Biomimetic organo-specific scaffolds reveal lineage-specific adaptations of breast cancer cells in bone metastasis

Bone metastasis is a major clinical complication of breast cancer, regulated by dynamic interactions between disseminated tumor cells and the bone extracellular matrix (ECM). Experimental models that accurately replicate the biochemical, structural, and mechanical features of the bone niche remain limited. Here, we engineered three-dimensional organo-specific ECM scaffolds to investigate how bone-mimetic matrices regulate breast cancer cell behavior, phenotypic plasticity, and therapeutic response. Collagen-based scaffolds mimicking primary breast tumor ECM and collagen–hydroxyapatite (coll-HA) scaffolds reproducing bone ECM were developed. Physicochemical characterization confirmed that coll-HA scaffolds showed effective hydroxyapatite integration, trabecular-like organization, physiological porosity, and elastic properties consistent with the bone metastatic niche. Upon cellularization with breast cancer cells, the scaffolds reproduced key histological features and tumor cell morphologies observed in human bone metastasis. Using four breast cancer cell lines representative of distinct molecular subtypes and degree of bone tropism, we demonstrated that organo-specific ECMs profoundly influence cell growth dynamics and phenotypic plasticity. In the bone-mimetic niche, tumor cells exhibited reduced proliferation and adopted subtype-specific epithelial–mesenchymal states. Transcriptomic profiling revealed lineage-dependent metabolic reprogramming and modulation of bone metastasis-associated signaling. The bone-mimetic ECM also enhanced tumor cell sensitivity to bone-targeted therapies and osteoclastogenic ability, highlighting the role of tumor–ECM interactions in shaping the osteolytic microenvironment. Collectively, organo-specific ECM scaffolds provide a physiologically relevant platform to study breast cancer adaptation to the bone microenvironment, offering mechanistic insights into microenvironment-driven plasticity, metabolism and therapeutic vulnerabilities, with implications for improving treatments for bone metastatic disease.