Sequential Proteomic and N-Glycoproteomic Analyses of Bronchoalveolar Lavage Fluids for Potential Biomarker Discovery of Lung Adenocarcinoma

Lung adenocarcinoma (LUAD) is the most common histological subtype of nonsmall-cell lung cancer. Herein, a multiomics method, which combined proteomic and N-glycoproteomic analyses, was developed to analyze the normal and cancerous bronchoalveolar lavage fluids (BALFs) from six LUAD patients to identify potential biomarkers of LUAD. The data-independent acquisition proteomic analysis was first used to analyze BALFs, which identified 59 differentially expressed proteins (DEPs). The bioinformatic analyses of 59 DEPs have shown that a potential marker protein, beta-1,4-galactosyltransferase 1 (B4GALT1), was consistently downregulated in all cancerous lung lobes (CLLs). As the downregulation of B4GALT1 may indicate changes in protein N-glycosylation, site-specific N-glycoproteome analysis of BALFs from the normal lung lobes (NLLs) and CLLs was further performed by using a fully automated glycopeptide enrichment and separation system. Comparing the glycan structures containing free GlcNAc in BALFs between NLLs and CLLs qualitatively, the percentage of unique glycan structure for free GlcNAc existing only in NLLs was 52.8%, which was significantly higher than the 46.3% existing only in CLLs. Furthermore, the sequential proteomic and N-glycoproteomic analyses allowed us to identify a panel of functionally related potential biomarkers consisting of one protein (B4GALT1) and four glycoproteins (NFKB1, F2, LTF, and DLD).