Application of Isobaric Tags for Relative and Absolute Quantification (iTRAQ) Coupled with Two-Dimensional Liquid Chromatography/Tandem Mass Spectrometry in Quantitative Proteomic Analysis for Discovery of Serum Biomarkers for Idiopathic Pulmonary Fibrosis

Zhang, Ying; Xin, Qian; Wu, Zhen Sen; Wang, Chaochao; Wang, Yongbin; Wu, Qian; Niu, Rui

doi:10.12659/msm.908702

Cited by 13 publications

(10 citation statements)

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“…Thus, this tool has both facilitated and hastened the identification of key proteins involved in the progression of different diseases [7,11]. Coincidently, several investigations on IPF have used proteomic approaches to characterize the molecular mechanisms involved in the disease progression [2,3,7,[12][13][14][15][16]; however, limited studies have aimed to identify the proteomic profile of EVs cargo secreted during IPF progression [8]. Thus, here we identified differentially expressed proteins contained within EVs cargo secreted by cell lines isolated from lungs bearing IPF.…”

Section: Introductionmentioning

confidence: 99%

Proteomic Analysis Reveals Key Proteins in Extracellular Vesicles Cargo Associated with Idiopathic Pulmonary Fibrosis In Vitro

et al. 2021

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Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, irreversible, and highly fatal disease. It is characterized by the increased activation of both fibroblast and myofibroblast that results in excessive extracellular matrix (ECM) deposition. Extracellular vesicles (EVs) have been described as key mediators of intercellular communication in various pathologies. However, the role of EVs in the development of IPF remains poorly understood. This study aimed to characterize the differentially expressed proteins contained within EVs cargo derived from the fibroblast cell lines LL97A (IPF-1) and LL29 (IPF-2) isolated from lungs bearing IPF as compared to those derived from the fibroblast cell lines CCD8Lu (NL-1) and CCD19Lu (NL-2) isolated from healthy donors. Isolated EVs were subjected to label-free quantitative proteomic analysis by LC-MS/MS, and as a result, 331 proteins were identified. Differentially expressed proteins were obtained after the pairwise comparison, including all experimental groups. A total of 86 differentially expressed proteins were identified in either one or more comparison groups. Of note, proteins involved in fibrogenic processes, such as tenascin-c (TNC), insulin-like-growth-factor-binding protein 7 (IGFBP7), fibrillin-1 (FBN1), alpha-2 collagen chain (I) (COL1A2), alpha-1 collagen chain (I) (COL1A1), and lysyl oxidase homolog 1 (LOXL1), were identified in EVs cargo isolated from IPF cell lines. Additionally, KEGG pathway enrichment analysis revealed that differentially expressed proteins participate in focal adhesion, PI3K-Akt, and ECM–receptor interaction signaling pathways. In conclusion, our findings reveal that proteins contained within EVs cargo might play key roles during IPF pathogenesis.

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Section: Introductionmentioning

confidence: 99%

Proteomic Analysis Reveals Key Proteins in Extracellular Vesicles Cargo Associated with Idiopathic Pulmonary Fibrosis In Vitro

et al. 2021

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“…They observed reduced glycolysis/gluconeogenesis and enhanced ascorbate and aldarate metabolism, and the imbalanced metabolism can be restored by pirfenidone [16]. Proteomic analysis also have been applied to identify serum biomarkers for IPF, they found that 97 out of total 394 proteins were associated with IPF, C-reactive protein (CRP), fibrinogen- α chain, haptoglobin, and kininogen-1 were useful candidate biomarkers for IPF [17]. Another proteome analysis for serum of IPF patients also found that CRP is a biomarker for the diagnosis of IPF [18].…”

Section: Introductionmentioning

confidence: 99%

Quantitative proteomic characterization of lung tissue in idiopathic pulmonary fibrosis

