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Ebert C, Walsh AM, Sereda L, Wilson CL, Schafer PH, Fischer A, Zhao L, Ramirez-Valle F, Gordon D, Schnapp LM. Circulating biomarker analyses in a longitudinal cohort of patients with IPF. Am J Physiol Lung Cell Mol Physiol 2024; 326:L303-L312. [PMID: 38226605 DOI: 10.1152/ajplung.00222.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/17/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is an incurable interstitial lung disease characterized by fibrosis. Two FDA-approved drugs, pirfenidone and nintedanib, only modestly prolong survival. In this study, we asked whether levels of select circulating biomarkers in patients with IPF demonstrated changes in response to treatment over time and whether treatment with pirfenidone and nintedanib led to differential biomarker expression. Serial plasma samples from 48 patients with IPF on usual treatment and six healthy volunteers were analyzed to identify differentially expressed blood protein. Hypothesis-driven potential biomarker selection was based on recent literature, internal preclinical data, and the PROLIFIC Consortium (Schafer P. 6th Annual IPF Summit. Boston, MA, 2022) proposed biomarkers of pulmonary fibrosis. We compared our findings to public databases to provide insights into relevant signaling pathways in IPF. Of the 26 proteins measured, we found that 11 (SP-D, TIMP1, MMP7, CYFRA21-1, YKL40, CA125, sICAM, IP-10, MDC, CXCL13) were significantly elevated in patients with IPF compared with healthy volunteers but their levels did not significantly change over time. In the IPF samples, seven proteins were elevated in the treatment group compared with the no-treatment group. However, protein profiles were not distinguishable between patients on pirfenidone versus nintedanib. We demonstrated that most proteins differentially detected in our samples were predicted to be secreted from the lung epithelial or interstitial compartments. However, a significant minority of the proteins are not known to be transcriptionally expressed by lung cells, suggesting an ongoing systemic response. Understanding the contributions of the systemic response in IPF may be important as new therapeutics are developed.NEW & NOTEWORTHY In this study, we confirmed protein expression differences in only a subset of predicted biomarkers from IPF and control subjects. Most differentially expressed proteins were predicted to be secreted from lung cells. However, a significant minority of the proteins are not known to be transcriptionally expressed by lung cells, suggesting an ongoing systemic response. The contributions of the systemic response in IPF may be important as new therapeutics are developed.
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Affiliation(s)
| | - Alice M Walsh
- Bristol Myers Squibb, Princeton, New Jersey, United States
| | - Larisa Sereda
- Bristol Myers Squibb, Princeton, New Jersey, United States
| | - Carole L Wilson
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Medical University of South Carolina, Charleston, South Carolina, United States
| | | | - Aryeh Fischer
- Bristol Myers Squibb, Princeton, New Jersey, United States
| | - Lei Zhao
- Bristol Myers Squibb, Princeton, New Jersey, United States
| | | | - David Gordon
- Bristol Myers Squibb, Princeton, New Jersey, United States
| | - Lynn M Schnapp
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Medical University of South Carolina, Charleston, South Carolina, United States
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2
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Qianman B, Wupuer A, Jiasharete T, Luo B, Nihemaiti M, Jielile J. iTRAQ-based proteomics reveals potential markers and treatment pathways for acute Achilles tendon rupture. J Orthop Surg Res 2023; 18:852. [PMID: 37946221 PMCID: PMC10636927 DOI: 10.1186/s13018-023-04346-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Due to its limited blood supply and irregular mechanical loading, the Achilles tendon is the most frequently ruptured tendon. Despite the rising incidence of acute Achilles tendon rupture (AATR), the optimal treatment remains controversial. Missed diagnoses and delayed treatments lead to poor outcomes and limited treatment options. This study aimed to identify potential biomarkers for diagnosing and developing therapies for AATR. METHODS We employed the coupled isobaric tag for relative and absolute quantitation-liquid chromatography-electrospray ionization-tandem mass spectrometry approach to investigate protein expression in tissues from AATR patients. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to identify differentially expressed proteins (DEPs) between AATR patients and healthy individuals. A protein-protein interaction (PPI) network of DEPs was constructed using the Search Tool for the Retrieval of Interacting Genes. The screened hub genes were selectively verified by immunohistochemical staining. RESULTS We identified 410 DEPs between AATR patients and controls. The DEPs were significantly enriched in GO terms such as the extracellular region, extracellular region part, and defense response, as well as KEGG pathways, including complement and coagulation cascades, focal adhesion, and regulation of actin cytoskeleton. The main hub nodes in the PPI network comprised fibronectin 1 (FN1), major histocompatibility complex, class I, B (HLA-B), filamin A (FLNA), heat shock 27-kDa protein 1 (HSPB1), heat shock protein family A member 5 (HSPA5), apolipoprotein A4 (APOA4), and myosin IC (MYO1C). Although APOA4 and collagens I, II, and III were detectable in healthy tendons, immunohistochemical staining confirmed higher expression of these proteins in the acutely ruptured Achilles tendon. CONCLUSIONS Our findings lay a foundation for further molecular studies of AATR. Inflammation and age-related degeneration may contribute to the pathogenesis of AATR. Moreover, the identified DEPs could be potential biomarkers for AATR diagnosis and treatment.
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Affiliation(s)
- Bayixiati Qianman
- Department of Osteopathy and Orthopedics (Ankle) Surgery, The Sixth Teaching Hospital of Xinjiang Medical University, No. 39 Wuxing South Road, Ürümqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Aikeremu Wupuer
- Department of Osteopathy and Orthopedics (Ankle) Surgery, The Sixth Teaching Hospital of Xinjiang Medical University, No. 39 Wuxing South Road, Ürümqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Tuomilisi Jiasharete
- Urumqi No.1 Middle School, No. 195, West 2nd Lane, Kanas Hubei Road, Urumqi Economic and Technological Development Zone (Toutunhe District), Ürümqi, 830015, Xinjiang Uygur Autonomous Region, China
| | - Biao Luo
- Department of Orthopaedics, Pingmei Shenma Medical Group General Hospital, No.1 South of Kuanggoong Middle Road, Xinhua District, Pingdingshan, 467000, Henan, China
| | - Meihua Nihemaiti
- Altay Traditional Chinese Medicine Hospital (Regional Kazakh Medical Hospital) in Xinjiang Uygur Autonomous Region, No. 40 Yingbin Road, Altay City, 836500, Xinjiang Uygur Autonomous Region, China
| | - Jiasharete Jielile
- Department of Osteopathy and Orthopedics (Ankle) Surgery, The Sixth Teaching Hospital of Xinjiang Medical University, No. 39 Wuxing South Road, Ürümqi, 830001, Xinjiang Uygur Autonomous Region, China.
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3
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Rezaeeyan H, Arabfard M, Rasouli HR, Shahriary A, Gh BFNM. Evaluation of common protein biomarkers involved in the pathogenesis of respiratory diseases with proteomic methods: A systematic review. Immun Inflamm Dis 2023; 11:e1090. [PMID: 38018577 PMCID: PMC10659759 DOI: 10.1002/iid3.1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/22/2023] [Accepted: 11/04/2023] [Indexed: 11/30/2023] Open
Abstract
AIM Respiratory disease (RD) is one of the most common diseases characterized by lung dysfunction. Many diagnostic mechanisms have been used to identify the pathogenic agents of responsible for RD. Among these, proteomics emerges as a valuable diagnostic method for pinpointing the specific proteins involved in RD pathogenesis. Therefore, in this study, for the first time, we examined the protein markers involved in the pathogenesis of chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), asthma, bronchiolitis obliterans (BO), and chemical warfare victims exposed to mustard gas, using the proteomics method as a systematic study. MATERIALS AND METHODS A systematic search was performed up to September 2023 on several databases, including PubMed, Scopus, ISI Web of Science, and Cochrane. In total, selected 4246 articles were for evaluation according to the criteria. Finally, 119 studies were selected for this systematic review. RESULTS A total of 13,806 proteins were identified, 6471 in COPD, 1603 in Asthma, 5638 in IPF, three in BO, and 91 in mustard gas exposed victims. Alterations in the expression of these proteins were observed in the respective diseases. After evaluation, the results showed that 31 proteins were found to be shared among all five diseases. CONCLUSION Although these 31 proteins regulate different factors and molecular pathways in all five diseases, they ultimately lead to the regulation of inflammatory pathways. In other words, the expression of some proteins in COPD and mustard-exposed patients increases inflammatory reactions, while in IPF, they cause lung fibrosis. Asthma, causes allergic reactions due to T-cell differentiation toward Th2.
