Pathway Discovery and Target Validation for Outgrowth of Breast Cancer Metastases

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PROJECT SUMMARY The overwhelming majority of deaths from cancer are attributable to metastasis, rather than growth of the primary tumor. In breast cancer, metastatic recurrence can occur years to decades after apparently successful surgery. Current methods do not allow individualized assessment of metastatic recurrence risk nor do they offer effective therapies for metastatic breast cancer patients. Breast cancer presents a unique research opportunity because the long interval between surgery and recurrence offers the potential to improve patient outcomes if effective anti-metastatic therapies could be developed. However, few drug discovery efforts to date have focused on the metastatic process specifically. The challenges we address are developing and applying methods to identify the basic mechanisms of metastasis, then prioritizing and validating genes and proteins as potential therapeutic targets. Our approach combines advances in experimental (Ewald) and computational (Bader) methods that we have developed to interrogate the metastatic process and to systematically dissect the genetic basis of human disease. Experimentally, we will use a pipeline that relies on organoids from primary human breast cancer tissue to model several distinct steps of metastasis: invasion into the surrounding matrix, dissemination of cancer cell clusters, and outgrowth of these clusters molecular models of distant organs. Computationally, we have developed and applied powerful methods to connect quantitative traits to their genetic basis across multiple complex human disease. We will now apply these computational methods to dissect the molecular basis of breast cancer metastasis. The central insight of our proposal is that the known heterogeneity of breast tumors, while confounding to other methods, enables our quantitative trait loci approach. We will exploit this heterogeneity with computational methods that have the potential to identify the molecular differences between primary human breast tumor organoids that demonstrate metastatic vs. non-metastatic cell behaviors (Aim 1). We will use network analysis techniques to prioritize these as targets, and then use a combination of mammalian genetic engineering and small molecule perturbations to validate targets first in the organoid system and then in accepted mouse PDX models for metastatic growth (Aim 2). Finally, we will combine our novel target based approaches with chemical and genetic perturbagens from the CTD2 Network and broader drug discovery efforts (Aim 3). In this way, we can build on existing knowledge to accelerate our progress towards improved patient outcomes. Success of this program will provide clinically actionable targets for preventing metastatic recurrence or treating patients with established breast cancer metastases. Importantly, our approaches can provide a general platform for dissecting metastasis across epithelial cancers.