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Duraloglu C, Baysal I, Yabanoglu-Ciftci S, Arica B. Nintedanib and miR-29b co-loaded lipoplexes in idiopathic pulmonary fibrosis: formulation, characterization, and in vitro evaluation. Drug Dev Ind Pharm 2024; 50:671-686. [PMID: 39099436 DOI: 10.1080/03639045.2024.2387166] [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: 03/21/2024] [Revised: 07/25/2024] [Accepted: 07/28/2024] [Indexed: 08/06/2024]
Abstract
OBJECTIVE This study was aimed to develop a cationic lipoplex formulation loaded with Nintedanib and miR-29b (LP-NIN-miR) as an alternative approach in the combination therapy of idiopathic pulmonary dibrosis (IPF) by proving its additive anti-fibrotic therapeutic effects through in vitro lung fibrosis model. SIGNIFICANCE This is the first research article reported that the LP-NIN-MIR formulations in the treatment of IPF. METHODS To optimize cationic liposomes (LPs), quality by design (QbD) approach was carried out. Optimized blank LP formulation was prepared with DOTAP, CHOL, DOPE, and DSPE-mPEG 2000 at the molar ratio of 10:10:1:1. Nintedanib loaded LP (LPs-NIN) were produced by microfluidization method and were incubated with miR-29b at room temperature for 30 min to obtain LP-NIN-miR. To evaluate the cellular uptake of LP-NIN-miR, NIH/3T3 cells were treated with 20 ng.mL-1 transforming growth factor-β1 (TGF-β1) for 96 h to establish the in vitro IPF model and incubated with LP-NIN-miR for 48 h. RESULTS The hydrodynamic diameter, polydispersity index (PDI), and zeta potential of the LP-NIN-miR were 87.3 ± 0.9 nm, 0.184 ± 0.003, and +24 ± 1 mV, respectively. The encapsulation efficiencies of Nintedanib and miR-29b were 99.8% ± 0.08% and 99.7% ± 1.2%, respectively. The results of the cytotoxicity study conducted with NIH/3T3 cells indicated that LP-NIN-miR is a safe delivery system. CONCLUSIONS The outcome of the transfection study proved the additive anti-fibrotic therapeutic effect of LP-NIN-miR and suggested that lipoplexes are effective delivery systems for drug and nucleic acid to the NIH/3T3 cells in the treatment of IPF.
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Affiliation(s)
- Ceren Duraloglu
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Ipek Baysal
- Vocational School of Health Services, Hacettepe University, Ankara, Turkey
| | | | - Betul Arica
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
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Toker Ç, Kuyucu Y, Şaker D, Kara S, Güzelel B, Mete UÖ. Investigation of miR-26b and miR-27b expressions and the effect of quercetin on fibrosis in experimental pulmonary fibrosis. J Mol Histol 2024; 55:25-35. [PMID: 37857923 DOI: 10.1007/s10735-023-10168-z] [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: 03/23/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023]
Abstract
In this study, investigation of the effects of Quercetin on Bleomycin-induced pulmonary fibrosis and fibrosis-associated molecules miR-26b and miR-27b was aimed. Control group was given 10% saline on the 0th day, and saline was administered for 21 days starting from the 8th day. Group 2 was given 50 mg/kg Quercetin for 21 days starting from the 8th day. Group 3 was given 10 mg/kg Bleomycin Sulfate on day 0, and sacrificed on the 22nd and 29th day. Group 4 was given 10 mg/kg Bleomycin Sulfate on the 0th day, and was given 50 mg/kg Quercetin for 14 days, and 21 days starting from day 8. Lung tissues were examined using light and electron microscopic, immunohistochemical and molecular biological methods. Injury groups revealed impaired alveolar structure, collagen accumulation and increased inflammatory cells in interalveolar septum. Fibrotic response was decreased and the alveolar structure was improved with Quercetin treatment. α-SMA expressions were higher in the injury groups, but lower in the treatment groups compared to the injury groups. E-cadherin expressions were decreased in the injury groups and showed stronger immunoreactivity in the treatment groups compared to the injury groups. miR-26b and miR-27b expressions were lower in the injury groups than the control groups, and higher in the treatment groups than the injury groups. Quercetin can be considered as a new treatment agent in the idiopathic pulmonary fibrosis, since it increases the expression levels of miR-26b and miR-27b which decrease in fibrosis, and has therapeutic effects on the histopathological changes.