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Affiliation(s)
- Hadi Rezaeeyan
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion MedicineIranian Blood Transfusion Organization (IBTO)TehranIran
| | - Masoud Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - Hamid R. Rasouli
- Trauma Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Alireza Shahriary
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - B. Fatemeh Nobakht M. Gh
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
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4
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Volpe MC, Ciucci G, Zandomenego G, Vuerich R, Ring NAR, Vodret S, Salton F, Marchesan P, Braga L, Marcuzzo T, Bussani R, Colliva A, Piazza S, Confalonieri M, Zacchigna S. Flt1 produced by lung endothelial cells impairs ATII cell transdifferentiation and repair in pulmonary fibrosis. Cell Death Dis 2023; 14:437. [PMID: 37454154 PMCID: PMC10349845 DOI: 10.1038/s41419-023-05962-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
Pulmonary fibrosis is a devastating disease, in which fibrotic tissue progressively replaces lung alveolar structure, resulting in chronic respiratory failure. Alveolar type II cells act as epithelial stem cells, being able to transdifferentiate into alveolar type I cells, which mediate gas exchange, thus contributing to lung homeostasis and repair after damage. Impaired epithelial transdifferentiation is emerging as a major pathogenetic mechanism driving both onset and progression of fibrosis in the lung. Here, we show that lung endothelial cells secrete angiocrine factors that regulate alveolar cell differentiation. Specifically, we build on our previous data on the anti-fibrotic microRNA-200c and identify the Vascular Endothelial Growth Factor receptor 1, also named Flt1, as its main functional target in endothelial cells. Endothelial-specific knockout of Flt1 reproduces the anti-fibrotic effect of microRNA-200c against pulmonary fibrosis and results in the secretion of a pool of soluble factors and matrix components able to promote epithelial transdifferentiation in a paracrine manner. Collectively, these data indicate the existence of a complex endothelial-epithelial paracrine crosstalk in vitro and in vivo and position lung endothelial cells as a relevant therapeutic target in the fight against pulmonary fibrosis.
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Affiliation(s)
- Maria Concetta Volpe
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Giulio Ciucci
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Giulia Zandomenego
- Department of Life Sciences, University of Trieste, Trieste, Italy
- Functional Cell Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Roman Vuerich
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Nadja Anneliese Ruth Ring
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Ludwig Boltzmann Gesellschaft Research Group Senescence and Healing of Wounds, Vienna, Austria
| | - Simone Vodret
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Francesco Salton
- Pulmonology Unit, University Hospital of Cattinara, Trieste, Italy
| | - Pietro Marchesan
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Luca Braga
- Functional Cell Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Thomas Marcuzzo
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Rossana Bussani
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Andrea Colliva
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Silvano Piazza
- Computational Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Marco Confalonieri
- Pulmonology Unit, University Hospital of Cattinara, Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Serena Zacchigna
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.
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5
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Genetic association of circulating C-reactive protein levels with idiopathic pulmonary fibrosis: a two-sample Mendelian randomization study. Respir Res 2023; 24:7. [PMID: 36624433 PMCID: PMC9830761 DOI: 10.1186/s12931-022-02309-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Several observational studies have found that idiopathic pulmonary fibrosis (IPF) is often accompanied by elevated circulating C-reactive protein (CRP) levels. However, the causal relationship between them remains to be determined. Therefore, our study aimed to explore the causal effect of circulating CRP levels on IPF risk by the two-sample Mendelian randomization (MR) analysis. METHODS We analyzed the data from two genome-wide association studies (GWAS) of European ancestry, including circulating CRP levels (204,402 individuals) and IPF (1028 cases and 196,986 controls). We primarily used inverse variance weighted (IVW) to assess the causal effect of circulating CRP levels on IPF risk. MR-Egger regression and MR-PRESSO global test were used to determine pleiotropy. Heterogeneity was examined with Cochran's Q test. The leave-one-out analysis tested the robustness of the results. RESULTS We obtained 54 SNPs as instrumental variables (IVs) for circulating CRP levels, and these IVs had no significant horizontal pleiotropy, heterogeneity, or bias. MR analysis revealed a causal effect between elevated circulating CRP levels and increased risk of IPF (ORIVW = 1.446, 95% CI 1.128-1.854, P = 0.004). CONCLUSIONS The present study indicated that elevated circulating CRP levels could increase the risk of developing IPF in people of European ancestry.
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Axelsson GT, Gudmundsson G, Pratte KA, Aspelund T, Putman RK, Sanders JL, Gudmundsson EF, Hatabu H, Gudmundsdottir V, Gudjonsson A, Hino T, Hida T, Hobbs BD, Cho MH, Silverman EK, Bowler RP, Launer LJ, Jennings LL, Hunninghake GM, Emilsson V, Gudnason V. The Proteomic Profile of Interstitial Lung Abnormalities. Am J Respir Crit Care Med 2022; 206:337-346. [PMID: 35438610 PMCID: PMC9890263 DOI: 10.1164/rccm.202110-2296oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Rationale: Knowledge on biomarkers of interstitial lung disease is incomplete. Interstitial lung abnormalities (ILAs) are radiologic changes that may present in its early stages. Objectives: To uncover blood proteins associated with ILAs using large-scale proteomics methods. Methods: Data from two prospective cohort studies, the AGES-Reykjavik (Age, Gene/Environment Susceptibility-Reykjavik) study (N = 5,259) for biomarker discovery and the COPDGene (Genetic Epidemiology of COPD) study (N = 4,899) for replication, were used. Blood proteins were measured using DNA aptamers, targeting more than 4,700 protein analytes. The association of proteins with ILAs and ILA progression was assessed with regression modeling, as were associations with genetic risk factors. Adaptive Least Absolute Shrinkage and Selection Operator models were applied to bootstrap data samples to discover sets of proteins predictive of ILAs and their progression. Measurements and Main Results: Of 287 associations, SFTPB (surfactant protein B) (odds ratio [OR], 3.71 [95% confidence interval (CI), 3.20-4.30]; P = 4.28 × 10-67), SCGB3A1 (Secretoglobin family 3A member 1) (OR, 2.43 [95% CI, 2.13-2.77]; P = 8.01 × 10-40), and WFDC2 (WAP four-disulfide core domain protein 2) (OR, 2.42 [95% CI, 2.11-2.78]; P = 4.01 × 10-36) were most significantly associated with ILA in AGES-Reykjavik and were replicated in COPDGene. In AGES-Reykjavik, concentrations of SFTPB were associated with the rs35705950 MUC5B (mucin 5B) promoter polymorphism, and SFTPB and WFDC2 had the strongest associations with ILA progression. Multivariate models of ILAs in AGES-Reykjavik, ILAs in COPDGene, and ILA progression in AGES-Reykjavik had validated areas under the receiver operating characteristic curve of 0.880, 0.826, and 0.824, respectively. Conclusions: Novel, replicated associations of ILA, its progression, and genetic risk factors with numerous blood proteins are demonstrated as well as machine-learning-based models with favorable predictive potential. Several proteins are revealed as potential markers of early fibrotic lung disease.
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Affiliation(s)
- Gisli Thor Axelsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland;,Icelandic Heart Association, Kopavogur, Iceland
| | - Gunnar Gudmundsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland;,Department of Respiratory Medicine, Landspitali University Hospital, Reykjavik, Iceland
| | | | - Thor Aspelund
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland;,Icelandic Heart Association, Kopavogur, Iceland
| | | | | | | | - Hiroto Hatabu
- Department of Radiology, and,Center for Pulmonary Functional Imaging, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Valborg Gudmundsdottir
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland;,Icelandic Heart Association, Kopavogur, Iceland
| | | | - Takuya Hino
- Center for Pulmonary Functional Imaging, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tomoyuki Hida
- Center for Pulmonary Functional Imaging, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts;,Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Brian D. Hobbs
- Pulmonary and Critical Care Division,,Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Michael H. Cho
- Pulmonary and Critical Care Division,,Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Edwin K. Silverman
- Pulmonary and Critical Care Division,,Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Russell P. Bowler
- National Jewish Health, Denver, Colorado;,School of Medicine, University of Colorado, Aurora, Colorado
| | - Lenore J. Launer
- Laboratory of Epidemiology and Population Sciences, Intramural Research Program, National Institute on Aging, Bethesda, Maryland; and
| | - Lori L. Jennings
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Gary M. Hunninghake
- Pulmonary and Critical Care Division,,Center for Pulmonary Functional Imaging, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Vilmundur Gudnason
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland;,Icelandic Heart Association, Kopavogur, Iceland
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7
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Velázquez-Enríquez JM, Ramírez-Hernández AA, Navarro LMS, Reyes-Avendaño I, González-García K, Jiménez-Martínez C, Castro-Sánchez L, Sánchez-Chino XM, Vásquez-Garzón VR, Baltiérrez-Hoyos R. Proteomic Analysis Reveals Differential Expression Profiles in Idiopathic Pulmonary Fibrosis Cell Lines. Int J Mol Sci 2022; 23:ijms23095032. [PMID: 35563422 PMCID: PMC9105114 DOI: 10.3390/ijms23095032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/18/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, irreversible lung disorder of unknown cause. This disease is characterized by profibrotic activation of resident pulmonary fibroblasts resulting in aberrant deposition of extracellular matrix (ECM) proteins. However, although much is known about the pathophysiology of IPF, the cellular and molecular processes that occur and allow aberrant fibroblast activation remain an unmet need. To explore the differentially expressed proteins (DEPs) associated with aberrant activation of these fibroblasts, we used the IPF lung fibroblast cell lines LL97A (IPF-1) and LL29 (IPF-2), compared to the normal lung fibroblast cell line CCD19Lu (NL-1). Protein samples were quantified and identified using a label-free quantitative proteomic analysis approach by liquid chromatography-tandem mass spectrometry (LC-MS/MS). DEPs were identified after pairwise comparison, including all experimental groups. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Protein–Protein Interaction (PPI) network construction were used to interpret the proteomic data. Eighty proteins expressed exclusively in the IPF-1 and IPF-2 clusters were identified. In addition, 19 proteins were identified up-regulated in IPF-1 and 10 in IPF-2; 10 proteins were down-regulated in IPF-1 and 2 in IPF-2 when compared to the NL-1 proteome. Using the search tool for retrieval of interacting genes/proteins (STRING) software, a PPI network was constructed between the DEPs and the 80 proteins expressed exclusively in the IPF-2 and IPF-1 clusters, containing 115 nodes and 136 edges. The 10 hub proteins present in the IPP network were identified using the CytoHubba plugin of the Cytoscape software. GO and KEGG pathway analyses showed that the hub proteins were mainly related to cell adhesion, integrin binding, and hematopoietic cell lineage. Our results provide relevant information on DEPs present in IPF lung fibroblast cell lines when compared to the normal lung fibroblast cell line that could play a key role during IPF pathogenesis.
