Mapping tumor heterogeneity: ex-vivo drug responses in matched primary and metastatic tumors using a 3D functional precision platform

Introduction: Tumors are known to develop genomic heterogeneity over time, particularly in metastatic disease, raising concerns that a single-site biopsy may be insufficient to accurately predict response to medications. Methods: We used our 3D microtumor functional profiling platform that preserves key features of the native tumor microenvironment. We tested (i) six split samples from primary tumors and (ii) seven samples from primary tumors (ovarian, colon, and breast cancer) matched with their locoregional or distant metastases. Fresh tissue specimens were processed within 24 hours after surgery and treated with NCCN guideline-recommended chemo or targeted therapies at concentrations over four orders of magnitude. Cytotoxicity was evaluated after three days to generate dose response curves. The response correlations between the split sample or between the two matched sites were quantified using the concordance correlation coefficient ({rho}c) for the drug efficacy metrics. Results: We compared a total of 275 drug responses. The six split samples resulted in a strong correlation between the two tumor areas ({rho}c=0.95, p<0.001), supporting high assay reproducibility across distinct regions of the same tumor. Locoregional metastases were highly correlated with their primaries (ovarian to omentum {rho}c=0.97, p<0.001; ovarian to liver capsule {rho}c=0.93, p<0.001; colon to peritoneum {rho}c=0.91, p<0.001). A lesser correlation was observed with lymphogenic metastases (breast to axilla {rho}c=0.87, p<0.001), and the correlations of hematogenic metastases were even lower (colon to lung {rho}c=0.69 p<0.001; ovarian to soft tissue/colon {rho}c=0.58, p<0.001). No correlation was observed among specimens that were resistant to all tested medications. Conclusion: Tumor drug responses were highly preserved in locoregional metastases, whereas somewhat greater divergence was observed in lymphogenic or hematogenic metastases. Single-site functional profiling may remain informative for identifying treatment resistance and might reduce the risk of ineffective therapy selection in metastatic disease.