Understanding patient-specific responses to anti-cancer therapies and how individual tumors interact with their tumor microenvironment (TME) is a challenging task. To measure the impact of the TME on diverse and clinically-relevant treatments, Zapatero, Tong, and colleagues coupled patient-derived organoid (PDO) and cancer-associated fibroblast (CAF) co-cultures with high-throughput mass cytometry-based assessment of cell state. Using a newly developed "Trellis" algorithm enabled integration and analysis of highly complex, multi-dimensional treatment response data. This work showed that tumor cell response to chemotherapy was associated with both intrinsic and non-intrinsic signaling states, whereby proliferative rate, growth factor signaling and CAFs interaction influenced chemoprotection. Further, the work suggests a potential role for the TME in promoting lineage plasticity associated with drug resistance. In all, the pipeline described provides a blueprint for exploring the intricate interplay of factors influencing cancer treatment response.