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Affiliation(s)
- Juan Manuel Velázquez-Enríquez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico; (J.M.V.-E.); (A.A.R.-H.); (I.R.-A.); (K.G.-G.)
| | - Alma Aurora Ramírez-Hernández
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico; (J.M.V.-E.); (A.A.R.-H.); (I.R.-A.); (K.G.-G.)
| | | | - Itayetzi Reyes-Avendaño
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico; (J.M.V.-E.); (A.A.R.-H.); (I.R.-A.); (K.G.-G.)
| | - Karina González-García
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico; (J.M.V.-E.); (A.A.R.-H.); (I.R.-A.); (K.G.-G.)
| | - Cristian Jiménez-Martínez
- Departamento de Ingeniería Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Unidad Profesional Adolfo López Mateos, Zacatenco, Av. Wilfrido Massieu Esq. Cda. Miguel Stampa S/N, Alcaldía Gustavo A. Madero, Mexico City 07738, Mexico;
| | - Luis Castro-Sánchez
- Conacyt-Centro Universitario de Investigaciones Biomédicas “CUIB”, Universidad de Colima, Colima 28045, Mexico;
| | - Xariss Miryam Sánchez-Chino
- Catedra-Conacyt, Departamento de Salud El Colegio de La Frontera Sur, Unidad Villahermosa, Tabasco 86280, Mexico;
| | | | - Rafael Baltiérrez-Hoyos
- Conacyt-Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico;
- Correspondence:
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8
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Shaikh A, Olkhanud PB, Gangaplara A, Kone A, Patel S, Gucek M, Fitzhugh CD. Thrombospondin-1, Platelet Factor 4, and Galectin-1 are Associated with Engraftment in Patients with Sickle Cell Disease Who Underwent Haploidentical HSCT. Transplant Cell Ther 2022; 28:249.e1-249.e13. [PMID: 35131485 PMCID: PMC9176382 DOI: 10.1016/j.jtct.2022.01.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022]
Abstract
Sickle cell disease (SCD) is an inherited red blood cell disorder that leads to significant morbidity and early mortality. The most widely available curative approach remains allogeneic hematopoietic stem cell transplantation (HSCT). HLA-haploidentical (haplo) HSCT expands the donor pool considerably and is a practical alternative for these patients, but traditionally with an increased risk of allograft rejection. Biomarkers in patient plasma could potentially help predict HSCT outcome and allow treatment at an early stage to reverse or prevent graft rejection. Reliable, noninvasive methods to predict engraftment or rejection early after HSCT are needed. We sought to detect variations in the plasma proteomes of patients who engrafted compared with those who rejected their grafts. We used a mass spectrometry-based proteomics approach to identify candidate biomarkers associated with engraftment and rejection by comparing plasma samples obtained from 9 engrafted patients and 10 patients who experienced graft rejection. A total of 1378 proteins were identified, 45 of which were differentially expressed in the engrafted group compared with the rejected group. Based on bioinformatics analysis results, information from the literature, and immunoassay availability, 7 proteins-thrombospondin-1 (Tsp-1), platelet factor 4 (Pf-4), talin-1, moesin, cell division control protein 42 homolog (CDC42), galectin-1 (Gal-1), and CD9-were selected for further analysis. We compared these protein concentrations among 35 plasma samples (engrafted, n = 9; rejected, n = 10; healthy volunteers, n = 8; nontransplanted SCD, n = 8). ELISA analysis confirmed the significant up-regulation of Tsp-1, Pf-4, and Gal-1 in plasma samples from engrafted patients compared with rejected patients, healthy African American volunteers, and the nontransplanted SCD group (P < .01). By receiver operating characteristic analysis, these 3 proteins distinguished engrafted patients from the other groups (area under the curve, >0.8; P < .05). We then evaluated the concentration of these 3 proteins in samples collected pre-HSCT and at days +30, +60, +100, and +180 post-HSCT. The results demonstrate that Tsp-1 and Pf-4 stratified engrafted patients as early as day 60 post-HSCT (P < .01), and that Gal-1 was significantly higher in engrafted patients as early as day 30 post-HSCT (P < .01). We also divided the rejected group into those who experienced primary (n = 5) and secondary graft rejection (n = 5) and found that engrafted patients had significantly higher Tsp-1 levels compared with patients who developed primary graft rejection at days +60 and +100 (P < .05), as well as higher Pf-4 levels compared with patients who developed primary graft rejection at post-transplantation (PT) day 100. Furthermore, Tsp-1 levels were significantly higher at PT days 60 and 100 and Pf-4 levels were higher at PT day 100 in engrafted patients compared with those who experienced secondary graft rejection. Increased concentrations of plasma Gal-1, Tsp-1, and Pf-4 could reflect increased T regulatory cells, IL-10, and TGF-β, which are essential players in the initiation of immunologic tolerance. These biomarkers may provide opportunities for preemptive intervention to minimize the incidence of graft rejection.
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Affiliation(s)
- Ahmad Shaikh
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland; Department of Biology, The Catholic University of America, Washington, DC; Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Purevdorj B Olkhanud
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Arunakumar Gangaplara
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Abdoul Kone
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Sajni Patel
- Proteomics Core, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Marjan Gucek
- Proteomics Core, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Courtney D Fitzhugh
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland.
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9
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Zheng P, Sun S, Wang J, Cheng ZJ, Lei KC, Xue M, Zhang T, Huang H, Zhang XD, Sun B. Integrative omics analysis identifies biomarkers of idiopathic pulmonary fibrosis. Cell Mol Life Sci 2022; 79:66. [PMID: 35015148 PMCID: PMC11075137 DOI: 10.1007/s00018-021-04094-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/30/2021] [Accepted: 12/15/2021] [Indexed: 12/17/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease characterized by chronic progressive pulmonary fibrosis and a poor prognosis. Genetic studies, including transcriptomic and proteomics, have provided new insight into revealing mechanisms of IPF. Herein we provided a novel strategy to identify biomarkers by integrative analysis of transcriptomic and proteomic profiles of IPF patients. We examined the landscape of IPF patients' gene expression in the transcription and translation phases and investigated the expression and functions of two new potential biomarkers. Differentially expressed (DE) mRNAs were mainly enriched in pathways associated with immune system activities and inflammatory responses, while DE proteins are related to extracellular matrix production and wound repair. The upregulated genes in both phases are associated with wound repair and cell differentiation, while the downregulated genes in both phases are associated with reduced immune activities and the damage of the alveolar tissues. On this basis, we identified thirteen potential marker genes. Among them, we validated the expression changes of butyrophilin-like 9 (BTNL9) and plasmolipin (PLLP) and investigated their functional pathways in the IPF mechanism. Both genes are downregulated in the tissues of IPF patients and Bleomycin-induced mice, and co-expression analysis indicates that they have a protective effect by inhibiting extracellular matrix production and promoting wound repair in alveolar epithelial cells.
