Multi-Omics Analysis Identifies Paxillin as a Biomarker of Doxorubicin Resistance via Cytoskeletal Remodeling and Immune Exhaustion

Chemotherapy resistance remains a primary cause of treatment failure in breast cancer, yet the global proteomic landscape driving this phenotype has not been completely understood. In this study, we employed a systematic multiomics approach, integrating quantitative proteomics of doxorubicin-resistant cells with transcriptomic and proteomic data from large-scale clinical cohorts (TCGA and FUSCC). Our analysis revealed a fundamental functional dichotomy in resistant cells, where a downregulation of metabolic processes contrasts with a robust upregulation of cytoskeletal and focal adhesion complexes. Through machine learning and interaction network analyses, we identified the focal adhesion scaffold paxillin (PXN) as a central hub driving resistance and a robust prognostic marker for poor recurrence-free survival in chemotherapy-treated patients. Mechanistically, PXN orchestrates a “cell adhesion-mediated drug resistance” program by an extracellular matrix-focal adhesion-cytoskeleton axis, driving extensive extracellular matrix remodeling and stiffening via the upregulation of cross-linking enzymes and protease inhibitors. This structural remodeling reprograms the tumor microenvironment, inducing an immunosuppressive state where PXN-high tumors exhibit increased CD8⁺ T cell infiltration, but these lymphocytes are functionally exhausted and fail to execute cytotoxic responses. In summary, our findings reveal a novel resistance axis where PXN connects the intracellular cytoskeleton and extracellular matrix remodeling. This reprograms the tumor microenvironment and immune cell cytotoxicity, highlighting PXN as a critical target for overcoming chemoresistance.