Fig. 1: Proteomic profile of tissues and fluids in a 59-HNSCC patient cohort.
From: Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer
a Experimental design to uncover the biological aspects and prognostic markers in the proteomes from multiple HNSCC sites. Created with BioRender.com. b Dynamic range of proteomics quantitative data for primary tumor malignant (n = 25 samples) and non-malignant (n = 27 samples) cells, lymph node malignant (n = 13 samples) and non-malignant (n = 27 samples) cells, buffy coat (n = 24 samples) and saliva cells (n = 24 samples). The bar sizes and respective numbers in the right-sided graph indicate the total number of proteins identified per site. c Groups identified by clustering of the protein datasets for the multisites using the Ward’s method based on Bray-Curtis distance (primary tumor – malignant: 2444 proteins; primary tumor – non-malignant: 1984 proteins; lymph node – malignant: 2308 proteins; lymph node – non-malignant: 2137 proteins; buffy coat: 2188 proteins; saliva: 1154 proteins). d Top-10 significant GO biological processes enriched for the PC groups of the global proteomes (adjusted p ≤ 0.05; two-sided Fisher’s exact test followed by Benjamini-Hochberg correction). Immune-related processes are labeled with a triangle. Predicted composition of immune populations based on proteomic data of non-malignant cells from primary tumors (e) and buffy coat (f) samples using CIBERSORTx version 1.0. Samples were clustered using the Euclidean method and Ward.D distance, and the pN status was annotated. EMT Epithelial-mesenchymal transition, HNSCC head and neck squamous cell carcinoma, LC-MS/MS liquid Chromatography with tandem mass spectrometry. Source data are provided as a Source Data file.