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Affiliation(s)
- Peiyan Zheng
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Shixue Sun
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Jingxian Wang
- National Joint Local Engineering Laboratory for Cell Engineering and Biomedicine Technique, Guizhou Province Key Laboratory of Regenerative Medicine, Key Laboratory of Adult Stem Cell Translational Research (Chinese Academy of Medical Sciences), Guizhou Medical University, Guizhou, 550025, China
| | - Zhangkai Jason Cheng
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Kuan Cheok Lei
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Mingshan Xue
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Teng Zhang
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Huimin Huang
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | | | - Baoqing Sun
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China.
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Proteomic analysis of serum samples of paracoccidioidomycosis patients with severe pulmonary sequel. PLoS Negl Trop Dis 2021; 15:e0009714. [PMID: 34424905 PMCID: PMC8425554 DOI: 10.1371/journal.pntd.0009714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 09/08/2021] [Accepted: 08/06/2021] [Indexed: 12/26/2022] Open
Abstract
Background Pulmonary sequelae (PS) in patients with chronic paracoccidioidomycosis (PCM) typically include pulmonary fibrosis and emphysema. Knowledge of the molecular pathways involved in PS of PCM is required for treatment and biomarker identification. Methodology/Principal findings This non-concurrent cohort study included 29 patients with pulmonary PCM that were followed before and after treatment. From this group, 17 patients evolved to mild/ moderate PS and 12 evolved severe PS. Sera from patients were evaluated before treatment and at clinical cure, serological cure, and apparent cure. A nanoACQUITY UPLC-Xevo QT MS system and PLGS software were used to identify serum differentially expressed proteins, data are available via ProteomeXchange with identifier PXD026906. Serum differentially expressed proteins were then categorized using Cytoscape software and the Reactome pathway database. Seventy-two differentially expressed serum proteins were identified in patients with severe PS compared with patients with mild/moderate PS. Most proteins altered in severe PS were involved in wound healing, inflammatory response, and oxygen transport pathways. Before treatment and at clinical cure, signaling proteins participating in wound healing, complement cascade, cholesterol transport and retinoid metabolism pathways were downregulated in patients with severe PS, whereas signaling proteins in gluconeogenesis and gas exchange pathways were upregulated. At serological cure, the pattern of protein expression reversed. At apparent cure pathways related with tissue repair (fibrosis) became downregulated, and pathway related oxygen transport became upregulated. Additionally, we identified 15 proteins as candidate biomarkers for severe PS. Conclusions/Significance Development of severe PS is related to increased expression of proteins involved in glycolytic pathway and oxygen exchange), indicative of the greater cellular activity and replication associated with early dysregulation of wound healing and aberrant tissue repair. Our findings provide new targets to study mechanisms of PS in PCM, as well as potential biomarkers. Pulmonary fibrosis is the main sequel of paracoccidioidomycosis (PCM), a fungal disease that affects mainly men, rural workers. The development of pulmonary fibrosis is complex and involves several mechanisms that culminate in aberrant collagen production and deposition in the lungs making it became stiff and blocking the air passages. These changes lead to difficulty in breathing and in PCM patients dyspnea in response to high or low levels of exertion is common. Therefore, these patients show incapacity to work and the decreased quality of life. With the possibility of identifying some marker, for example, it could help the indication of respiratory physiotherapy, professional rehabilitation, or therapeutic intervention. This is the first study to examine the pulmonary sequelae (PS) in patients with paracoccidioidomycosis using an approach combining proteomics with bioinformatics. Here, we identify the specific proteome pattern found in PCM patients with severe sequelae that distinguishes these patients from that with mild/moderate sequelae. Our results showed that time points immediately before treatment and at clinical cure are key moments at which PS can progress to severe PS due a dysregulation in wound healing with consequent delayed in the healing processes resulting in an aberrant scar. As such, we suggest that the prognoses for severe PS should be considered as soon as possible and as early as diagnosis of PCM. Furthermore, we used proteomics to identify possible serum biomarkers with which to predict the likely development of severe PS, to be validated in future studies.
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Proteomic Analysis Reveals Key Proteins in Extracellular Vesicles Cargo Associated with Idiopathic Pulmonary Fibrosis In Vitro. Biomedicines 2021; 9:biomedicines9081058. [PMID: 34440261 PMCID: PMC8394197 DOI: 10.3390/biomedicines9081058] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/29/2022] Open
Abstract
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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12
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Khan T, Dasgupta S, Ghosh N, Chaudhury K. Proteomics in idiopathic pulmonary fibrosis: the quest for biomarkers. Mol Omics 2021; 17:43-58. [PMID: 33073811 DOI: 10.1039/d0mo00108b] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a debilitating chronic progressive and fibrosing lung disease that culminates in the destruction of alveolar integrity and dismal prognosis. Its etiology is unknown and pathophysiology remains unclear. While great advances have been made in elucidating the pathogenesis mechanism, considerable gaps related to information on pathogenetic pathways and key protein targets involved in the clinical course of the disease exist. These issues need to be addressed for better clinical management of this highly challenging disease. Omics approach has revolutionized the entire area of disease understanding and holds promise in its translation to clinical biomarker discovery. This review outlines the contribution of proteomics towards identification of important biomarkers in IPF in terms of their clinical utility, i.e. prognosis, differential diagnosis, disease progression and treatment monitoring. The major dysregulated pathways associated with IPF are also discussed. Based on numerous proteomics studies on human and animal models, it is proposed that IPF pathogenesis involves complex interactions of several pathways such as oxidative stress, endoplasmic reticulum stress, unfolded protein response, coagulation system, inflammation, abnormal wounding, fibroblast proliferation, fibrogenesis and deposition of extracellular matrix. These pathways and their key path-changing mediators need further validation in large well-planned multi-centric trials at various geographical locations for successful development of clinical biomarkers of this confounding disease.
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Affiliation(s)
- Tila Khan
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Sanjukta Dasgupta
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Nilanjana Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
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Mishra S, Shah MI, Udhaya Kumar S, Thirumal Kumar D, Gopalakrishnan C, Al-Subaie AM, Magesh R, George Priya Doss C, Kamaraj B. Network analysis of transcriptomics data for the prediction and prioritization of membrane-associated biomarkers for idiopathic pulmonary fibrosis (IPF) by bioinformatics approach. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 123:241-273. [PMID: 33485486 DOI: 10.1016/bs.apcsb.2020.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a rare yet crucial persistent lung disorder that actuates scarring of lung tissues, which makes breathing difficult. Smoking, environmental pollution, and certain viral infections could initiate lung scarring. However, the molecular mechanism involved in IPF remains elusive. To develop an efficient therapeutic arsenal against IPF, it is vital to understand the pathology and deviations in biochemical pathways that lead to disorder. In this study, we availed network analysis and other computational pipelines to delineate the prominent membrane proteins as diagnostic biomarkers and therapeutic targets for IPF. This study yielded a significant role of glycosaminoglycan binding, endothelin, and GABA-B receptor signaling pathway in IPF pathogenesis. Furthermore, ADCY8, CRH, FGB, GPR17, MCHR1, NMUR1, and SAA1 genes were found to be immensely involved with IPF, and the enrichment pathway analysis suggests that most of the pathways were corresponding to membrane transport and signal transduction functionalities. This analysis could help in better understanding the molecular mechanism behind IPF to develop an efficient therapeutic target or biomarkers for IPF.
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Affiliation(s)
- Smriti Mishra
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, India; Navipoint Health India Pvt Ltd, Moula-Ali, Hyderabad, Telangana, India
| | - Mohammad Imran Shah
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, India; Navipoint Health India Pvt Ltd, Moula-Ali, Hyderabad, Telangana, India
| | - S Udhaya Kumar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - D Thirumal Kumar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | | | - Abeer Mohammed Al-Subaie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - R Magesh
- Faculty of Biomedical Sciences, Technology & Research, Department of Biotechnology, Sri Ramachandra University, Chennai, Tamil Nadu, India
| | - C George Priya Doss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Balu Kamaraj
- Department of Neuroscience Technology, College of Applied Medical Sciences in Jubail, Imam Abdulrahman Bin Faisal University, Jubail, Saudi Arabia
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14
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Nieto‐Fontarigo JJ, González‐Barcala FJ, Andrade‐Bulos LJ, San‐José ME, Cruz MJ, Valdés‐Cuadrado L, Crujeiras RM, Arias P, Salgado FJ. iTRAQ-based proteomic analysis reveals potential serum biomarkers of allergic and nonallergic asthma. Allergy 2020; 75:3171-3183. [PMID: 32424932 DOI: 10.1111/all.14406] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/16/2020] [Accepted: 04/30/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Asthma is heterogeneous disease with different phenotypes, endotypes and severities. Definition of these subgroups requires the identification of biomarkers in biological samples, and serum proteomics is a useful and minimally invasive method for this purpose. Therefore, the aim of this study was to detect serum proteins whose abundance is distinctively associated with different asthma phenotypes (allergic vs nonallergic) or severities. METHODS For each group of donors (32 healthy controls, 43 allergic rhinitis patients and 192 asthmatics with different phenotypes and severities), we generated two pools of sera that were analysed by a shotgun MS approach based on combinatorial peptide ligand libraries and iTRAQ-LC-MS/MS. RESULTS MS analyses identified 18 proteins with a differential abundance. Functional/network study of these proteins identified key processes for asthma pathogenesis, such as complement activation, extracellular matrix organization, platelet activation and degranulation, or post-translational protein phosphorylation. Furthermore, our results highlighted an enrichment of the "Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)" route in allergic asthma and the lectin pathway of complement activation in nonallergic asthma. Thus, several proteins (eg IGFALS, HSPG2, FCN2 or MASP1) displayed a differential abundance between the different groups of donors. Particularly, our results revealed IGFALS as a useful biomarker for moderate-severe allergic asthma. CONCLUSION Our data suggest a set of serum biomarkers, especially IGFALS, capable of differentiating allergic from nonallergic asthma. These proteins reveal different pathophysiological mechanisms and may be useful in the future for diagnosis, prognosis or targeted therapy purposes.
