Dia-PASEF Proteomics of Tumor and Stroma LMD Enriched from Archived HNSCC Samples.

ABSTRACT: We employed laser microdissection to selectively harvest tumor cells and stroma from the microenvironment of formalin-fixed, paraffin-embedded head and neck squamous cell carcinoma (HNSCC) tissues. The captured HNSCC tissue fractions were analyzed by quantitative mass spectrometry-based proteomics using a data independent analysis approach. In paired samples, we achieved excellent proteome coverage having quantified 6,668 proteins with a median quantitative coefficient of variation under 10%. We observed significant differences in relevant functional pathways between the spatially resolved tumor and stroma regions. Our results identified extracellular matrix (ECM) as a major component enriched in the stroma, including many cancer associated fibroblast signature proteins in this compartment

SUBMITTER: Panigrahi A 

PROVIDER: S-EPMC11326218 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature