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Effendi WI, Nagano T. Epigenetics Approaches toward Precision Medicine for Idiopathic Pulmonary Fibrosis: Focus on DNA Methylation. Biomedicines 2023; 11:biomedicines11041047. [PMID: 37189665 DOI: 10.3390/biomedicines11041047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Genetic information is not transmitted solely by DNA but by the epigenetics process. Epigenetics describes molecular missing link pathways that could bridge the gap between the genetic background and environmental risk factors that contribute to the pathogenesis of pulmonary fibrosis. Specific epigenetic patterns, especially DNA methylation, histone modifications, long non-coding, and microRNA (miRNAs), affect the endophenotypes underlying the development of idiopathic pulmonary fibrosis (IPF). Among all the epigenetic marks, DNA methylation modifications have been the most widely studied in IPF. This review summarizes the current knowledge concerning DNA methylation changes in pulmonary fibrosis and demonstrates a promising novel epigenetics-based precision medicine.
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Goobie GC, Li X, Ryerson CJ, Carlsten C, Johannson KA, Fabisiak JP, Lindell KO, Chen X, Gibson KF, Kass DJ, Nouraie SM, Zhang Y. PM 2.5 and constituent component impacts on global DNA methylation in patients with idiopathic pulmonary fibrosis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120942. [PMID: 36574806 DOI: 10.1016/j.envpol.2022.120942] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/14/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive interstitial lung disease (ILD) whose outcomes are worsened with air pollution exposures. DNA methylation (DNAm) patterns are altered in lungs and blood from patients with IPF, but the relationship between air pollution exposures and DNAm patterns in IPF remains unexplored. This study aimed to evaluate the association of PM2.5 and constituent components with global DNAm in patients with IPF. Patients enrolled in either the University of Pittsburgh Simmons Center for ILD Registry (Simmons) or the U.S.-wide Pulmonary Fibrosis Foundation (PFF) Patient Registry with peripheral blood DNA samples were included. The averages of monthly exposures to PM2.5 and constituents over 1-year and 3-months pre-blood collection were matched to patient residential coordinates using satellite-derived hybrid models. Global DNAm percentage (%5 mC) was determined using the ELISA-based MethylFlash assay. Associations of pollutants with %5 mC were assessed using beta-regression, Cox models for mortality, and linear regression for baseline lung function. Mediation proportion was determined for models where pollutant-mortality and pollutant-%5 mC associations were significant. Inclusion criteria were met by 313 Simmons and 746 PFF patients with IPF. Higher PM2.5 3-month exposures prior to blood collection were associated with higher %5 mC in Simmons (β = 0.02, 95%CI 0.0003-0.05, p = 0.047), with trends in the same direction in the 1-year period in both cohorts. Higher exposures to sulfate, nitrate, ammonium, and black carbon constituents were associated with higher %5 mC in multiple models. Percent 5 mC was not associated with IPF mortality or lung function, but was found to mediate between 2 and 5% of the associations of PM2.5, sulfate, and ammonium with mortality. In conclusion, we found that higher global DNAm is a novel biomarker for increased PM2.5 and anthropogenic constituent exposure in patients with IPF. Mechanistic research is needed to determine if DNAm has pathogenic relevance in mediating associations between pollutants and mortality in IPF.
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Affiliation(s)
- Gillian C Goobie
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA; Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
| | - Xiaoyun Li
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Christopher J Ryerson
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada; Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada.
| | - Christopher Carlsten
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada; Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Vancouver, BC, Canada.
| | - Kerri A Johannson
- Division of Respiratory Medicine, Department of Medicine, University of Calgary, Calgary, AB, Canada.
| | - James P Fabisiak
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Kathleen O Lindell
- Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; College of Nursing, Medical University of South Carolina, Charleston, SC, USA.
| | - Xiaoping Chen
- Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Kevin F Gibson
- Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Daniel J Kass
- Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - S Mehdi Nouraie
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Yingze Zhang
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA; Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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3
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Li J, Wang R, Shi W, Chen X, Yi J, Yang X, Jin S. Epigenetic regulation in radiation-induced pulmonary fibrosis. Int J Radiat Biol 2022; 99:384-395. [PMID: 35895014 DOI: 10.1080/09553002.2022.2089365] [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: 10/16/2022]
Abstract
PURPOSE Radiation-induced pulmonary fibrosis (RIPF) is a common and serious adverse effect of radiotherapy for thoracic tumors, which occurs in the irreversible stage of radiation-induced lung injury (RILI) >6 months after irradiation. It is characterized by progressive and irreversible destruction of lung tissue and deterioration of lung function, which may impair quality of life and lead to respiratory failure and death. We hope this will draw attention to the involvement of epigenetics in the regulation of RIPF. CONCLUSIONS This review summarizes research progress on the role and mechanism of DNA methylation, noncoding RNA and RNA methylation in RIPF or RILI, and the possible role and mechanism of histone modification in RIPF. We have noticed that in tissue fibrosis, the epigenetic regulation mechanisms inside and outside the nucleus can influence each other. We speculate that RIPF may be regulated by an epigenetic regulatory network during its development, and believe that TGF-β, SNAIL, PTEN and EZH2 are four targets worthy of in-depth study.
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Affiliation(s)
- Jiale Li
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Rui Wang
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Wen Shi
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Xiaoyi Chen
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Junxuan Yi
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Xiangshan Yang
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Shunzi Jin
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
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4
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Salani F, Latarani M, Casadei-Gardini A, Gangadharannambiar P, Fornaro L, Vivaldi C, Pecora I, Massa V, Marisi G, Canale M, Ulivi P, Scartozzi M, Eccleston M, Masi G, Crea F. Predictive significance of circulating histones in hepatocellular carcinoma patients treated with sorafenib. Epigenomics 2022; 14:507-517. [PMID: 35473355 DOI: 10.2217/epi-2021-0383] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: Predictive biomarkers for advanced hepatocellular carcinoma are lacking. EZH2 drives sorafenib resistance through H3K27me3 and is counteracted by SETD2, which catalyzes H3K36me3. The authors tested the predictive power of circulating H3K27me3 and H3K36me3 in advanced hepatocellular carcinoma patients treated with sorafenib. Methods: A total of 80 plasma samples were tested for histone variants by ELISA. Changes from baseline to best response or progressive disease were correlated with patient survival. Results: A higher EZH2/SETD2 ratio predicted worse prognosis in this setting. H3K27me3 and H3K36me3 decreased from baseline to best response. The H3K27me3/H3K36me3 ratio increased from baseline to progressive disease. Higher ratios at best response were associated with shorter progression-free survival. Conclusion: The authors suggest that circulating H3K27me3/H3K36me3 ratio level acts as a predictive biomarker for sorafenib treatment outcomes in patients with advanced hepatocellular carcinoma.