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Affiliation(s)
- Juan José Nieto‐Fontarigo
- Department of Biochemistry and Molecular Biology Faculty of Biology‐Biological Research Centre (CIBUS) Universidade de Santiago de Compostela Santiago de Compostela Spain
| | - Francisco Javier González‐Barcala
- Department of Medicine Universidade de Santiago de Compostela Santiago de Compostela Spain
- Department of Respiratory Medicine University Hospital of Santiago de Compostela Santiago de Compostela Spain
- Health Research Institute of Santiago de Compostela (IDIS) Santiago de Compostela Spain
- Spanish Biomedical Research Networking Centre‐CIBERES Madrid Spain
| | - Luis Juan Andrade‐Bulos
- Department of Biochemistry and Molecular Biology Faculty of Biology‐Biological Research Centre (CIBUS) Universidade de Santiago de Compostela Santiago de Compostela Spain
| | - María Esther San‐José
- Clinical Analysis Service University Hospital of Santiago de Compostela Santiago de Compostela Spain
| | - María Jesús Cruz
- Spanish Biomedical Research Networking Centre‐CIBERES Madrid Spain
- Department of Respiratory Medicine‐Hospital Vall d'Hebron Universitat Autònoma de Barcelona Barcelona Spain
| | - Luis Valdés‐Cuadrado
- Department of Medicine Universidade de Santiago de Compostela Santiago de Compostela Spain
- Department of Respiratory Medicine University Hospital of Santiago de Compostela Santiago de Compostela Spain
- Health Research Institute of Santiago de Compostela (IDIS) Santiago de Compostela Spain
| | - Rosa María Crujeiras
- Department of Statistics, Mathematical Analysis and Optimization Universidade de Santiago de Compostela Santiago de Compostela Spain
| | - Pilar Arias
- Department of Biochemistry and Molecular Biology Faculty of Biology‐Biological Research Centre (CIBUS) Universidade de Santiago de Compostela Santiago de Compostela Spain
| | - Francisco Javier Salgado
- Department of Biochemistry and Molecular Biology Faculty of Biology‐Biological Research Centre (CIBUS) Universidade de Santiago de Compostela Santiago de Compostela Spain
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15
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HSP90 Inhibition and Modulation of the Proteome: Therapeutical Implications for Idiopathic Pulmonary Fibrosis (IPF). Int J Mol Sci 2020; 21:ijms21155286. [PMID: 32722485 PMCID: PMC7432830 DOI: 10.3390/ijms21155286] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 01/05/2023] Open
Abstract
Idiopathic Pulmonary fibrosis (IPF) is a catastrophic disease with poor outcomes and limited pharmacological approaches. Heat shock protein 90 (HSP90) has been recently involved in the wound-healing pathological response that leads to collagen deposition in patients with IPF and its inhibition represents an exciting drug target against the development of pulmonary fibrosis. Under physiological conditions, HSP90 guarantees proteostasis through the refolding of damaged proteins and the degradation of irreversibly damaged ones. Additionally, its inhibition, by specific HSP90 inhibitors (e.g., 17 AAG, 17 DAG, and AUY-922) has proven beneficial in different preclinical models of human disease. HSP90 inhibition modulates a complex subset of kinases and interferes with intracellular signaling pathways and proteome regulation. In this review, we evaluated the current evidence and rationale for the use of HSP90 inhibitors in the treatment of pulmonary fibrosis, discussed the intracellular pathways involved, described the limitations of the current understanding and provided insights for future research.
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Wan XL, Zhou ZL, Wang P, Zhou XM, Xie MY, Mei J, Weng J, Xi HT, Chen C, Wang ZY, Wang ZB. Small molecule proteomics quantifies differences between normal and fibrotic pulmonary extracellular matrices. Chin Med J (Engl) 2020; 133:1192-1202. [PMID: 32433051 PMCID: PMC7249707 DOI: 10.1097/cm9.0000000000000754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Pulmonary fibrosis is a respiratory disease caused by the proliferation of fibroblasts and accumulation of the extracellular matrix (ECM). It is known that the lung ECM is mainly composed of a three-dimensional fiber mesh filled with various high-molecular-weight proteins. However, the small-molecular-weight proteins in the lung ECM and their differences between normal and fibrotic lung ECM are largely unknown. METHODS Healthy adult male Sprague-Dawley rats (Rattus norvegicus) weighing about 150 to 200 g were randomly divided into three groups using random number table: A, B, and C and each group contained five rats. The rats in Group A were administered a single intragastric (i.g.) dose of 500 μL of saline as control, and those in Groups B and C were administered a single i.g. dose of paraquat (PQ) dissolved in 500 μL of saline (20 mg/kg). After 2 weeks, the lungs of rats in Group B were harvested for histological observation, preparation of de-cellularized lung scaffolds, and proteomic analysis for small-molecular-weight proteins, and similar procedures were performed on Group C and A after 4 weeks. The differentially expressed small-molecular-weight proteins (DESMPs) between different groups and the subcellular locations were analyzed. RESULTS Of the 1626 small-molecular-weight proteins identified, 1047 were quantifiable. There were 97 up-regulated and 45 down-regulated proteins in B vs. A, 274 up-regulated and 31 down-regulated proteins in C vs. A, and 237 up-regulated and 28 down-regulated proteins identified in C vs. B. Both the up-regulated and down-regulated proteins in the three comparisons were mainly distributed in single-organism processes and cellular processes within biological process, cell and organelle within cellular component, and binding within molecular function. Further, more up-regulated than down-regulated proteins were identified in most sub-cellular locations. The interactions of DESMPs identified in extracellular location in all comparisons showed that serum albumin (Alb) harbored the highest degree of node (25), followed by prolyl 4-hydroxylase beta polypeptide (12), integrin β1 (10), apolipoprotein A1 (9), and fibrinogen gamma chain (9). CONCLUSIONS Numerous PQ-induced DESMPs were identified in de-cellularized lungs of rats by high throughput proteomics analysis. The DESMPs between the control and treatment groups showed diversity in molecular functions, biological processes, and pathways. In addition, the interactions of extracellular DESMPs suggested that the extracellular proteins Alb, Itgb1, Apoa1, P4hb, and Fgg in ECM could be potentially used as biomarker candidates for pulmonary fibrosis. These results provided useful information and new insights regarding pulmonary fibrosis.
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Affiliation(s)
- Xin-Long Wan
- Platform for Radiation Protection and Emergency Preparedness of Southern Zhejiang, School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Center for Health Assessment, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zhi-Liang Zhou
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Peng Wang
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Xiao-Ming Zhou
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Meng-Ying Xie
- Department of Geriatric Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Jin Mei
- Institute of Bioscaffold Transplantation and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jie Weng
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Hai-Tao Xi
- Institute of Bioscaffold Transplantation and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Chan Chen
- Department of Geriatric Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Zhi-Yi Wang
- Center for Health Assessment, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Department of Emergency Medicine and General Practice, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Institute of Bioscaffold Transplantation and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zhi-Bin Wang
- Institute of Bioscaffold Transplantation and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
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Label-free plasma proteomics identifies haptoglobin-related protein as candidate marker of idiopathic pulmonary fibrosis and dysregulation of complement and oxidative pathways. Sci Rep 2020; 10:7787. [PMID: 32385381 PMCID: PMC7211010 DOI: 10.1038/s41598-020-64759-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/19/2020] [Indexed: 02/06/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a lung parenchymal disease of unknown cause usually occurring in older adults. It is a chronic and progressive condition with poor prognosis and diagnosis is largely clinical. Currently, there exist few biomarkers that can predict patient outcome or response to therapies. Together with lack of markers, the need for novel markers for the detection and monitoring of IPF, is paramount. We have performed label-free plasma proteomics of thirty six individuals, 17 of which had confirmed IPF. Proteomics data was analyzed by volcano plot, hierarchical clustering, Partial-least square discriminant analysis (PLS-DA) and Ingenuity pathway analysis. Univariate and multivariate statistical analysis overlap identified haptoglobin-related protein as a possible marker of IPF when compared to control samples (Area under the curve 0.851, ROC-analysis). LXR/RXR activation and complement activation pathways were enriched in t-test significant proteins and oxidative regulators, complement proteins and protease inhibitors were enriched in PLS-DA significant proteins. Our pilot study points towards aberrations in complement activation and oxidative damage in IPF patients and provides haptoglobin-related protein as a new candidate biomarker of IPF.