Tian

Gao

et al. 2019

Clin Proteom

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BackgroundIdiopathic pulmonary fibrosis (IPF) is a progressive, eventually fatal disease. IPF is characterized by excessive accumulation of the extracellular matrix (ECM) in the alveolar parenchyma and progressive lung scarring. The pathogenesis of IPF and whether the ECM involved in the process remain unknown.MethodsTo identify potential treatment target and ECM associated proteins that may be involved in the development of IPF, we employed isobaric tag for relative and absolute quantitation (iTRAQ) combined liquid chromatography–tandem mass spectrometry (LC–MS/MS) approach to examine protein expression in lung tissues from IPF patients.ResultsA total of 662 proteins with altered expression (455 upregulated proteins and 207 downregulated proteins) were identified in lung tissue of IPF patients compared with control. KEGG pathway enrichment analysis showed that the altered proteins in lung tissue mainly belonged to the PI3K-Akt signaling, focal adhesion, ECM-receptor interaction, and carbon metabolism pathways. According to the bioinformatic definition of the matrisome, 229 matrisome proteins were identified in lung tissue. These proteins comprised the ECM of lung, of which 104 were core matrisome proteins, and 125 were matrisome-associated proteins. Of the 229 ECM quantified proteins, 56 significantly differentially expressed proteins (19 upregulated proteins and 37 downregulated proteins) were detected in IPF lung tissue samples. In addition to proteins with well-known functions such as COL1A1, SCGB1A1, TAGLN, PSEN2, TSPAN1, CTSB, AGR2, CSPG2, and SERPINB3, we identified several novel ECM proteins with unknown function deposited in IPF lung tissue including LGALS7, ASPN, HSP90AA1 and HSP90AB1. Some of these differentially expressed proteins were further verified using Western blot analysis and immunohistochemical staining.ConclusionsThis study provides a list of proteomes that were detected in IPF lung tissue by iTRAQ technology combined with LC–MS/MS. The findings of this study will contribute better understanding to the pathogenesis of IPF and facilitate the development of therapeutic targets.Electronic supplementary materialThe online version of this article (10.1186/s12014-019-9226-4) contains supplementary material, which is available to authorized users.

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“…Subsequently, the monomers polymerized with fibrinogen beta ( Fgb ) and fibrinogen gamma ( Fgg ), forming the insoluble fibrin matrix. The level of Fga was higher in patients with IPF compared with that in healthy controls ( 43 ). Moreover, previous research found that the lack of a C-terminal fragment of Fga preceded the progress of fibrosis in patients with liver diseases ( 44 ).…”

Section: Discussionmentioning

confidence: 95%

Identification of Genetic Signature Associated With Aging in Pulmonary Fibrosis

Chen

Wang

et al. 2021

Front. Med.

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Background: Aging is a strong risk factor and an independent prognostic factor in idiopathic pulmonary fibrosis (IPF). In this study, we aimed to conduct a comprehensive analysis based on gene expression profiles for the role of aging in pulmonary fibrosis.Method: Four datasets (GSE21411, GSE24206, GSE47460, and GSE101286) for patients with clinical IPF and one dataset for bleomycin (BLM)-induced pulmonary fibrosis (BIPF) mouse model (GSE123293) were obtained from Gene Expression Omnibus (GEO). According to different age ranges, both patients with IPF and BIPF mice were divided into young and aged groups. The differently expressed genes (DEGs) were systemically analyzed using Gene Ontology (GO) functional, Kyoto Encyclopedia of Genes and Genomes (KEGG), and hub genes analysis. Finally, we verified the role of age and core genes associated with age in vivo.Results:Via the expression profile comparisons of aged and young patients with IPF, we identified 108 aging-associated DEGs, with 21 upregulated and 87 downregulated. The DEGs were associated with “response to glucocorticoid,” “response to corticosteroid,” and “rhythmic process” in GO biological process (BP). For KEGG analysis, the top three significantly enriched KEGG pathways of the DEGs included “IL-17 signaling pathway,” “Mineral absorption,” and “HIF-1-signaling pathway.” Through the comparisons of aged and young BIPF mice, a total number of 778 aging-associated DEGs were identified, with 453 genes increased and 325 genes decreased. For GO and KEGG analysis, the DEGs were enriched in extracellular matrix (ECM) and collagen metabolism. The common DEGs of patients with IPF and BIPF mice were enriched in the BP category, including “induction of bacterial agglutination,” “hyaluronan biosynthetic process,” and “positive regulation of heterotypic cell-cell adhesion.” We confirmed that aged BIPF mice developed more serious pulmonary fibrosis. Finally, the four aging-associated core genes (Slc2a3, Fga, Hp, and Thbs1) were verified in vivo.Conclusion: This study provides new insights into the impact of aging on pulmonary fibrosis. We also identified four aging-associated core genes (Slc2a3, Fga, Hp, and Thbs1) related to the development of pulmonary fibrosis.

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Application of Isobaric Tags for Relative and Absolute Quantification (iTRAQ) Coupled with Two-Dimensional Liquid Chromatography/Tandem Mass Spectrometry in Quantitative Proteomic Analysis for Discovery of Serum Biomarkers for Idiopathic Pulmonary Fibrosis

Cited by 13 publications

References 84 publications

Proteomic Analysis Reveals Key Proteins in Extracellular Vesicles Cargo Associated with Idiopathic Pulmonary Fibrosis In Vitro

Proteomic Analysis Reveals Key Proteins in Extracellular Vesicles Cargo Associated with Idiopathic Pulmonary Fibrosis In Vitro

Quantitative proteomic characterization of lung tissue in idiopathic pulmonary fibrosis

Identification of Genetic Signature Associated With Aging in Pulmonary Fibrosis

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