Fig. 2
Differential protein expression in patients with different response groups. (A) Spatial proteomics profiling was conducted on tissue samples from R/M HNSCC tumor tissues. Demarcation of tissues was achieved through masking PanCk + and PanCk- regions to delineate tumor and stromal compartments, respectively. The morphology markers included PanCk (green), CD45 (red), and SYTO 13 (blue) for the tumor cells, immune cells, and nucleus, respectively. Segmentation of tumors focused on regions of interest (ROIs) to distinctly identify the Tumor mask in green and the Stromal mask in yellow. (B) Utilizing the PanCk+/- feature, masks were generated to liberate barcodes for digital counting via the Nanostring nCounter platform. (C) MA plots of Mean Expression (AveExpr) vs. fold change (logFC) visualize the expression of protein biomarkers within tumor compartments in patients with complete response (CR) versus patients with progressive disease (PD). (D) MA plots of Mean Expression (AveExpr) vs. fold change (logFC) visualize the expression of protein biomarkers within tumor compartments in patients with disease control status (CR/PR/SD) versus patients with PD. Color coding represents markers that are not differentially expressed (gray), significantly upregulated (red), and downregulated (blue), based on a false discovery rate (FDR) of < 0.05 following multiple testing adjustments