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Structural and metabolic alterations in erythrocytes play an important role in the pathophysiology of Chronic Obstructive Pulmonary Disease (COPD). Whether these dysfunctions are related to the modulation of erythrocyte membrane proteins in patients diagnosed with COPD remains to be determined. Herein, a comparative proteomic profiling of the erythrocyte membrane fraction isolated from peripheral blood of smokers diagnosed with COPD and smokers with no COPD was performed using differential (16)O/(18)O stable isotope labeling. A total of 219 proteins were quantified as being significantly differentially expressed within the erythrocyte membrane proteomes of smokers with COPD and healthy smokers. Functional pathway analysis showed that the most enriched biofunctions were related to cell-to-cell signaling and interaction, hematological system development, immune response, oxidative stress and cytoskeleton. Chorein (VPS13A), a cytoskeleton related protein whose defects had been associated with the presence of cell membrane deformation of circulating erythrocytes was found to be down-regulated in the membrane fraction of erythrocytes obtained from COPD patients. Methemoglobin reductase (CYB5R3) was also found to be underexpressed in these cells, suggesting that COPD patients may be at higher risk for developing methemoglobinemia. This article is part of a Special Issue entitled: Integrated omics.

A comprehensive proteomic profiling of nasal epithelium (NE) is described. This study relies on simple subcellular fractionation used to obtain soluble- and membrane-enriched fractions followed by 2-dimensional liquid chromatography (2D-LC) separation and tandem mass spectrometry (MS/MS). The cells were collected using a brushing technique applied on NE of clinically evaluated volunteers. Subsequently, the soluble- and the membrane-protein enriched fractions were prepared and analyzed in parallel using 2D-LC-MS/MS. In a set of 1482 identified proteins, 947 (63.9%) proteins were found to be associated to membrane fraction. Grand average hydropathy value index (GRAVY) analysis, the transmembrane protein mapping and annotations of primary location deposited in the Human Protein Reference Database (HPRD) confirmed an enrichment of hydrophobic proteins on this dataset. Ingenuity Pathway Analysis (IPA) of soluble fraction revealed an enrichment of molecular and cellular functions associated with cell death, protein folding and drug metabolism while in membrane fraction showed an enrichment of functions associated with molecular transport, protein trafficking and cell-to-cell signaling and interaction. The IPA showed similar enrichment of functions associated with cellular growth and proliferation in both soluble and membrane subproteomes. This finding was in agreement with protein content analysis using exponentially modified protein abundance index (emPAI). A comparison of our data with previously published studies focusing on respiratory tract epithelium revealed similarities related to identification of proteins associated with physical barrier function and immunological defence. In summary, we extended the NE molecular profile by identifying and characterizing proteins associated to pivotal functions of a respiratory epithelium, including the control of fluid volume and ionic composition at the airways' surface, physical barrier maintenance, detoxification and immunological defence. The extent of similarities supports the applicability of a less invasive analysis of NE to assess prognosis and treatment response of lung diseases such as asthma, cystic fibrosis and chronic obstructive pulmonary disease., Graphical abstract This work represents the most complete proteome characterization of nasal epithelium (NE) describing its relevant functions. NE usefulness in lung biomedical research is highlighted based on observed similarities with bronchial epithelial proteome. Research highlights ► Sub-fractionation of nasal epithelial cells (NEC) to improve the detection of low abundance proteins. ► Global proteome characterization based on a gel-free SCX-RPLC- chromatography coupled with MS/MS approach. ► Characterization of cell membrane proteins using a methanol-based solubilization before tryptic digestion. ► Pathway Analysis to profile molecular and cellular functions overrepresented in nasal epithelium. ► Extensive comparison of our data with previously published studies focusing on respiratory tract epithelium.

The extracellular matrix (ECM) is the connective tissue component generated and secreted by cells to provide structural and functional support, while extracellular vesicles are distinct membrane-enclosed structures present outside of eucaryotic cells that carry out distinct biological functions. Different cell types release distinct populations of vesicles that fulfill various functions. Exosomes are vesicles commonly secreted by a variety of cells, whereas matrix vesicles (MVs) are specifically produced and secreted by bone cells to facilitate the formation of the ECM. This article focuses on the characteristics of the ECM and extracellular vesicles, and reviews the latest progress in applying proteomic technologies to analyze these features. The findings and implications in developmental biology, tumor biology, immunology, biomarker discovery, and vaccine research are also discussed.