LMTK3 regulates breast cancer angiogenesis via a context-dependent mesenchymal-epithelial transition program

Abstract Angiogenesis constitutes a critical rate-limiting determinant of tumor progression in breast cancer (BC). Resistance to conventional anti-angiogenic therapies in BC highlights an unmet need to identify upstream molecular regulators coordinating malignant cell plasticity and vascular remodeling. Lemur tail kinase 3 (LMTK3) is a well-established oncogenic kinase; however, its specific role within the tumor angiogenic microenvironment remains undefined. Here, we identify LMTK3 as a context-dependent driver of angiogenesis through a mesenchymal-epithelial transition (MET) program. By integrating single-cell RNA sequencing with functional validation, we uncover a ‘Simpson’s paradox’ (where a correlation present in different groups disappears or reverses when combined): In mesenchymal-like triple-negative breast cancer (TNBC), LMTK3 promotes a pro-angiogenic, ‘partial EMT’ (p-EMT) state characterized by sustained ERK signaling and elevated secretion of angiogenic factors, including angiogenin. Conversely, in luminal-like cells, LMTK3 enforces a hyperepithelialized state that suppresses angiogenic phenotypes. Consequently, LMTK3 emerges as a central regulator of angiogenic plasticity, and its targeted inhibition offers a promising strategy to abrogate the pro-angiogenic p-EMT state and promote vascular normalization in TNBC.