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Affiliation(s)
- Francesca Salani
- Sant'Anna School of Advanced Studies, Institute of Life Sciences, Piazza Martiri della Libertà 33, Pisa, 56124, Italy.,Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, MK7 6AA, UK.,Medical Oncology Department, Pisa University, Via Savi 10, Pisa, 56126, Italy
| | - Maryam Latarani
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, MK7 6AA, UK
| | - Andrea Casadei-Gardini
- Department of Oncology, Vita-Salute San Raffaele University, Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Scientific Institute Hospital, Milan, Italy
| | | | - Lorenzo Fornaro
- Medical Oncology Department, Azienda Ospedaliero-Universitaria Pisana, Via Roma 67, 56100, Pisa
| | - Caterina Vivaldi
- Department of Translational Research and New Technologies for Medicine and Surgery, University of Pisa, Via Savi 10, Pisa, 56126, Italy
| | - Irene Pecora
- Unit of Medical Oncology, Ospedale Misericordia di Grosseto,Via Senese, 161, Grosseto, 58100, Italy
| | - Valentina Massa
- Medical Oncology Department, Pisa University, Via Savi 10, Pisa, 56126, Italy
| | - Giorgia Marisi
- Biosciences Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico Istituto Romagnolo per lo Studio dei Tumori 'Dino Amadori,' Meldola, 47014, Italy
| | - Matteo Canale
- Biosciences Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico Istituto Romagnolo per lo Studio dei Tumori 'Dino Amadori,' Meldola, 47014, Italy
| | - Paola Ulivi
- Biosciences Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico Istituto Romagnolo per lo Studio dei Tumori 'Dino Amadori,' Meldola, 47014, Italy
| | - Mario Scartozzi
- Department of Medical Sciences and Public Health, University of Cagliari, Via Università, 40, Cagliari CA, 09124, Italy
| | - Mark Eccleston
- Belgian Volition SPRL, Parc Scientifique Créalys, Rue Phocas Lejeune 22, Isnes, BE, 5032, Belgium
| | - Gianluca Masi
- Department of Translational Research and New Technologies for Medicine and Surgery, University of Pisa, Via Savi 10, Pisa, 56126, Italy
| | - Francesco Crea
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, MK7 6AA, UK
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Faniyi AA, Hughes MJ, Scott A, Belchamber KBR, Sapey E. Inflammation, Ageing and Diseases of the Lung: Potential therapeutic strategies from shared biological pathways. Br J Pharmacol 2021; 179:1790-1807. [PMID: 34826882 DOI: 10.1111/bph.15759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 10/07/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022] Open
Abstract
Lung diseases disproportionately affect elderly individuals. The lungs form a unique environment: a highly elastic organ with gaseous exchange requiring the closest proximity of inhaled air containing harmful agents and the circulating blood volume. The lungs are highly susceptible to senescence, with age and "inflammageing" creating a pro-inflammatory environment with a reduced capacity to deal with challenges. Whilst lung diseases may have disparate causes, the burden of ageing and inflammation provides a common process which can exacerbate seemingly unrelated pathologies. However, these shared pathways may also provide a common route to treatment, with increased interest in drugs which target ageing processes across respiratory diseases. In this review, we will examine the evidence for the increased burden of lung disease in older adults, the structural and functional changes seen with advancing age and assess what our expanding knowledge of inflammation and ageing pathways could mean for the treatment of lung disease.
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Affiliation(s)
- A A Faniyi
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, U.K
| | - M J Hughes
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, U.K
| | - A Scott
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, U.K
| | - K B R Belchamber
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, U.K
| | - E Sapey
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, U.K
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The Crucial Role of NLRP3 Inflammasome in Viral Infection-Associated Fibrosing Interstitial Lung Diseases. Int J Mol Sci 2021; 22:ijms221910447. [PMID: 34638790 PMCID: PMC8509020 DOI: 10.3390/ijms221910447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/17/2021] [Accepted: 09/24/2021] [Indexed: 12/11/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF), one of the most common fibrosing interstitial lung diseases (ILD), is a chronic-age-related respiratory disease that rises from repeated micro-injury of the alveolar epithelium. Environmental influences, intrinsic factors, genetic and epigenetic risk factors that lead to chronic inflammation might be implicated in the development of IPF. The exact triggers that initiate the fibrotic response in IPF remain enigmatic, but there is now increasing evidence supporting the role of chronic exposure of viral infection. During viral infection, activation of the NLRP3 inflammasome by integrating multiple cellular and molecular signaling implicates robust inflammation, fibroblast proliferation, activation of myofibroblast, matrix deposition, and aberrant epithelial-mesenchymal function. Overall, the crosstalk of the NLRP3 inflammasome and viruses can activate immune responses and inflammasome-associated molecules in the development, progression, and exacerbation of IPF.
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7
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Mechanism of Fei-Xian Formula in the Treatment of Pulmonary Fibrosis on the Basis of Network Pharmacology Analysis Combined with Molecular Docking Validation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:6658395. [PMID: 34394391 PMCID: PMC8357467 DOI: 10.1155/2021/6658395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 06/21/2021] [Accepted: 07/16/2021] [Indexed: 01/05/2023]
Abstract
Objective This study aimed to clarify the mechanism of Fei-Xian formula (FXF) in the treatment of pulmonary fibrosis based on network pharmacology analysis combined with molecular docking validation. Methods Firstly, ingredients in FXF with pharmacological activities, together with specific targets, were identified based on the BATMA-TCM and TCMSP databases. Then, targets associated with pulmonary fibrosis, which included pathogenic targets as well as those known therapeutic targets, were screened against the CTD, TTD, GeneCards, and DisGeNet databases. Later, Cytoscape was employed to construct a candidate component-target network of FXF for treating pulmonary fibrosis. In addition, for nodes within the as-constructed network, topological parameters were calculated using CytoHubba plug-in, and the degree value (twice as high as the median degree value for all the nodes) was adopted to select core components as well as core targets of FXF for treating pulmonary fibrosis, which were subsequently utilized for constructing the core network. Furthermore, molecular docking study was carried out on those core active ingredients together with the core targets using AutoDock Vina for verifying results of network pharmacology analysis. At last, OmicShare was employed for enrichment analysis of the core targets. Results Altogether 12 active ingredients along with 13 core targets were identified from our constructed core component-target network of FXF for the treatment of pulmonary fibrosis. As revealed by enrichment analysis, the 13 core targets mostly concentrated in regulating biological functions, like response to external stimulus (from oxidative stress, radiation, UV, chemical substances, and virus infection), apoptosis, cell cycle, aging, immune process, and protein metabolism. In addition, several pathways, like IL-17, AGE-RAGE, TNF, HIF-1, PI3K-AKT, NOD-like receptor, T/B cell receptor, and virus infection-related pathways, exerted vital parts in FXF in the treatment of pulmonary fibrosis. Conclusions FXF can treat pulmonary fibrosis through a “multicomponent, multitarget, and multipathway” mean. Findings in this work lay foundation for further exploration of the FXF mechanism in the treatment of pulmonary fibrosis.
