Genetic barcoding uncovers the clonal makeup of solid and liquid biopsies and their ability to capture intra-tumoral heterogeneity

Abstract Intratumoral heterogeneity (ITH) is fueling tumor progression in breast cancer, as specific clones present within a tumor may have a selective advantage to colonize distant organs and escape therapy. Accurate sampling of ITH is therefore a pressing challenge in clinical oncology to adequately predict recurrence and inform rational and personalized therapies. Here, we used genetic barcoding to track the spatiotemporal composition of human breast cancer clones in six preclinical models—across two cell lines and four patient-derived xenografts (PDXs). This allowed a direct side-by-side quantitative comparison of both intra-tumor clonal composition and how that composition was reflected in needle biopsies and cell-free DNA (cfDNA). These analyses highlighted several biologically and clinically relevant findings. First, the use of barcoding revealed that clonal diversity in the center of non-necrotic primary tumors was significantly higher than in the periphery. Second, cfDNA barcode analysis suggested that DNA ‘shedding’ in the vasculature varied widely, not only depending on necrosis and tumor burden but also across models. Third, combining information captured in both solid and liquid biopsies can provide a more robust assessment of tumor clonal composition. Taken together, these results showcase the utility of these barcoded models to optimize the use of solid and liquid biopsies as surrogates of tumor heterogeneity.