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Affiliation(s)
- Çağrı Toker
- Department of Histology and Embryology, Faculty of Medicine, Çukurova University, 01330, Adana, Turkey
| | - Yurdun Kuyucu
- Department of Histology and Embryology, Faculty of Medicine, Çukurova University, 01330, Adana, Turkey.
| | - Dilek Şaker
- Department of Histology and Embryology, Faculty of Medicine, Çukurova University, 01330, Adana, Turkey
| | - Samet Kara
- Department of Histology and Embryology, Faculty of Medicine, Çukurova University, 01330, Adana, Turkey
| | - Bilge Güzelel
- Department of Histology and Embryology, Faculty of Medicine, Çukurova University, 01330, Adana, Turkey
| | - Ufuk Özgü Mete
- Department of Histology and Embryology, Faculty of Medicine, Çukurova University, 01330, Adana, Turkey
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Lettieri S, Bertuccio FR, del Frate L, Perrotta F, Corsico AG, Stella GM. The Plastic Interplay between Lung Regeneration Phenomena and Fibrotic Evolution: Current Challenges and Novel Therapeutic Perspectives. Int J Mol Sci 2023; 25:547. [PMID: 38203718 PMCID: PMC10779349 DOI: 10.3390/ijms25010547] [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: 12/13/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Interstitial lung diseases (ILDs) are a heterogeneous group of pulmonary disorders characterized by variable degrees of inflammation, interstitial thickening, and fibrosis leading to distortion of the pulmonary architecture and gas exchange impairment. Among them, idiopathic pulmonary fibrosis (IPF) displays the worst prognosis. The only therapeutic options consist of the two antifibrotic drugs, pirfenidone and nintedanib, which limit fibrosis progression but do not reverse the lung damage. The shift of the pathogenetic paradigm from inflammatory disease to epithelium-derived disease has definitively established the primary role of type II alveolar cells, which lose their epithelial phenotype and acquire a mesenchymal phenotype with production of collagen and extracellular matrix (EMC) deposition. Some predisposing environmental and genetic factors (e.g., smoke, pollution, gastroesophageal reflux, variants of telomere and surfactant genes) leading to accelerated senescence set a pro-fibrogentic microenvironment and contribute to the loss of regenerative properties of type II epithelial cells in response to pathogenic noxae. This review provides a complete overview of the different pathogenetic mechanisms leading to the development of IPF. Then, we summarize the currently approved therapies and the main clinical trials ongoing. Finally, we explore the potentialities offered by agents not only interfering with the processes of fibrosis but also restoring the physiological properties of alveolar regeneration, with a particular focus on potentialities and concerns about cell therapies based on mesenchymal stem cells (MSCs), whose anti-inflammatory and immunomodulant properties have been exploited in other fibrotic diseases, such as graft versus host disease (GVHD) and COVID-19-related ARDS.
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Affiliation(s)
- Sara Lettieri
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy; (S.L.); (F.R.B.); (L.d.F.); (A.G.C.)
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Francesco R. Bertuccio
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy; (S.L.); (F.R.B.); (L.d.F.); (A.G.C.)
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Lucia del Frate
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy; (S.L.); (F.R.B.); (L.d.F.); (A.G.C.)
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Fabio Perrotta
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, 80055 Naples, Italy;
| | - Angelo G. Corsico
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy; (S.L.); (F.R.B.); (L.d.F.); (A.G.C.)
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giulia M. Stella
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy; (S.L.); (F.R.B.); (L.d.F.); (A.G.C.)