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8
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Guiot J, Njock MS, André B, Gester F, Henket M, de Seny D, Moermans C, Malaise MG, Louis R. Serum IGFBP-2 in systemic sclerosis as a prognostic factor of lung dysfunction. Sci Rep 2021; 11:10882. [PMID: 34035374 PMCID: PMC8149825 DOI: 10.1038/s41598-021-90333-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/07/2021] [Indexed: 01/17/2023] Open
Abstract
Systemic sclerosis (SSc) is a rare connective tissue disease associated with rapid evolving interstitial lung disease (ILD), driving its mortality. Specific biomarkers associated with the progression of this lung disease are highly needed. We aimed to identify specific biomarkers of SSc-ILD to predict the evolution of the disease. For this, we compared prospectively serum levels of several biomarkers associated with lung fibrosis in SSc patients (n = 102), among which SSc-no ILD (n = 63) and SSc-ILD (n = 39), compared to healthy subjects (HS) (n = 39). We also performed a longitudinal study in a subgroup of 28 patients analyzing biomarkers variations and pulmonary function tests over a period of 2 years. Serum level of IGFBP-2 was significantly increased in SSc patients compared to HS, and negatively correlated with pulmonary function (assessed by carbon monoxide transfer coefficient (KCO)) (r = - 0.29, p < 0.01). Two-year longitudinal analysis in a subgroup of 28 SSc patients determined that IGFBP-2 variation was positively correlated with KCO at 2-year follow-up (r = 0.6, p < 0.001). SSc patients with a lower variation of IGFBP-2 (less than 22%) presented significant deterioration of pulmonary function at 2-year follow-up (p < 0.01). ROC curve analysis enabled us to identify that baseline IGFBP-2 > 105 ng/ml was associated with a poor outcome (KCO < 70% predicted) at 2-year follow-up (AUC = 0.75, p < 0.05). We showed for the first time that serum levels of IGFBP-2 might be a prognostic factor of the development of SSc-ILD.
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Affiliation(s)
- Julien Guiot
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
| | - Makon-Sébastien Njock
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium.
- Laboratory of Rheumatology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium.
| | - Béatrice André
- Laboratory of Rheumatology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
| | - Fanny Gester
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
| | - Monique Henket
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
| | - Dominique de Seny
- Laboratory of Rheumatology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
| | - Catherine Moermans
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
| | - Michel G Malaise
- Laboratory of Rheumatology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
| | - Renaud Louis
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
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9
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Inflammatory profile of induced sputum composition in systemic sclerosis and comparison with healthy volunteers. Sci Rep 2021; 11:10679. [PMID: 34021175 PMCID: PMC8139955 DOI: 10.1038/s41598-021-87701-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/25/2021] [Indexed: 12/29/2022] Open
Abstract
Systemic sclerosis (SSc) is a potentially serious and disabling connective tissue disease specially in case of interstitial lung disease (SSc-ILD). The aim of our study was to evaluate the potential utility of dosing in the induced sputum (IS) and to compare their levels in SSc-ILD and SSc-nonILD patients, as well as in healthy volunteers (HV). IS and sera values were also compared. In a prospective cross-sectional analysis, we studied the IS and serum provided from 25 SSc patients, 15 SSc-nonILD and 10 SSc-ILD, compared to 25 HV. We analyzed sputum cell composition and quantified in the supernatant and corresponding serum by commercially available immunoassays: IGFBP-1, IGFBP-2, IGFBP-3, TGF-β, IL-8, TNF-α, YKL-40, MMP-7 and MMP-9. Lung function was studied by the determination of FEV-1 (%), FVC (%), DLCO (%) and KCO (%). The IS of SSc patients had a lower weight than HV (p<0.05, p<0.01) without any significant difference with regard to the cellularity. IGFBP-1 (p < 0.0001), TGF-β (p < 0.05), IL-8 (p < 0.05), YKL-40 (p < 0.0001) and MMP-7 (p < 0.01) levels were increased in the IS of SSc patients compared to HV. Only IL-8 serum levels (p < 0.001) were increased in SSc patients compared to HV. Neither in IS nor in serum were observed differences between SSc-ILD and SSc-nonILD patients. Correlations were observed between IS IL-8 levels and FEV-1 (%) (r = = − 0.53, p < 0.01), FVC (%) (r = − 0.51, p < 0.01) and annualized ∆KCO (%) (r = 0.57, p < 0.05), between IS TGF-β levels and annualized ∆FEV-1 (%) (r = = − 0.57, p < 0.05), between IS IGFBP-2 levels and annualized ∆KCO (%) (r = 0.56, p < 0.05). Our study showed that SSc patients exhibit raised IS levels of IGFBP-1, TGF-β, IL-8, YKL-40 and MMP-7, molecules known to be involved in lung remodeling and fibrotic process, without any significant difference between SSc-ILD and SSc-nonILD patients. IL-8, TGF-β and IGFBP-2 are correlated with lung function in SSc patients which emphasize clinical relevance. IS analysis represents a new approach to understand lung inflammatory process in SSc patients. A longitudinal study is needed to evaluate their pathophysiological relevance.