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Identification of Urinary Biomarkers for Exercise-Induced Immunosuppression by iTRAQ Proteomics. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3030793. [PMID: 32047808 PMCID: PMC7003279 DOI: 10.1155/2020/3030793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/20/2019] [Accepted: 12/30/2019] [Indexed: 12/16/2022]
Abstract
Purpose To identify noninvasive immune biomarkers of exercise-induced immunosuppression using the iTRAQ proteomics technique. Methods Fifteen healthy males were recruited and subjected to a four-week incremental treadmill running training program. After each week of training, WBC counts and CD4+ and CD8+ lymphocytes were measured to monitor the immune function status. iTRAQ proteomics technology was used to identify differential proteins and their characteristics in urine. Results Our data showed that the WBC counts, CD4+ lymphocytes, and CD4+/CD8+ ratio decreased by more than 10% after four weeks of training, suggesting exercise-induced immunosuppression. A total of 1854 proteins were identified in urine during the incremental running using the iTRAQ technology. Compared with the urine before training, there were 89, 52, 77, and 148 proteins significantly upregulated and 66, 27, 68, and 114 proteins significantly downregulated after each week, respectively. Among them, four upregulated proteins, SEMG-1, PIP, PDGFRL, and NDPK, increased their abundance with the increased exercise intensity. Bioinformatics analysis indicates that these proteins are involved in stress response and immune function. Conclusion Four weeks of incremental treadmill running induced immunosuppression in healthy males. By using iTRAQ proteomics, four proteins in the urine, SEMG-1, PIP, PDGFRL, and NDPK, were found to increase incrementally with the increased exercise intensity, which have the potential to be used as noninvasive immune biomarkers of exercise-induced immunosuppression.
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19
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Sullivan DI, Kass DJ. Signals and signposts: Biomarkers in IPF and PAH at the crossroads of clinical relevance. Respirology 2019; 24:1044-1045. [PMID: 31486582 PMCID: PMC8491577 DOI: 10.1111/resp.13694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 08/14/2019] [Indexed: 01/10/2023]
Abstract
See related Article and Article
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Affiliation(s)
- Daniel I Sullivan
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel J Kass
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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20
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Peripheral blood proteomic profiling of idiopathic pulmonary fibrosis biomarkers in the multicentre IPF-PRO Registry. Respir Res 2019; 20:227. [PMID: 31640794 PMCID: PMC6805665 DOI: 10.1186/s12931-019-1190-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/20/2019] [Indexed: 01/28/2023] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease for which diagnosis and management remain challenging. Defining the circulating proteome in IPF may identify targets for biomarker development. We sought to quantify the circulating proteome in IPF, determine differential protein expression between subjects with IPF and controls, and examine relationships between protein expression and markers of disease severity. Methods This study involved 300 patients with IPF from the IPF-PRO Registry and 100 participants without known lung disease. Plasma collected at enrolment was analysed using aptamer-based proteomics (1305 proteins). Linear regression was used to determine differential protein expression between participants with IPF and controls and associations between protein expression and disease severity measures (percent predicted values for forced vital capacity [FVC] and diffusion capacity of the lung for carbon monoxide [DLco]; composite physiologic index [CPI]). Multivariable models were fit to select proteins that best distinguished IPF from controls. Results Five hundred fifty one proteins had significantly different levels between IPF and controls, of which 47 showed a |log2(fold-change)| > 0.585 (i.e. > 1.5-fold difference). Among the proteins with the greatest difference in levels in patients with IPF versus controls were the glycoproteins thrombospondin 1 and von Willebrand factor and immune-related proteins C-C motif chemokine ligand 17 and bactericidal permeability-increasing protein. Multivariable classification modelling identified nine proteins that, when considered together, distinguished IPF versus control status with high accuracy (area under receiver operating curve = 0.99). Among participants with IPF, 14 proteins were significantly associated with FVC % predicted, 23 with DLco % predicted, 14 with CPI. Four proteins (roundabout homolog-2, spondin-1, polymeric immunoglobulin receptor, intercellular adhesion molecule 5) demonstrated the expected relationship across all three disease severity measures. When considered in pathways analyses, proteins associated with the presence or severity of IPF were enriched in pathways involved in platelet and haemostatic responses, vascular or platelet derived growth factor signalling, immune activation, and extracellular matrix organisation. Conclusions Patients with IPF have a distinct circulating proteome and can be distinguished using a nine-protein profile. Several proteins strongly associate with disease severity. The proteins identified may represent biomarker candidates and implicate pathways for further investigation. Trial registration ClinicalTrials.gov (NCT01915511).
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21
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Tatsuno K, Midorikawa Y, Takayama T, Yamamoto S, Nagae G, Moriyama M, Nakagawa H, Koike K, Moriya K, Aburatani H. Impact of AAV2 and Hepatitis B Virus Integration Into Genome on Development of Hepatocellular Carcinoma in Patients with Prior Hepatitis B Virus Infection. Clin Cancer Res 2019; 25:6217-6227. [PMID: 31320595 DOI: 10.1158/1078-0432.ccr-18-4041] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/29/2019] [Accepted: 07/11/2019] [Indexed: 12/31/2022]
Abstract
PURPOSE Hepatitis B viral (HBV) DNA is frequently integrated into the genomes of hepatocellular carcinoma (HCC) in patients with chronic HBV infection (chronic HBV, hereafter), whereas the frequency of HBV integration in patients after the disappearance of HBV (prior HBV, hereafter) has yet to be determined. This study aimed to detect integration of HBV and adeno-associated virus type 2 (AAV2) into the human genome as a possible oncogenic event. EXPERIMENTAL DESIGN Virome capture sequencing was performed, using HCC and liver samples obtained from 243 patients, including 73 with prior HBV without hepatitis C viral (HCV) infection and 81 with chronic HBV. RESULTS Clonal HBV integration events were identified in 11 (15.0%) cases of prior HBV without HCV and 61 (75.3%) cases of chronic HBV (P < 0.001). Several driver genes were commonly targeted by HBV, leading to transcriptional activation of these genes; TERT [four (5.4%) vs. 15 (18.5%)], KMT2B [two (2.7%) vs. five (6.1%)], CCNE1 [zero vs. one (1.2%)], CCNA2 [zero vs. one (1.2%)]. Conversely, CCNE1 and CCNA2 were, respectively, targeted by AAV2 only in prior HBV. In liver samples, HBV genome recurrently integrated into fibrosis-related genes FN1, HS6ST3, KNG1, and ROCK1 in chronic HBV. There was not history of alcohol abuse and 3 patients with a history of nucleoside analogue treatment for HBV in 8 prior HBV with driver gene integration. CONCLUSIONS Despite the seroclearance of hepatitis B surface antigen, HBV or AAV2 integration in prior HBV was not rare; therefore, such patients are at risk of developing HCC.
