An in vivo platform to jointly monitor cellular and metabolic responses to chemotherapy.

Abstract

How drug treatments reshape immune and metabolic states within intact tumors remains difficult to study with existing methods. We introduce a spatial pharmacology platform that enables parallel analysis of multiple agents within a single tumor, linking local drug exposure to immune and metabolic remodeling. Using a microdevice for localized drug delivery, we created a large-scale paired CyCIF-MALDI dataset spanning 1.5 million cells across 27 MMTV-PyMT tumor sections and nine treatment programs, enabling integrated spatial pharmacology at unprecedented scale. Metabolic signatures robustly predict proteomic spatial neighborhoods establishing metabolism as a powerful predictor of tumor organization and immune phenotype. Within this framework, we identify a dominant metabolic axis defined by the myeloid polarization between CSF1R+ tumor-associated macrophages and MPO+ infiltrating myeloid cells localized near regions of drug-induced tumor cell death. Finally, we detect putative lipid-associated macrophage (LAM)-like populations within drug-resistant treatment regions.