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10
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Bowman WS, Echt GA, Oldham JM. Biomarkers in Progressive Fibrosing Interstitial Lung Disease: Optimizing Diagnosis, Prognosis, and Treatment Response. Front Med (Lausanne) 2021; 8:680997. [PMID: 34041256 PMCID: PMC8141562 DOI: 10.3389/fmed.2021.680997] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
Interstitial lung disease (ILD) comprises a heterogenous group of diffuse lung disorders that commonly result in irreversible pulmonary fibrosis. While idiopathic pulmonary fibrosis (IPF) is the prototypical progressive fibrosing ILD (PF-ILD), a high proportion of patients with other ILD subtypes develop a PF-ILD phenotype. Evidence exists for shared pathobiology leading to progressive fibrosis, suggesting that biomarkers of disease activity may prove informative across the wide spectrum of ILDs. Biomarker investigation to date has identified a number of molecular markers that predict relevant ILD endpoints, including disease presence, prognosis, and/or treatment response. In this review, we provide an overview of potentially informative biomarkers in patients with ILD, including those suggestive of a PF-ILD phenotype. We highlight the recent genomic, transcriptomic, and proteomic investigations that identified these biomarkers and discuss the body compartments in which they are found, including the peripheral blood, airway, and lung parenchyma. Finally, we identify critical gaps in knowledge within the field of ILD biomarker research and propose steps to advance the field toward biomarker implementation.
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Affiliation(s)
- Willis S Bowman
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California, Davis, Davis, CA, United States
| | - Gabrielle A Echt
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California, Davis, Davis, CA, United States
| | - Justin M Oldham
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California, Davis, Davis, CA, United States
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11
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Cavalier E, Guiot J, Lechner K, Dutsch A, Eccleston M, Herzog M, Bygott T, Schomburg A, Kelly T, Holdenrieder S. Circulating Nucleosomes as Potential Markers to Monitor COVID-19 Disease Progression. Front Mol Biosci 2021; 8:600881. [PMID: 33816549 PMCID: PMC8012533 DOI: 10.3389/fmolb.2021.600881] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/22/2021] [Indexed: 12/13/2022] Open
Abstract
The severity of coronavirus disease 2019 (COVID-19) varies significantly with cases spanning from asymptomatic to lethal with a subset of individuals developing Severe Acute Respiratory Syndrome (SARS) and death from respiratory failure. To determine whether global nucleosome and citrullinated nucleosome levels were elevated in COVID-19 patients, we tested two independent cohorts of COVID-19 positive patients with quantitative nucleosome immunoassays and found that nucleosomes were highly elevated in plasma of COVID-19 patients with a severe course of the disease relative to healthy controls and that both histone 3.1 variant and citrullinated nucleosomes increase with disease severity. Elevated citrullination of circulating nucleosomes is indicative of neutrophil extracellular trap formation, neutrophil activation and NETosis in severely affected individuals. Importantly, using hospital setting (outpatient, inpatient or ICU) as a proxy for disease severity, nucleosome levels increased with disease severity and may serve as a guiding biomarker for treatment. Owing to the limited availability of mechanical ventilators and extracorporal membrane oxygenation (ECMO) equipment, there is an urgent need for effective tools to rapidly assess disease severity and guide treatment selection. Based on our studies of two independent cohorts of COVID-19 patients from Belgium and Germany, we suggest further investigation of circulating nucleosomes and citrullination as biomarkers for clinical triage, treatment allocation and clinical drug discovery.
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Affiliation(s)
- Etienne Cavalier
- Clinical Chemistry Department, Centre Hospitalier Universitaire de Liege, Domaine Universitaire Du Sart-Tilman, Liège, Belgium
| | - Julien Guiot
- Pneumology Department, Centre Hospitalier Universitaire de Liege, Domaine Universitaire Du Sart-Tilman, Liège, Belgium
| | - Katharina Lechner
- Department of Cardiology, German Heart Centre Munich, Technical University Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich, Munich Heart Alliance, Munich, Germany
| | - Alexander Dutsch
- Department of Cardiology, German Heart Centre Munich, Technical University Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich, Munich Heart Alliance, Munich, Germany
| | | | | | | | - Adrian Schomburg
- Eisbach Bio GmbH, Munich, Germany.,Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Munich, Germany.,Volition Germany GmbH, Gräfelfing, Germany
| | | | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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12
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Verhoeven JGHP, Baan CC, Peeters AMA, Clahsen-van Groningen MC, Nieboer D, Herzog M, Eccleston M, Hesselink DA, Boer K. Circulating cell-free nucleosomes as biomarker for kidney transplant rejection: a pilot study. Clin Epigenetics 2021; 13:32. [PMID: 33573704 PMCID: PMC7879674 DOI: 10.1186/s13148-020-00969-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/04/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is an unmet need for noninvasive markers specific for kidney transplant rejection. Such a marker may eventually overcome the need for a transplant biopsy. In this pilot study, the potential of circulating cell-free nucleosomes (CCFN) to serve as a biomarker for kidney transplant rejection was evaluated. METHODS Forty de novo kidney transplant recipients were prospectively followed as part of a randomized, controlled clinical trial. Total CCFN (H3) and CCFN with the histone modifications H3K36me3 and H3 citrulline were measured in patients at four fixed time points: before transplantation and on days 3-6, 30 and 180 after kidney transplantation. In addition, serum collected at times of transplant rejection (n = 14) was analyzed. CCFN were measured with a Nu.Q™ Assay kit (VolitionRx), an ELISA-based assay using antibodies directed against nucleosomes. RESULTS For total CCFN (H3), H3K36me3, and H3 citrulline, the same pattern was seen over time: Concentrations were elevated shortly after transplantation (day 3-6) followed by a decline reaching baseline (pre-transplantation) values at days 30 and 180. At times of acute rejection, the median concentration of total CCFN (H3) was significantly higher compared to the stable situation (day 30): 4309 (3435-5285) versus 2885 (1668-3923) ng/mL, p < 0.05, respectively. Total CCFN (H3) had an acceptable ability to discriminate rejection from no rejection (AUC-ROC = 0.73) with a negative predictive value of 92.9%. For both histone modifications (H3K36me3 and H3 citrulline), there was no significant difference between episodes of acute rejection and the stable situation (day 30). CONCLUSION In this pilot study, total CCFN (H3) concentrations are increased at times of acute kidney transplant rejection. The high negative predictive value implies that whenever a patient experiences loss of renal transplant function and the total CCFN (H3) is not increased, causes other than acute rejection should be considered. Clinical implementation of total CCFN (H3) measurement may avoid unnecessary and potentially harmful kidney transplant biopsies.
