In vivo proteomic labeling reveals diverse proteomes for therapeutic targets

Proteomics is transforming medical sciences, but bridging isolated samples with intact in vivo microenvironments remains a major hurdle. We present an in vivo proteomic labeling (IVPL) platform built on a new substrate, Btn-Ph-3F, and engineered ascorbate peroxidase (APEX2)-EGFP^f/f mice. Btn-Ph-3F shows high stability in organs possessing complex microenvironments, while APEX2-EGFP^f/f mice readily cross with commercial Cre lines, enabling specific proteomic labeling for customized cell groups in distant organs. IVPL robustly profiles in situ proteomes of intestinal epithelium, mammary gland, and tumor-infiltrating T_reg cells, and, critically, labels trace exogenous proteomes from patient-derived exosomes in live mice. We identify lactate dehydrogenase A-like 6A (LDHAL6A) as a persisting exosomal effector that promotes malignant programs in recipient cells. Inhibition of LDHAL6A combined with paclitaxel treatment markedly suppresses triple-negative breast cancer growth and metastasis. Collectively, our work not only establishes an advanced model for IVPL but also profiles ultimately exosomal actors in recipient organs for targeted therapy.