In‐Depth Proteomic Analysis of Human Bronchoalveolar Lavage Fluid toward the Biomarker Discovery for Lung Cancers

Abstract

Purpose Lung cancer is among the most common cancers. Bronchoalveolar lavage fluid (BALF) can be easily obtained from patients with lung cancers. The aim is to develop a novel proteomic method of the molecule‐based sensitive detection of biomarkers from BALF. Experimental Design BALF samples are collected from segmental bronchus of 14 patients with lung cancers from Kyung Hee University Hospital. First, BALF proteome is depleted using a depletion column, and then peptides are prepared from the enriched low abundant proteins and fractionated by high pH reverse phase liquid chromatography prior to LC‐MS/MS. Data are available via ProteomeXchange with identifier PXD012645. Results A novel method is developed for in‐depth proteomic analysis of BALF by combining antibody‐based depletion of high abundant proteins from BALF with high pH peptide fractionation. Peptides are analyzed on a high resolution Orbitrap Fusion mass spectrometer. MaxQuant search result in the identification of 4615 protein groups mapped to 4534 genes. Conclusions and Clinical Relevance It is found that the method outperformed conventional BALF proteomic methods and it is believed that this method will facilitate the biomarker research for lung cancer. In addition, it is shown that BALF will be a great source of biomarkers of lung diseases.

Lacritin proteoforms prevent tear film collapse and maintain epithelial homeostasis

“…All focused attention on lacritin's two C-terminal amphipathic α-helices required for ligation of heparanase-modified cell surface syndecan-1 ( 53 , 63 ) necessary for epithelial targeting. Their similarity to N- and C-termini of processed lipid stabilizing pulmonary surfactant protein B ( 32 , 33 , 34 ), together with lacritin's detection in broncheoalveolar lavage ( 19 , 20 ), and selective lacritin and C-terminal proteoform deficiency in dry eye were rationale for testing with tear lipids.…”

“…Also, in dry eye, surprisingly few tear proteins are selectively deficient. Of tear deficient proteins curiously also constituents of broncheoalveolar lung lavage ( 19 , 20 ) are: zymogen granule protein 16B, annexin A5, alpha-2-glycoprotein 1, deleted in malignant brain tumors1, lipocalin-1, submaxillary gland androgen regulator protein 3B, immunoglobulin heavy constant alpha 1, polymeric immmunoglobulin and lacritin. Lacritin is a basal tearing agonist ( 21 , 22 , 23 , 24 ) that in addition transiently stimulates autophagy in ocular surface epithelia ( 25 ) to restore oxidative phosphorylation under conditions of inflammatory stress ( 25 ).…”

Is the Proteome of Bronchoalveolar Lavage Extracellular Vesicles a Marker of Advanced Lung Cancer?

“…Deep protein coverage is paramount for identifying cancer signatures as well as contributing to the design of novel therapies [ 4 ]. Recent methodologies combining antibody-based depletion of high abundant BALF proteins, high pH peptide fractionation, and label-free quantitation on a high-resolution Orbitrap Fusion Lumos instrument demonstrated superior protein coverage [ 16 ]. In this study, we demonstrated the enrichment of sEVs by the sequential centrifugation method and quantification, resulted in a total of 7484 protein isoforms.…”

“…Abundant proteins like albumin partially hamper the protein coverage obtainable by direct LC-MS analysis of acellular BAL samples. Therefore, Sim et al [ 16 ] established a novel methodology based on combining antibody-based depletion of high abundant BALF proteins, high pH peptide fractionation, and label-free quantitation on a high-resolution Orbitrap Fusion Lumos instrument. However, antibody depletion of abundant proteins risks the removal of clinically relevant target proteins.…”

Proteome analysis of bronchoalveolar lavage fluids reveals host and fungal proteins highly expressed during invasive pulmonary aspergillosis in mice and humans

“…However, this approach suffers from a major limitation: the abundance of host proteins hampers the detection of pathogen-derived proteins that are usually present at lower concentrations. Recent advances in gel-free sample preparation methods and instrumentation developments for bottomup proteomics using liquid chromatography tandem mass spectrometry (LC-MS/MS) allow exhaustive analysis of even low abundant proteins in complex biological samples due to improvements in speed, mass resolution, sensitivity, as well as ion separation and dissociation technologies [17][18][19][20].…”