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Affiliation(s)
- Jeroen G H P Verhoeven
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Room Na-524, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands. .,Rotterdam Transplant Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Carla C Baan
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Room Na-524, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.,Rotterdam Transplant Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Annemiek M A Peeters
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Room Na-524, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.,Rotterdam Transplant Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Daan Nieboer
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | | | - Dennis A Hesselink
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Room Na-524, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.,Rotterdam Transplant Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Karin Boer
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center Rotterdam, Room Na-524, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.,Rotterdam Transplant Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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13
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Hamanaka RB, Mutlu GM. Metabolic requirements of pulmonary fibrosis: role of fibroblast metabolism. FEBS J 2021; 288:6331-6352. [PMID: 33393204 DOI: 10.1111/febs.15693] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/22/2020] [Accepted: 12/31/2020] [Indexed: 12/27/2022]
Abstract
Fibrosis is a pathologic condition characterized by excessive deposition of extracellular matrix and chronic scaring that can affect every organ system. Organ fibrosis is associated with significant morbidity and mortality, contributing to as many as 45% of all deaths in the developed world. In the lung, many chronic lung diseases may lead to fibrosis, the most devastating being idiopathic pulmonary fibrosis (IPF), which affects approximately 3 million people worldwide and has a median survival of 3.8 years. Currently approved therapies for IPF do not significantly extend lifespan, and thus, there is pressing need for novel therapeutic strategies to treat IPF and other fibrotic diseases. At the heart of pulmonary fibrosis are myofibroblasts, contractile cells with characteristics of both fibroblasts and smooth muscle cells, which are the primary cell type responsible for matrix deposition in fibrotic diseases. Much work has centered around targeting the extracellular growth factors and intracellular signaling regulators of myofibroblast differentiation. Recently, metabolic changes associated with myofibroblast differentiation have come to the fore as targetable mechanisms required for myofibroblast function. In this review, we will discuss the metabolic changes associated with myofibroblast differentiation, as well as the mechanisms by which these changes promote myofibroblast function. We will then discuss the potential for this new knowledge to lead to the development of novel therapies for IPF and other fibrotic diseases.
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Affiliation(s)
- Robert B Hamanaka
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, IL, USA
| | - Gökhan M Mutlu
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, IL, USA
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14
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Dao L, Ragoonanan D, Yi S, Swinford R, Petropoulos D, Mahadeo KM, Li S. The Organ Trail: A Review of Biomarkers of Organ Failure. Front Oncol 2020; 10:579219. [PMID: 33262945 PMCID: PMC7686565 DOI: 10.3389/fonc.2020.579219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/15/2020] [Indexed: 11/13/2022] Open
Abstract
Pediatric organ failure and transplant populations face significant risks of morbidity and mortality. The risk of organ failure itself may be disproportionately higher among pediatric oncology patients, as cancer may originate within and/or metastasize to organs and adversely affect their function. Additionally, cancer directed therapies are frequently toxic to organs and may contribute to failure. Recent reports suggest that nearly half of providers find it difficult to provide prognostic information regarding organ failure due to unknown disease trajectories. Unfortunately, there is a lack of uniform methodology in detecting the early symptoms of organ failure, which may delay diagnosis, initiation of treatment and hinder prognostic planning. There remains a wide array of outstanding scientific questions regarding organ failure in pediatrics but emerging data may change the landscape of prognostication. Liquid biopsy, in which disease biomarkers are detected in bodily fluids, offers a noninvasive alternative to tissue biopsy and may improve prompt detection of organ failure and prognostication. Here, we review potential liquid biopsy biomarkers for organ failure, which may be particularly useful among pediatric oncology patients. We synthesized information from publications obtained on PubMed, Google Scholar, clinicaltrials.gov, and Web of Science and categorized our findings based on the type of biomarker used to detect organ failure. We highlight the advantages and disadvantages specific to each type of organ failure biomarker. While much work needs to be done to advance this field and validate its applicability to pediatric cancer patients facing critical care complications, herein, we highlight promising areas for future discovery.
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Affiliation(s)
- Long Dao
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Dristhi Ragoonanan
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sofia Yi
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Rita Swinford
- Division of Pediatric Nephrology, University of Texas Health Science Center Houston, Houston, TX, United States
| | - Demetrios Petropoulos
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Kris M Mahadeo
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Shulin Li
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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15
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Goobie GC, Nouraie M, Zhang Y, Kass DJ, Ryerson CJ, Carlsten C, Johannson KA. Air Pollution and Interstitial Lung Diseases: Defining Epigenomic Effects. Am J Respir Crit Care Med 2020; 202:1217-1224. [PMID: 32569479 PMCID: PMC7605178 DOI: 10.1164/rccm.202003-0836pp] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 06/10/2020] [Indexed: 12/15/2022] Open
Affiliation(s)
- Gillian C. Goobie
- Department of Human Genetics, Graduate School of Public Health and
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Yingze Zhang
- Department of Human Genetics, Graduate School of Public Health and
- Department of Medicine and
| | | | - Christopher J. Ryerson
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, British Columbia, Canada; and
| | - Christopher Carlsten
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, British Columbia, Canada; and
| | - Kerri A. Johannson
- Division of Respiratory Medicine, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
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16
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Insights into the Role of Bioactive Food Ingredients and the Microbiome in Idiopathic Pulmonary Fibrosis. Int J Mol Sci 2020; 21:ijms21176051. [PMID: 32842664 PMCID: PMC7503951 DOI: 10.3390/ijms21176051] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 02/08/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic disease mainly associated with aging and, to date, its causes are still largely unknown. It has been shown that dietary habits can accelerate or delay the occurrence of aging-related diseases; however, their potential role in IPF development has been underestimated so far. The present review summarizes the evidence regarding the relationship between diet and IPF in humans, and in animal models of pulmonary fibrosis, in which we discuss the bioactivity of specific dietary food ingredients, including fatty acids, peptides, amino acids, carbohydrates, vitamins, minerals and phytochemicals. Interestingly, many animal studies reveal preventive and therapeutic effects of particular compounds. Furthermore, it has been recently suggested that the lung and gut microbiota could be involved in IPF, a relationship which may be linked to changes in immunological and inflammatory factors. Thus, all the evidence so far puts forward the idea that the gut-lung axis could be modulated by dietary factors, which in turn have an influence on IPF development. Overall, the data reviewed here support the notion of identifying food ingredients with potential benefits in IPF, with the ultimate aim of designing nutritional approaches as an adjuvant therapeutic strategy.