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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Sabater L, Gossart JB, Hernandez I, Rico D, Blanchard A, Borthwick LA, Fisher AJ, Majo J, Jiwa K, Collins A, Abbate G, Oakley F, Mann DA, Mann J. miRNA Expression in Fibroblastic Foci within Idiopathic Pulmonary Fibrosis Lungs Reveals Novel Disease-Relevant Pathways. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:417-429. [PMID: 36690076 DOI: 10.1016/j.ajpath.2022.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/22/2023]
Abstract
miRNAs are a class of noncoding RNAs of approximately 22 nucleotides long that play an important role in regulating gene expression at a post-transcriptional level. Aberrant levels of miRNAs have been associated with profibrotic processes in idiopathic pulmonary fibrosis (IPF). However, most of these studies used whole IPF tissue or in vitro monocultures in which fibrosis has been artificially induced. In this study, we used laser microdissection to collect fibroblastic foci (FF), the key pathologic lesion in IPF, then isolate miRNAs and compare their expression levels with those found in whole IPF lung tissue and/or in vitro cultured fibroblast from IPF or normal lungs. Sequencing libraries were generated, and data generated were bioinformatically analyzed. A total of 18 miRNAs were significantly overexpressed in FF tissue when compared with whole IPF tissue; of these molecules, 15 were unique to FF. Comparison of FF with cultured IPF fibroblasts also revealed differences in miRNA composition that impact on several signaling pathways. The miRNA composition of FF is both overlapping and distinct from that of whole IPF tissue or cultured IPF fibroblasts and highlights the importance of characterizing FF biology as a phenotypically and functionally discrete tissue microenvironment.
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Affiliation(s)
- Laura Sabater
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jean B Gossart
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Inmaculada Hernandez
- Computational Epigenomics Laboratory, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Daniel Rico
- Computational Epigenomics Laboratory, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andy Blanchard
- GlaxoSmithKline Medicines Research Centre, Stevenage, United Kingdom
| | - Lee A Borthwick
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andrew J Fisher
- Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Joaquim Majo
- Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Kasim Jiwa
- Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Amy Collins
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; FibroFind Ltd, FibroFind Laboratories, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Giuseppe Abbate
- FibroFind Ltd, FibroFind Laboratories, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Fiona Oakley
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; FibroFind Ltd, FibroFind Laboratories, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Derek A Mann
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; FibroFind Ltd, FibroFind Laboratories, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jelena Mann
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; FibroFind Ltd, FibroFind Laboratories, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom.
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Abstract
The lungs are continually subjected to noxious and inert substances, are immunologically active, and are in a constant state of damage and repair. This makes the pulmonary system particularly vulnerable to diseases of aging. Aging can be understood as random molecular damage that is unrepaired and accumulates over time, resulting in cellular defects and tissue dysfunction. The breakdown of cellular mechanisms, including stem cell exhaustion, genomic instability, telomere attrition, epigenetic alteration, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, altered intercellular communication, and changes in the extracellular matrix is thought to advance the aging process itself. Chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), and cancers illustrate a pathologic breakdown in these mechanisms beyond normal aging. The immune system becomes less effective with advancing age. There is a low-level state of chronic inflammation termed inflammaging which is thought to be driven by immunosenescence, the changes in the innate and adaptive immune systems with advancing age that lead to dysregulation and decreased effectiveness of the immune system. These processes of aging lead to expected changes in the form and function of the respiratory system, most notably a loss of lung elasticity, decrease in respiratory muscle strength, increase in ventilation-perfusion mismatching, and stiffening of the vasculature. The astute clinician is aware of these expected findings and does not often attribute dyspnea to aging alone. Maintaining a low threshold to investigate for comorbid disease and understanding how pulmonary disease presents differently in the elderly than in younger adults can improve clinical outcomes. © 2022 American Physiological Society. Compr Physiol 12:3509-3522, 2022.
