PROJECT SUMMARY Patients with aggressive cancers often present with no pharmacologically actionable mutations and poor or no sensitivity to immune checkpoint blockade, thus deriving only modest improvement in disease-free survival from targeted therapy and immunotherapy. Tumor heterogeneity adds further complexity by fostering reprogramming, adaptation, selection, and ultimately expansion of drug-resistant cells, as well as emergence of an immunosuppressive tumor microenvironment (TME), both of which are ultimately responsible for patient relapse and poor outcome. Addressing these challenges—i.e., identifying more universal, mechanism-based targets for pharmacological intervention and assessing their potential value in highly heterogeneous tumors—is critically dependent on the availability of accurate, comprehensive, and cell type-specific molecular interaction networks (cellular networks, hereafter), which underlie both the cell-autonomous behavior of cancer cells and their interaction with other TME subpopulations. The proposed Cancer Systems Therapeutics (CaST) Center, will continue its highly productive collaboration within the U54 Cancer Systems Biology Center (CSBC) network by extending its successful network-based methodologies—which integrate cutting edge computational advances and novel experimental technologies, including use of 3D structure and multi-omics-based evidence. This will support studying cancer as a fully integrated system of co-evolving, interacting subpopulations, comprising both molecularly distinct, coexisting malignant cell states as well as non-malignant cell states recruited to the tumor microenvironment and potentially reprogrammed to implement a pro-malignant, immunosuppressive milieu. The ultimate goal of this proposal is to leverage recent advances by CaST center investigators to elucidate the Mechanism of Action of clinically relevant drugs and late-stage experimental compounds to target individual subpopulation to either drive combination therapy or to rescue immunotherapy in drug resistant tumors.

PROJECT NARRATIVE The proposed Center for Cancer Systems Therapeutics (CaST) will seek to perform systematic, single-cell- level elucidation of stable cell states and state transitions in tumor-related cells and in their tumor microenvironment (TME) to identify and target complementary dependencies leading to mechanism-based combination therapy trials. This will provide a more holistic understanding of the fundamental steps underlying tumor initiation and progression and of the critical mechanisms that can be targeted pharmacologically to transform cancer treatment. Critically, we have shown that the Systems Biology framework developed by CaST Center investigators can effectively generalize to virtually any tumor of interest leading to highly innovative, biomarker-based interventional trials, thus accelerating progression from biological analysis to cures.