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17
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Guiot J, Henket M, Andre B, Herzog M, Hardat N, Njock MS, Moermans C, Malaise M, Louis R. A new nucleosomic-based model to identify and diagnose SSc-ILD. Clin Epigenetics 2020; 12:124. [PMID: 32807242 PMCID: PMC7430109 DOI: 10.1186/s13148-020-00915-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/30/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Systemic sclerosis (SSc) is a rare connective tissue disease associated with rapid evolving interstitial lung disease (SSc-ILD), driving its mortality. Specific biomarkers associated with the evolution of the lung disease are highly needed. We aimed to identify specific biomarkers of SSc-ILD to predict the evolution of the disease. Nucleosomes are stable DNA/protein complexes that are shed into the blood stream making them ideal candidates for biomarkers. METHODS We studied circulating cell-free nucleosomes (cf-nucleosomes) in SSc patients, 31 with ILD (SSc-ILD) and 67 without ILD. We analyzed plasma levels for cf-nucleosomes and investigated whether global circulating nucleosome levels in association with or without other biomarkers of interest for systemic sclerosis or lung fibrosis (e.g., serum growth factors: IGFBP-1 and the MMP enzyme: MMP-9), could be suitable potential biomarkers for the correct identification of SSc-ILD disease. RESULTS We found that H3.1 nucleosome levels were significantly higher in patients with SSc-ILD compared SSc patients without ILD (p < 0.05) and levels of MMP-9 were significantly increased in patients with SSc-ILD compared to SSc patients without ILD (p < 0.05). Conversely, IGFBP-1 was significantly reduced in patients with SSc-ILD compared to SSc without ILD (p < 0.001). The combination of cf-nucleosomes H3.1 coupled to MMP-9 and IGFBP-1 increased the sensitivity for the differential detection of SSc-ILD. High levels of accuracy were reached with this combined model: its performances are strong with 68.4% of positive predictive value and 77.2% of negative predictive value for 90% of specificity. With our model, we identified a significant negative correlation with FVC % pred (r = -0.22) and TLC % pred (r = -0.31). The value of our model at T1 (baseline) has a predictive power over the Rodnan score at T2 (after 6-18 months), showed by a significant linear regression with R2 = 19% (p = 0.013). We identified in the sole group of SSc-ILD patients a significant linear regression with a R2 = 54.4% with the variation of DLCO between T1 and T2 (p < 0.05). CONCLUSION In our study, we identified a new blood-based model with nucleosomic biomarker in order to diagnose SSc-ILD in a SSc cohort. This model is correlated with TLC and FVC at baseline and predictive of the skin evolution and the DLCO. Further longitudinal exploration studies should be performed in order to evaluate the potential of such diagnostic and predictive model.
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Affiliation(s)
- Julien Guiot
- Pneumology Department, CHU Liège, Domaine Universitaire du Sart-Tilman, B35, B4000, Liège, Belgium.
| | - Monique Henket
- Pneumology Department, CHU Liège, Domaine Universitaire du Sart-Tilman, B35, B4000, Liège, Belgium
| | - Béatrice Andre
- Rheumatology Department, CHU Liège, Domaine Universitaire du Sart-Tilman, B35, B4000, Liège, Belgium
| | - Marielle Herzog
- Belgian Volition SPRL, Parc Scientifique Créalys, 22 rue Phocas lejeune, B5032, Isnes, Belgium
| | - Nathalie Hardat
- Belgian Volition SPRL, Parc Scientifique Créalys, 22 rue Phocas lejeune, B5032, Isnes, Belgium
| | - Makon-Sebastien Njock
- Pneumology Department, CHU Liège, Domaine Universitaire du Sart-Tilman, B35, B4000, Liège, Belgium
- Rheumatology Department, CHU Liège, Domaine Universitaire du Sart-Tilman, B35, B4000, Liège, Belgium
| | - Catherine Moermans
- Pneumology Department, CHU Liège, Domaine Universitaire du Sart-Tilman, B35, B4000, Liège, Belgium
| | - Michel Malaise
- Rheumatology Department, CHU Liège, Domaine Universitaire du Sart-Tilman, B35, B4000, Liège, Belgium
| | - Renaud Louis
- Pneumology Department, CHU Liège, Domaine Universitaire du Sart-Tilman, B35, B4000, Liège, Belgium
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18
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Guiot J, Cambier M, Boeckx A, Henket M, Nivelles O, Gester F, Louis E, Malaise M, Dequiedt F, Louis R, Struman I, Njock MS. Macrophage-derived exosomes attenuate fibrosis in airway epithelial cells through delivery of antifibrotic miR-142-3p. Thorax 2020; 75:870-881. [PMID: 32759383 PMCID: PMC7509395 DOI: 10.1136/thoraxjnl-2019-214077] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 05/31/2020] [Accepted: 06/11/2020] [Indexed: 12/14/2022]
Abstract
Introduction Idiopathic pulmonary fibrosis (IPF) is a progressive fibrosing interstitial lung disease of unknown aetiology and cure. Recent studies have reported a dysregulation of exosomal microRNAs (miRs) in the IPF context. However, the impact of IPF-related exosomal miRs on the progression of pulmonary fibrosis is unknown. Methods Two independent cohorts were enrolled at the ambulatory care polyclinic of Liège University. Exosomes from sputum were obtained from 19 patients with IPF and 23 healthy subjects (HSs) (cohort 1), and the ones from plasma derived from 14 patients with IPF and 14 HSs (cohort 2). Exosomal miR expression was performed by quantitative reverse transcription–PCR. The functional role of exosomal miRs was assessed in vitro by transfecting miR mimics in human alveolar epithelial cells and lung fibroblasts. Results Exosomal miR analysis showed that miR-142-3p was significantly upregulated in sputum and plasma of patients with IPF (8.06-fold, p<0.0001; 1.64 fold, p=0.008, respectively). Correlation analysis revealed a positive association between exosomal miR-142-3p and the percentage of macrophages from sputum of patients with IPF (r=0.576, p=0.012), suggesting macrophage origin of exosomal miR-142-3p upregulation. The overexpression of miR-142-3p in alveolar epithelial cells and lung fibroblasts was able to reduce the expression of transforming growth factor β receptor 1 (TGFβ-R1) and profibrotic genes. Furthermore, exosomes isolated from macrophages present antifibrotic properties due in part to the repression of TGFβ-R1 by miR-142-3p transfer in target cells. Discussion Our results suggest that macrophage-derived exosomes may fight against pulmonary fibrosis progression via the delivery of antifibrotic miR-142–3 p to alveolar epithelial cells and lung fibroblasts.
