Data Sheet 1_Plasma multi-omics reveals molecular remodeling and prognostic biomarkers in advanced breast cancer treated with trastuzumab deruxtecan.docx

However, treatment outcomes remain heterogeneous, and circulating molecular correlates of treatment and prognosis are incompletely defined.</p>Methods<p>Twenty-nine patients receiving T-DXd were included in the clinical cohort, of whom 16 provided paired pre- and post-two-cycle plasma for multi-omics profiling.

Proteomics used 4D-DIA LC-MS/MS; metabolomics used UHPLC-high-resolution MS in positive/negative modes. Treatment-associated features were identified by paired statistics, fold change, and multivariate criteria, followed by enrichment, correlation, joint pathway mapping, and exploratory PFS-oriented Cox/LASSO-Cox analyses.</p>Results<p>Proteomics identified 4,444 proteins; 508 were differentially expressed (136 up, 372 down), enriched in translation/ribosome, complement/coagulation, acute-phase, cytoskeletal/adhesion, and lipid transport pathways.