Spatial proteomic profiling reveals an association between NF1-Ras/Raf/MEK signaling and immune cell infiltration in locally advanced triple-negative breast cancer

Background Triple-negative breast cancer (TNBC) is a highly aggressive malignancy characterized by significant molecular heterogeneity with a limited range of targeted therapy options. Better resolution of the spatial interactions between tumor cells and the immune microenvironment is essential for identifying actionable vulnerabilities. Methods Here we employed GeoMx Digital Spatial Profiling (DSP) to investigate the proteomic landscape of 72 immuno-oncology biomarkers in normal breast, primary breast cancer, and metastatic axillary lymph node tissues of treatment-naïve TNBC patients (n=29) who underwent upfront breast surgery. Results Through comprehensive profiling, we identified the tumor suppressor protein, neurofibromin (NF1), as one of the vulnerabilities in TNBC. Spatially resolved analysis revealed that NF1 downregulation is strongly associated with Ras/Raf/MEK pathway activation. This downregulation of NF1 level was characteristic of tumor regions with a high representation of tumor infiltrating lymphocytes (TILs). Furthermore, low NF1 levels significantly correlated with reduced disease-free survival, suggesting its potential clinical utility as a biomarker. We also observed a high degree of proteomic similarity between primary breast tumors and the matched lymph node metastases. Conclusions These findings advance our understanding of TNBC spatial proteomic profiles and suggest that targeting the NF1-Ras/Raf/MEK axis may offer novel strategy for clinical management of TNBC patients with immune “hot” tumors.