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Affiliation(s)
- Julien Guiot
- Department of Pneumology, GIGA-I3 Research Group, University of Liège (ULiege) and University Hospital of Liège (CHU Liege), Liège, Belgium
| | - Maureen Cambier
- Laboratory of Molecular Angiogenesis, GIGA Research, University of Liège, Liège, Belgium
| | - Amandine Boeckx
- Laboratory of Molecular Angiogenesis, GIGA Research, University of Liège, Liège, Belgium
| | - Monique Henket
- Department of Pneumology, GIGA-I3 Research Group, University of Liège (ULiege) and University Hospital of Liège (CHU Liege), Liège, Belgium
| | - Olivier Nivelles
- Laboratory of Molecular Angiogenesis, GIGA Research, University of Liège, Liège, Belgium
| | - Fanny Gester
- Department of Pneumology, GIGA-I3 Research Group, University of Liège (ULiege) and University Hospital of Liège (CHU Liege), Liège, Belgium
| | - Edouard Louis
- Department of Gastroenterology, GIGA-I3 Research Group, University of Liège (ULiege) and University Hospital of Liège (CHU Liege), Liège, Belgium
| | - Michel Malaise
- Department of Rheumatology, GIGA-I3 Research Group, University of Liège (ULiege) and University Hospital of Liège (CHU Liege), Liège, Belgium
| | - Franck Dequiedt
- GIGA-Molecular Biology of Diseases, Laboratory of Gene expression and Cancer, GIGA Research, University of Liège, Liège, Belgium
| | - Renaud Louis
- Department of Pneumology, GIGA-I3 Research Group, University of Liège (ULiege) and University Hospital of Liège (CHU Liege), Liège, Belgium
| | - Ingrid Struman
- Laboratory of Molecular Angiogenesis, GIGA Research, University of Liège, Liège, Belgium
| | - Makon-Sébastien Njock
- Department of Pneumology, GIGA-I3 Research Group, University of Liège (ULiege) and University Hospital of Liège (CHU Liege), Liège, Belgium
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Kang N, Eccleston M, Clermont PL, Latarani M, Male DK, Wang Y, Crea F. EZH2 inhibition: a promising strategy to prevent cancer immune editing. Epigenomics 2020; 12:1457-1476. [PMID: 32938196 PMCID: PMC7607396 DOI: 10.2217/epi-2020-0186] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
Immunotherapies are revolutionizing the clinical management of a wide range of cancers. However, intrinsic or acquired unresponsiveness to immunotherapies does occur due to the dynamic cancer immunoediting which ultimately leads to immune escape. The evolutionarily conserved histone modifier enhancer of zeste 2 (EZH2) is aberrantly overexpressed in a number of human cancers. Accumulating studies indicate that EZH2 is a main driver of cancer cells' immunoediting and mediate immune escape through downregulating immune recognition and activation, upregulating immune checkpoints and creating an immunosuppressive tumor microenvironment. In this review, we overviewed the roles of EZH2 in cancer immunoediting, the preclinical and clinical studies of current pharmacologic EZH2 inhibitors and the prospects for EZH2 inhibitor and immunotherapy combination for cancer treatment.
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Affiliation(s)
- Ning Kang
- Department of Experimental Therapeutics, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Mark Eccleston
- Belgian Volition SPRL, Parc Scientifique Créalys, Rue Phocas Lejeune 22, BE-5032 Isnes, Belgium
| | - Pier-Luc Clermont
- Faculty of Medicine, Université Laval, 1050, avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Maryam Latarani
- Cancer Research Group, School of Life Health & Chemical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK
| | - David Kingsley Male
- Cancer Research Group, School of Life Health & Chemical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK
| | - Yuzhuo Wang
- Department of Experimental Therapeutics, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Urologic Sciences, The Vancouver Prostate Centre, The University of British Columbia, 2660 Oak St, Vancouver, BC, V6H 3Z6, Canada
| | - Francesco Crea
- Cancer Research Group, School of Life Health & Chemical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK
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Poulet C, Njock MS, Moermans C, Louis E, Louis R, Malaise M, Guiot J. Exosomal Long Non-Coding RNAs in Lung Diseases. Int J Mol Sci 2020; 21:E3580. [PMID: 32438606 PMCID: PMC7279016 DOI: 10.3390/ijms21103580] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Within the non-coding genome landscape, long non-coding RNAs (lncRNAs) and their secretion within exosomes are a window that could further explain the regulation, the sustaining, and the spread of lung diseases. We present here a compilation of the current knowledge on lncRNAs commonly found in Chronic Obstructive Pulmonary Disease (COPD), asthma, Idiopathic Pulmonary Fibrosis (IPF), or lung cancers. We built interaction networks describing the mechanisms of action for COPD, asthma, and IPF, as well as private networks for H19, MALAT1, MEG3, FENDRR, CDKN2B-AS1, TUG1, HOTAIR, and GAS5 lncRNAs in lung cancers. We identified five signaling pathways targeted by these eight lncRNAs over the lung diseases mentioned above. These lncRNAs were involved in ten treatment resistances in lung cancers, with HOTAIR being itself described in seven resistances. Besides, five of them were previously described as promising biomarkers for the diagnosis and prognosis of asthma, COPD, and lung cancers. Additionally, we describe the exosomal-based studies on H19, MALAT1, HOTAIR, GAS5, UCA1, lnc-MMP2-2, GAPLINC, TBILA, AGAP2-AS1, and SOX2-OT. This review concludes on the need for additional studies describing the lncRNA mechanisms of action and confirming their potential as biomarkers, as well as their involvement in resistance to treatment, especially in non-cancerous lung diseases.
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Affiliation(s)
- Christophe Poulet
- Department of Rheumatology, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (M.-S.N.); (M.M.)
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
| | - Makon-Sébastien Njock
- Department of Rheumatology, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (M.-S.N.); (M.M.)
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Respiratory Diseases, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
| | - Catherine Moermans
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Respiratory Diseases, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
| | - Edouard Louis
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Gastroenterology, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
| | - Renaud Louis
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Respiratory Diseases, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
| | - Michel Malaise
- Department of Rheumatology, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (M.-S.N.); (M.M.)
