Hepatoblasts are isolated from Kras mutant/p53 mutant mice and transduced with vectors expressing a gene or shRNA of interest. Cells are transplanted orthotopically into the liver where they produce a cancer mirroring the human disease (Saborowski et al., Proc Natl Acad Sci U S A, 2013).

  1. Zuber, J., Rappaport, A.R., Luo, W., Wang, E., Chen, C., Vaseva, A.V., Shi, J., Weissmueller, S., Fellmann, C., Taylor, M.J., et al. (2011). An integrated approach to dissecting oncogene addiction implicates a Myb-coordinated self-renewal program as essential for leukemia maintenance. Genes Dev 25, 1628-1640.

  2. Zuber, J., Shi, J., Wang, E., Rappaport, A.R., Herrmann, H., Sison, E.A., Magoon, D., Qi, J., Blatt, K., Wunderlich, M., et al. (2011). RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 478, 524-528.

  3. Chen, C., Liu, Y., Lu, C., Cross, J.R., Morris, J.P.T., Shroff, A.S., Ward, P.S., Bradner, J.E., Thompson, C., and Lowe, S.W. (2013). Cancer-associated IDH2 mutants drive an acute myeloid leukemia that is susceptible to Brd4 inhibition. Genes Dev 27, 1974-1985.

  4. Davare, M.A., Saborowski, A., Eide, C.A., Tognon, C., Smith, R.L., Elferich, J., Agarwal, A., Tyner, J.W., Shinde, U.P., Lowe, S.W., et al. (2013). Foretinib is a potent inhibitor of oncogenic ROS1 fusion proteins. Proc Natl Acad Sci U S A 110, 19519-19524.

  5. Saborowski, A., Saborowski, M., Davare, M.A., Druker, B.J., Klimstra, D.S., and Lowe, S.W. (2013). Mouse model of intrahepatic cholangiocarcinoma validates FIG-ROS as a potent fusion oncogene and therapeutic target. Proc Natl Acad Sci U S A 110, 19513-19518.