A proteogenomic atlas of 1032 brain metastases identifies molecular subtypes, immune landscapes, and therapeutic vulnerabilities

The molecular heterogeneity of brain metastases hampers therapeutic development for cures. To address this unmet and urgent need, we construct a comprehensive multi-omic, single cell, and spatially resolved atlas of 1,032 pan-cancer brain metastases, identifying four robust molecular subtypes with distinct biological programs and clinical associations. These brain metastases subtypes (BrMS) are defined by unique biological states: neural-like (BrMS1), metabolic (BrMS3), highly proliferative/immune-excluded (BrMS4), and an immune-infiltrated (BrMS2) state featuring a coordinated epithelial-mesenchymal transition program. Patient-derived organoids coupled with targeted drug screening indicate subtype-specific molecular dependencies and putative targets, notably mTOR signaling activation in BrMS3 and CDK4/6 axis activation in BrMS4, while BrMS1 and BrMS2 display distinct radiobiologic and immunologic signatures. This atlas provides a rigorous classification framework of BrMs and offers insights into subtype-specific molecular vulnerabilities. The molecular heterogeneity of brain metastases (BrMs) poses challenges for their treatment. Here, the authors generate a multi-omic, single cell, and spatially resolved atlas of 1,032 pan-cancer BrMs and identify four molecular subtypes with distinct biological and clinical features.