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
| | - Julien Guiot
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Respiratory Diseases, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
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21
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Diagnostic and Prognostic Biomarkers for Chronic Fibrosing Interstitial Lung Diseases With a Progressive Phenotype. Chest 2020; 158:646-659. [PMID: 32268131 DOI: 10.1016/j.chest.2020.03.037] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/05/2020] [Accepted: 03/19/2020] [Indexed: 12/19/2022] Open
Abstract
Biomarkers have the potential to become central to the clinical evaluation and monitoring of patients with chronic fibrosing interstitial lung diseases (ILDs) with a progressive phenotype. Here we summarize the current understanding of putative serum, BAL fluid, and genetic biomarkers in this setting, according to their hypothesized pathobiologic mechanisms: evidence of epithelial cell dysfunction (eg, Krebs von den Lungen-6 antigen), fibroblast proliferation and extracellular matrix production or turnover (eg, matrix metalloproteinase-1), or immune dysregulation (eg, CC chemokine ligand 18). While most of the available data come from idiopathic pulmonary fibrosis (IPF), the prototypic progressive fibrosing ILD, data are available in the broader patient population of chronic fibrosing ILDs. A number of these biomarkers show promise, however, none have been validated. In this review article, we assess both the status of proposed biomarkers for chronic fibrosing lung diseases with a progressive phenotype in predicting disease risk or predisposition, diagnosis, prognosis, and treatment response and provide a direct comparison between IPF and other chronic fibrotic ILDs. We also reflect on the current clinical usefulness and future direction of research for biomarkers in the setting of chronic fibrosing ILDs with a progressive phenotype.
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Bonhomme O, André B, Gester F, de Seny D, Moermans C, Struman I, Louis R, Malaise M, Guiot J. Biomarkers in systemic sclerosis-associated interstitial lung disease: review of the literature. Rheumatology (Oxford) 2020; 58:1534-1546. [PMID: 31292645 PMCID: PMC6736409 DOI: 10.1093/rheumatology/kez230] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 05/09/2019] [Indexed: 12/18/2022] Open
Abstract
SSc is a rare disease of unknown origin associated with multiple organ involvement. One of the major complications that drives the mortality of SSc patients is interstitial lung disease. The course of SSc-interstitial lung disease progression has a wide spectrum. Since the treatment is based on aggressive immunosuppression it should not be given to stable or non-progressing disease. The correct identification of disease with high risk of progression remains a challenge for early therapeutic intervention, and biomarkers remain urgently needed. In fact, eight categories of biomarkers have been identified and classified according to the different biological pathways involved. The purpose of this article is to describe the main biomarkers thought to be of interest with clinical value in the diagnosis and prognosis of SSc-interstitial lung disease.
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Affiliation(s)
| | | | | | | | | | - Ingrid Struman
- Molecular Angiogenesis Laboratory, GIGA R, University of Liege, Liège, Belgium
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Ma J, Zhou Y, Li W, Xiao L, Yang M, Tan Q, Xu Y, Chen W. Association between Plasma HMGB-1 and Silicosis: A Case-Control Study. Int J Mol Sci 2018; 19:ijms19124043. [PMID: 30558126 PMCID: PMC6320808 DOI: 10.3390/ijms19124043] [Citation(s) in RCA: 3] [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: 11/23/2018] [Accepted: 12/10/2018] [Indexed: 12/31/2022] Open
Abstract
High-mobility group box-1 (HMGB-1) has been associated with fibrotic diseases. However, the role of HMGB-1 in silicosis is still uncertain. In this study, we conducted a case-control study involving 74 patients with silicosis and 107 age/gender-matched healthy controls in China. An Enzyme-linked immunosorbent assay (ELISA) was used to examine the concentrations of plasma HMGB-1 among all subjects. A logistic regression model and receiver operating characteristic curve (ROC) analysis were performed to assess the relationships between HMGB-1 and silicosis. We observed that plasma HMGB-1 concentrations were significantly increased in silicosis patients when compared with healthy controls (p < 0.05). Each 1 ng/mL increase in plasma HMGB-1 was positively associated with increased odds of silicosis, and the odds ratio (OR) (95% confidence interval) was 1.86 (1.52, 2.27). Additionally, compared with subjects with lower HMGB-1 concentrations, increased odds of silicosis were observed in those with higher HMGB-1 concentrations, and the OR was 15.33 (6.70, 35.10). Nonlinear models including a natural cubic spline function of continuous HMGB-1 yielded similar results. In ROC analyses, we found that plasma HMGB-1 >7.419 ng/mL had 81.6% sensitivity and 80.4% specificity for silicosis, and the area under the curve (AUC) was 0.84. Our results demonstrated that elevated plasma HMGB-1 was positivity associated with increased OR of silicosis.
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Affiliation(s)
- Jixuan Ma
- Department of Occupational & Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Yun Zhou
- Department of Occupational & Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Wei Li
- Department of Occupational & Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Lili Xiao
- Department of Occupational & Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Meng Yang
- Department of Occupational & Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Qiyou Tan
- Department of Occupational & Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Yiju Xu
- Department of Occupational & Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Weihong Chen
- Department of Occupational & Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Abstract
Idiopathic Pulmonary Fibrosis (IPF) is a devastating chronic, progressive and irreversible disease that remains refractory to current therapies. Matrix metalloproteinases (MMPs) and their inhibitors, tissue inhibitors of MMPs (TIMPs), have been implicated in the development of pulmonary fibrosis since decades. Coagulation signalling deregulation, which influences several key inflammatory and fibro-proliferative responses, is also essential in IPF pathogenesis, and a growing body of evidence indicates that Protease-Activated Receptors (PARs) inhibition in IPF may be promising for future evaluation. Therefore, proteases and anti-proteases aroused great biomedical interest over the past years, owing to the identification of their potential roles in lung fibrosis. During these last decades, numerous other proteases and anti-proteases have been studied in lung fibrosis, such as matriptase, Human airway trypsin-like protease (HAT), Hepatocyte growth factor activator (HGFA)/HGFA activator inhibitor (HAI) system, Plasminogen activator inhibitor (PAI)-1, Protease nexine (PN)-1, cathepsins, calpains, and cystatin C. Herein, we provide a general overview of the proteases and anti-proteases unbalance during lung fibrogenesis and explore potential therapeutics for IPF.
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