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Affiliation(s)
- Kenji Tatsuno
- Genome Science Division, RCAST, University of Tokyo, Tokyo, Japan
| | - Yutaka Midorikawa
- Genome Science Division, RCAST, University of Tokyo, Tokyo, Japan. .,Department of Digestive Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Tadatoshi Takayama
- Department of Digestive Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Shogo Yamamoto
- Genome Science Division, RCAST, University of Tokyo, Tokyo, Japan
| | - Genta Nagae
- Genome Science Division, RCAST, University of Tokyo, Tokyo, Japan
| | - Mitsuhiko Moriyama
- Department of Gastroenterology and Hepatology, Nihon University School of Medicine, Tokyo, Japan
| | - Hayato Nakagawa
- Department of Gastroenterology, University of Tokyo, Tokyo, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, University of Tokyo, Tokyo, Japan
| | - Kyoji Moriya
- Department of Infectious Diseases, University of Tokyo, Tokyo, Japan
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22
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Moodley YP, Corte TJ, Oliver BG, Glaspole IN, Livk A, Ito J, Peters K, Lipscombe R, Casey T, Tan DBA. Analysis by proteomics reveals unique circulatory proteins in idiopathic pulmonary fibrosis. Respirology 2019; 24:1111-1114. [PMID: 31393655 DOI: 10.1111/resp.13668] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 04/13/2019] [Accepted: 06/04/2019] [Indexed: 11/26/2022]
Abstract
BACKGROUND AND OBJECTIVE Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic disease that has a poor 3-year median survival rate with unclear pathophysiology. Radiological features include bibasal, subpleural fibrosis and honeycombing while its pathology is characterized by fibroblastic foci and honeycombing. Proteomic analysis of circulating molecules in plasma may identify factors that characterize IPF and may assist in the diagnosis, prognostication and determination of pathogenic pathways in this condition. METHODS Two independent quantitative proteomic techniques were used, isobaric tags for relative and absolute quantitation (iTRAQ) and multiple reaction monitoring (MRM), to identify differentially expressed plasma proteins in a group of IPF patients in comparison to healthy controls with normal lung function matched for age and gender. RESULTS Five proteins were identified to be differentially expressed in IPF compared to healthy controls (upregulation of platelet basic protein and downregulation of actin, cytoplasmic 2, antithrombin-III, extracellular matrix protein-1 and fibronectin). CONCLUSION This study further validates the combinational use of non-targeted discovery proteomics (iTRAQ) with targeted quantitation by mass spectrometry (MRM) of soluble biomarkers to identify potentially important molecules and pathways for pulmonary diseases such as IPF.
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Affiliation(s)
- Yuben P Moodley
- School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia.,Stem Cell Unit, Institute for Respiratory Health, Perth, WA, Australia.,Department of Respiratory Medicine, Fiona Stanley Hospital, Perth, WA, Australia.,National Health and Medical Research Council Centre of Research Excellence in Pulmonary Fibrosis, University of Sydney, Sydney, NSW, Australia
| | - Tamera J Corte
- National Health and Medical Research Council Centre of Research Excellence in Pulmonary Fibrosis, University of Sydney, Sydney, NSW, Australia.,Department of Respiratory Medicine, Royal Prince Alfred Hospital, Sydney, NSW, Australia.,School of Medicine, University of Sydney, Sydney, NSW, Australia
| | - Brian G Oliver
- Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Ian N Glaspole
- National Health and Medical Research Council Centre of Research Excellence in Pulmonary Fibrosis, University of Sydney, Sydney, NSW, Australia.,Department of Allergy and Respiratory Medicine, The Alfred Hospital, Melbourne, VIC, Australia.,Faculty of Medicine, Monash University, Melbourne, VIC, Australia
| | | | - Jason Ito
- Proteomics International, Perth, WA, Australia
| | | | | | - Tammy Casey
- Proteomics International, Perth, WA, Australia
| | - Dino B A Tan
- School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia.,Stem Cell Unit, Institute for Respiratory Health, Perth, WA, Australia
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23
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Du C, Weng Y, Lou J, Zeng G, Liu X, Jin H, Lin S, Tang L. Isobaric tags for relative and absolute quantitation‑based proteomics reveals potential novel biomarkers for the early diagnosis of acute myocardial infarction within 3 h. Int J Mol Med 2019; 43:1991-2004. [PMID: 30896787 PMCID: PMC6443345 DOI: 10.3892/ijmm.2019.4137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 03/04/2019] [Indexed: 12/13/2022] Open
Abstract
Acute myocardial infarction (AMI) is one of the most common and life-threatening cardiovascular diseases. However, the ability to diagnose AMI within 3 h is currently lacking. The present study aimed to identify the differentially expressed proteins of AMI within 3 h and to investigate novel biomarkers using isobaric tags for relative and absolute quantitation (ITRAQ) technology. A total of 30 beagle dogs were used for establishing the MI models successfully by injecting thrombin powder and a polyethylene microsphere suspension. Serum samples were collected prior to (0 h) and following MI (1, 2 and 3 h). ITRAQ-coupled liquid chromatography-mass spectrometry (LC-MS) technology was used to identify the differentially expressed proteins. The bioinformatics analysis selected several key proteins in the initiation of MI. Further analysis was performed using STRING software. Finally, western blot analysis was used to evaluate the results obtained from ITRAQ. In total, 28 proteins were upregulated and 23 were downregulated in the 1 h/0 h group, 28 proteins were upregulated and 26 were downregulated in the 2 h/0 h group, and 24 proteins were upregulated and 19 were downregulated in the 3 h/0 h group. The Gene Ontology (GO) annotation and functional enrichment analysis identified 19 key proteins. Protein-protein interactions (PPIs) were investigated using the STRING database. GO enrichment analysis revealed that a number of key proteins, including ATP synthase F1 subunit β (ATP5B), cytochrome c oxidase subunit 2 and cytochrome c, were components of the electron transport chain and were involved in energy metabolism. The western blot analysis demonstrated that the expression of ATP5B decreased significantly at all three time points (P<0.01), which was consistent with the ITRAQ results, whereas the expression of fibrinogen γ chain increased at 2 and 3 h (P<0.01) and the expression of integrator complex subunit 4 increased at all three time points (P<0.01), which differed from the ITRAQ results. According to the proteomics of the beagle dog MI model, ATP5B may serve as the potential biomarkers of AMI. Mitochondrial dysfunction and disruption of the electron transport chain may be critical indicators of early MI within 3 h. These finding may provide a novel direction for the diagnosis of AMI.
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Affiliation(s)
- Changqing Du
- Department of Cardiology, Zhejiang Hospital, Hangzhou, Zhejiang 310013, P.R. China
| | - Yingzheng Weng
- Department of Medicine, School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Jiangjie Lou
- Department of Medicine, School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Guangzhong Zeng
- Department of Cardiology, Pingxiang City People's Hospital, Pingxiang, Jiangxi 337055, P.R. China
| | - Xiaowei Liu
- Department of Cardiology, Zhejiang Hospital, Hangzhou, Zhejiang 310013, P.R. China
| | - Hongfeng Jin
- Department of Cardiology, Zhejiang Hospital, Hangzhou, Zhejiang 310013, P.R. China
| | - Senna Lin
- Department of Medicine, The Second College of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Lijiang Tang
- Department of Cardiology, Zhejiang Hospital, Hangzhou, Zhejiang 310013, P.R. China
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Tian Y, Li H, Gao Y, Liu C, Qiu T, Wu H, Cao M, Zhang Y, Ding H, Chen J, Cai H. Quantitative proteomic characterization of lung tissue in idiopathic pulmonary fibrosis. Clin Proteomics 2019; 16:6. [PMID: 30774578 PMCID: PMC6364390 DOI: 10.1186/s12014-019-9226-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 01/27/2019] [Indexed: 02/06/2023] Open
Abstract
Background Idiopathic 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. Methods To 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. Results A 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. Conclusions This 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.
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Affiliation(s)
- Yaqiong Tian
- 1Department of Respiratory Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
| | - Hui Li
- 1Department of Respiratory Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
| | - Yujuan Gao
- 1Department of Respiratory Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
| | - Chuanmei Liu
- 2Department of Respiratory Medicine, Yi Ji Shan Hospital of Wannan Medical College, No. 2 Zheshan West Road, Wuhu, 241001 Anhui People's Republic of China
| | - Ting Qiu
- Department of Respiratory Medicine, KunShan Hospital of Traditional Chinese Medicine, No. 189 Chaoyang Road, Kunshan, 215300 Jiangsu People's Republic of China
| | - Hongyan Wu
- 4Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
| | - Mengshu Cao
- 1Department of Respiratory Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
| | - Yingwei Zhang
- 1Department of Respiratory Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
| | - Hui Ding
- 5Department of Respiratory Medicine, Yixing People Hospital, Affiliated Jiangsu University, No. 75 Tongzhenguan Road, Yixing, 214200 Jiangsu People's Republic of China
| | - Jingyu Chen
- 6Jiangsu Key Laboratory of Organ Transplantation, Wuxi People's Hospital, Nanjing Medical University, No. 299 Qingyang Road, Wuxi, 214023 Jiangsu People's Republic of China
| | - Hourong Cai
- 1Department of Respiratory Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
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25
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Analytical techniques for characterization of biological molecules - proteins and aptamers/oligonucleotides. Bioanalysis 2018; 11:103-117. [PMID: 30475073 DOI: 10.4155/bio-2018-0225] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
With the advent of the high-throughput technologies and exciting times for biology, the discipline of analytical methodology is experiencing a surge in the growth and the scope. Over the years, multitude of analytical techniques have evolved from a work-intensive, low sensitivity and high volume of reagent and sample consumption endeavor to automated, better selectivity, lower limit of quantification and cost-effective techniques for biological research. In this review, we give an overview of the currently available wide range of cell-based and noncell based and structural based analytical techniques, their principle and biological applications. The analytical techniques discussed in this paper includes surface plasmon resonance, electrophoresis, enzyme linked immunosorbent assay, Western blotting, flow cytometry, fluorescence activated cell sorting, mass spectrometry, nuclear magnetic resonance and x-ray crystallography.
