Abstract Breast tumors comprise several sub-populations of cells, so-called “clones”, with specific cellular and molecular characteristics. Some cancer clones can be more ‘aggressive’ than others in particular tumor microenvironments (TMEs), contributing to metastatic progression and drug resistance. Understanding the specific genes/pathways deregulated in these aggressive cancer cells is essential for developing new tailored treatment strategies. To accomplish this, we optimized the use of a lentiviral-based barcoding technique (Berthelet, J., et.al., Sci Adv 2021, Serrano, A., et.al., Nat Rev Cancer 2022) where cancer cells from cell lines and patient-derived xenografts are tagged with optical barcodes and transplanted into the mammary fat pads of immunodeficient mice. Upon resection of tumors and collection of metastatic organs at the experimental endpoint, we analyzed clonal fate and fitness using flow cytometry and imaging. The subsequent molecular characterization of individual clones was determined by bulk and single-cell RNA sequencing. We also leverage the use of these barcoded models to investigate the mechanisms of innate and acquired resistance to Sacituzumab Govitecan (SG), a drug recently approved for the treatment of patients with advanced breast cancer. Our studies revealed unique gene signatures and pathways associated with preferential organ tropism (in the lungs, liver and brain TMEs) and SG resistance. This comprehensive analysis, currently validated using autopsy samples and patient databases, will support the design of new predictive markers and targeted therapies for metastatic breast cancer. Citation Format: Sreeja Reddy Gadipally, Jean Berthelet, Samuel C. Lee, Dharmesh D. Bhuva, Michael Roach, Farrah El-Saafin, Caroline Bell, Yunjian Wu, David Baloyan, Christphe Ginestier, Charafe Jauffret Emmanuelle, Melissa Davis, Robin L. Anderson, Luciano Martelotto, Belinda Yeo, Delphine Merino. Exploring breast cancer heterogeneity in the context of metastatic tumour microenvironments and therapy resistance [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr B005.
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