e15199 Background: Trastuzumab deruxtecan (T-DXd) has transformed the treatment of breast cancer brain metastases (BCBM). However, approximately half of patients exhibit acquired resistance, and no predictive biomarkers have been clinically established. Since antibody-drug conjugate (ADC) efficacy depends on the unique brain microenvironment and intracellular processing, we applied spatial multiomics to resolve tumor- and niche-specific resistance mechanisms. Methods: Pre-treatment BCBM specimens from T-DXd responders (R) and non-responders (NR) were profiled using Bruker GeoMX for spatial proteomics and whole transcriptome analysis (n = 2 R, 2 NR; 5-10 ROIs per specimen). Additionally, Bruker CosMX single-cell spatial transcriptomics was employed for pathway enrichment and cell crosstalk analyses (n = 3 R, 3 NR; 200 ROIs per specimen). Results: GeoMX analysis identified fibronectin as a potential spatial biomarker—the significantly stronger spatial correlation with T cell markers (CD3, CD4, CD8) in NR (p 3.4, FDR q < 0.01 for all). These findings are mechanistically consistent with the requirements of efficient intracellular processing and lysosomal cleavage for ADC payload release. Conclusions: To summarize, two plausible mechanisms of T-DXd resistance in BCBM were identified: 1) remodeling of the immune-glial niche associated with fibronectin and S100A8/9, and 2) impaired intracellular trafficking. Hence, the novelty of this research lies in uncovering potential biomarkers beyond the HER2 and topoisomerase I genes. Future work will explore these spatial signatures as high resolution biomarkers to stratify patients and nominate strategies to restore ADC efficacy in the CNS.
Das et al. (2026) studied this question.