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26
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Walraven M, Hinz B. Therapeutic approaches to control tissue repair and fibrosis: Extracellular matrix as a game changer. Matrix Biol 2018; 71-72:205-224. [DOI: 10.1016/j.matbio.2018.02.020] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/22/2018] [Accepted: 02/23/2018] [Indexed: 02/08/2023]
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27
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Belushkin A, Yesilkoy F, Altug H. Nanoparticle-Enhanced Plasmonic Biosensor for Digital Biomarker Detection in a Microarray. ACS NANO 2018; 12:4453-4461. [PMID: 29715005 DOI: 10.1021/acsnano.8b00519] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nanoplasmonic devices have become a paradigm for biomolecular detection enabled by enhanced light-matter interactions in the fields from biological and pharmaceutical research to medical diagnostics and global health. In this work, we present a bright-field imaging plasmonic biosensor that allows visualization of single subwavelength gold nanoparticles (NPs) on large-area gold nanohole arrays (Au-NHAs). The sensor generates image heatmaps that reveal the locations of single NPs as high-contrast spikes, enabling the detection of individual NP-labeled molecules. We implemented the proposed method in a sandwich immunoassay for the detection of biotinylated bovine serum albumin (bBSA) and human C-reactive protein (CRP), a clinical biomarker of acute inflammatory diseases. Our method can detect 10 pg/mL of bBSA and 27 pg/mL CRP in 2 h, which is at least 4 orders of magnitude lower than the clinically relevant concentrations. Our sensitive and rapid detection approach paired with the robust large-area plasmonic sensor chips, which are fabricated using scalable and low-cost manufacturing, provides a powerful platform for multiplexed biomarker detection in various settings.
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Affiliation(s)
- Alexander Belushkin
- Institute of BioEngineering , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Filiz Yesilkoy
- Institute of BioEngineering , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Hatice Altug
- Institute of BioEngineering , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
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28
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Honda H, Fujimoto M, Serada S, Urushima H, Mishima T, Lee H, Ohkawara T, Kohno N, Hattori N, Yokoyama A, Naka T. Leucine-rich α-2 glycoprotein promotes lung fibrosis by modulating TGF- β signaling in fibroblasts. Physiol Rep 2017; 5:5/24/e13556. [PMID: 29279415 PMCID: PMC5742708 DOI: 10.14814/phy2.13556] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 11/24/2022] Open
Abstract
TGF‐β has an important role in fibrotic diseases, including idiopathic pulmonary fibrosis (IPF). Detailed analysis of TGF‐β signaling in pulmonary fibrosis at the molecular level is needed to identify novel therapeutic targets. Recently, leucine‐rich alpha‐2 glycoprotein (LRG) was reported to function as a modulator of TGF‐β signaling in angiogenesis and tumor progression. However, the involvement of LRG in fibrotic disorders, including IPF, has not yet been investigated. In this study, we investigated the role of LRG in fibrosis by analyzing LRG knockout (KO) mice with bleomycin‐induced lung fibrosis, an animal model of pulmonary fibrosis. The amount of LRG in the lungs of wild‐type (WT) mice was increased by bleomycin administration prior to fibrosis development. In LRG KO mice, lung fibrosis was significantly suppressed, as indicated by attenuated Masson's trichrome staining and lower collagen content than those in WT mice. Moreover, in the lungs of LRG KO mice, phosphorylation of Smad2 was reduced and expression of α‐SMA was decreased relative to those in WT mice. In vitro experiments indicated that LRG enhanced the TGF‐β‐induced phosphorylation of Smad2 and the expression of Serpine1 and Acta2, the downstream of Smad2, in fibroblasts. Although endoglin, an accessory TGF‐β receptor, is essential for LRG to promote TGF‐β signaling in endothelial cells during angiogenesis, we found that endoglin did not contribute to the ability of LRG to enhance Smad2 phosphorylation in fibroblasts. Taken together, our data suggest that LRG promotes lung fibrosis by modulating TGF‐β‐induced Smad2 phosphorylation and activating profibrotic responses in fibroblasts.
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Affiliation(s)
- Hiromi Honda
- Center for Intractable Immune Disease, Kochi Medical School, Kochi University, Nankoku, Japan.,Laboratory of Immune Signal, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan
| | - Minoru Fujimoto
- Center for Intractable Immune Disease, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Satoshi Serada
- Center for Intractable Immune Disease, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Hayato Urushima
- Department of Anatomy and Regenerative Biology, Osaka City University Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Takashi Mishima
- Laboratory of Immune Signal, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan
| | - Hyun Lee
- Center for Intractable Immune Disease, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Tomoharu Ohkawara
- Center for Intractable Immune Disease, Kochi Medical School, Kochi University, Nankoku, Japan
| | | | - Noboru Hattori
- Department of Molecular and Internal Medicine, Graduate School of Biomedical Science, Hiroshima University, Minami-ku, Hiroshima, Japan
| | - Akihito Yokoyama
- Department of Haematology and Respiratory Medicine, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Tetsuji Naka
- Center for Intractable Immune Disease, Kochi Medical School, Kochi University, Nankoku, Japan.,Laboratory of Immune Signal, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan
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Wu J, Li X, Zhao M, Huang H, Sun W, Gao Y. Early Detection of Urinary Proteome Biomarkers for Effective Early Treatment of Pulmonary Fibrosis in a Rat Model. Proteomics Clin Appl 2017; 11. [DOI: 10.1002/prca.201700103] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 09/12/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Jianqiang Wu
- Department of Pathophysiology; Institute of Basic Medical Sciences; Chinese Academy of Medical Sciences; School of Basic Medicine; Peking Union Medical College; Beijing China
| | - Xundou Li
- Department of Pathophysiology; Institute of Basic Medical Sciences; Chinese Academy of Medical Sciences; School of Basic Medicine; Peking Union Medical College; Beijing China
| | - Mindi Zhao
- Department of Pathophysiology; Institute of Basic Medical Sciences; Chinese Academy of Medical Sciences; School of Basic Medicine; Peking Union Medical College; Beijing China
| | - He Huang
- Department of Biochemistry and Molecular Biology; School of Life Sciences; Beijing Normal University; Gene Engineering and Biotechnology Beijing Key Laboratory; Beijing China
| | - Wei Sun
- Core Facility of Instrument; Institute of Basic Medical Sciences; Chinese Academy of Medical Sciences; School of Basic Medicine; Peking Union Medical College; Beijing China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology; School of Life Sciences; Beijing Normal University; Gene Engineering and Biotechnology Beijing Key Laboratory; Beijing China
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Greiffo FR, Eickelberg O, Fernandez IE. Systems medicine advances in interstitial lung disease. Eur Respir Rev 2017; 26:26/145/170021. [PMID: 28954764 DOI: 10.1183/16000617.0021-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/15/2017] [Indexed: 01/17/2023] Open
Abstract
Fibrotic lung diseases involve subject-environment interactions, together with dysregulated homeostatic processes, impaired DNA repair and distorted immune functions. Systems medicine-based approaches are used to analyse diseases in a holistic manner, by integrating systems biology platforms along with clinical parameters, for the purpose of understanding disease origin, progression, exacerbation and remission.Interstitial lung diseases (ILDs) refer to a heterogeneous group of complex fibrotic diseases. The increase of systems medicine-based approaches in the understanding of ILDs provides exceptional advantages by improving diagnostics, unravelling phenotypical differences, and stratifying patient populations by predictable outcomes and personalised treatments. This review discusses the state-of-the-art contributions of systems medicine-based approaches in ILDs over the past 5 years.
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Affiliation(s)
- Flavia R Greiffo
- Comprehensive Pneumology Center, Ludwig-Maximilians-Universität, University Hospital Grosshadern and Helmholtz Zentrum München and Member of the German Center for Lung Research, Munich, Germany
| | - Oliver Eickelberg
- Comprehensive Pneumology Center, Ludwig-Maximilians-Universität, University Hospital Grosshadern and Helmholtz Zentrum München and Member of the German Center for Lung Research, Munich, Germany.,Division of Respiratory Sciences and Critical Care Medicine, Dept of Medicine, University of Colorado, Denver, CO, USA
| | - Isis E Fernandez
- Comprehensive Pneumology Center, Ludwig-Maximilians-Universität, University Hospital Grosshadern and Helmholtz Zentrum München and Member of the German Center for Lung Research, Munich, Germany
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