Engineering the Cancer Genome

Over the past several years, my laboratory has employed gene targeting technology to create a series of mouse models of cancer that share genetic and pathological features of the cognate diseases in humans. We have focused particularly on models of lung cancer, both adenocarcinoma and small cell lung cancer. These models have been subjected to various types of molecular characterization, including mRNA profiling and exome/whole-genome sequencing. These efforts have defined genes and pathways that promote tumor progression and metastasis, including in the case of the adenocarcinoma model down-regulation of the lineage-restricted transcription factor Nkx2.1 and other transcriptional regulators that are involved in inducing and enforcing various differentiation states that might limit tumor progression. We have also studied the involvement of subpopulations of tumor cells in this model in which the Wnt signaling pathway is active. Data from lineage tracing experiments are consistent with this population having increased tumor propagating potential. In order to functionally characterize these and other cancer genes, we have recently developed methods to mutate genes in developing tumors using the CRISPR/Cas9 system. Using tri-functional lentiviral, we have developed tumors that have undergone Cas9-mediated mutation of a series of genes of interest. Several examples of the application of this method will be reviewed. As another example of cancer genome manipulation, we have engineered tumors of the lung and other sites to express specific T cell antigens and/or NK cell ligands. These models have allowed a detailed investigation of adaptive and innate immune responses to a developing tumor. We have used the models to explore mechanisms of immune suppression in cancer and develop methods to elicit improved anti-tumor immune responses.