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Affiliation(s)
- Julia Budde
- New York City Health and Hospitals/Metropolitan Hospital, New York, New York, USA
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Cadena-Suárez AR, Hernández-Hernández HA, Alvarado-Vásquez N, Rangel-Escareño C, Sommer B, Negrete-García MC. Role of MicroRNAs in Signaling Pathways Associated with the Pathogenesis of Idiopathic Pulmonary Fibrosis: A Focus on Epithelial-Mesenchymal Transition. Int J Mol Sci 2022; 23:ijms23126613. [PMID: 35743055 PMCID: PMC9224458 DOI: 10.3390/ijms23126613] [Citation(s) in RCA: 1] [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: 05/10/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 12/15/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive disease with high mortality and unclear etiology. Previous evidence supports that the origin of this disease is associated with epigenetic alterations, age, and environmental factors. IPF initiates with chronic epithelial lung injuries, followed by basal membrane destruction, which promotes the activation of myofibroblasts and excessive synthesis of extracellular matrix (ECM) proteins, as well as epithelial-mesenchymal transition (EMT). Due to miRNAs’ role as regulators of apoptosis, proliferation, differentiation, and cell-cell interaction processes, some studies have involved miRNAs in the biogenesis and progression of IPF. In this context, the analysis and discussion of the probable association of miRNAs with the signaling pathways involved in the development of IPF would improve our knowledge of the associated molecular mechanisms, thereby facilitating its evaluation as a therapeutic target for this severe lung disease. In this work, the most recent publications evaluating the role of miRNAs as regulators or activators of signal pathways associated with the pathogenesis of IPF were analyzed. The search in Pubmed was made using the following terms: “miRNAs and idiopathic pulmonary fibrosis (IPF)”; “miRNAs and IPF and signaling pathways (SP)”; and “miRNAs and IPF and SP and IPF pathogenesis”. Additionally, we focus mainly on those works where the signaling pathways involved with EMT, fibroblast differentiation, and synthesis of ECM components were assessed. Finally, the importance and significance of miRNAs as potential therapeutic or diagnostic tools for the treatment of IPF are discussed.
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Affiliation(s)
- Ana Ruth Cadena-Suárez
- Laboratorio de Biología Molecular, Instituto Nacional de Enfermedades Respiratorias (INER) “Ismael Cosío Villegas”, Calz. Tlalpan 4502, Col. Sección XVI, Mexico City 14080, Mexico; (A.R.C.-S.); (H.A.H.-H.)
| | - Hilda Arely Hernández-Hernández
- Laboratorio de Biología Molecular, Instituto Nacional de Enfermedades Respiratorias (INER) “Ismael Cosío Villegas”, Calz. Tlalpan 4502, Col. Sección XVI, Mexico City 14080, Mexico; (A.R.C.-S.); (H.A.H.-H.)
| | - Noé Alvarado-Vásquez
- Departamento de Bioquímica, Instituto Nacional de Enfermedades Respiratorias (INER) “Ismael Cosío Villegas”, Calz. Tlalpan 4502, Col. Sección XVI, Mexico City 14080, Mexico;
| | - Claudia Rangel-Escareño
- Departamento de Genomica Computacional, Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Col. Arenal Tepepan, Mexico City 14610, Mexico;
- Escuela de Ingenieria y Ciencias, Tecnológico de Monterrey, Epigmenio González 500, San Pablo 76130, Mexico
| | - Bettina Sommer
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias (INER) “Ismael Cosío Villegas”, Calz. Tlalpan 4502, Col. Sección XVI, Mexico City 14080, Mexico;
| | - María Cristina Negrete-García
- Laboratorio de Biología Molecular, Instituto Nacional de Enfermedades Respiratorias (INER) “Ismael Cosío Villegas”, Calz. Tlalpan 4502, Col. Sección XVI, Mexico City 14080, Mexico; (A.R.C.-S.); (H.A.H.-H.)
- Correspondence:
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Aomatsu A, Kaneko S, Yanai K, Ishii H, Ito K, Hirai K, Ookawara S, Kobayashi Y, Sanui M, Morishita Y. MicroRNA expression profiling in acute kidney injury. Transl Res 2022; 244:1-31. [PMID: 34871811 DOI: 10.1016/j.trsl.2021.11.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 11/27/2021] [Accepted: 11/30/2021] [Indexed: 02/05/2023]
Abstract
The aim of this study was to identify miRNAs that regulate AKI and develop their applications as diagnostic biomarkers and therapeutic agents. First, kidney tissues from two different AKI mouse models, namely, AKI induced by the administration of lipopolysaccharide (LPS) causing sepsis (LPS-AKI mice) and AKI induced by renal ischemia-reperfusion injury (IRI-AKI mice), were exhaustively screened for their changes of miRNA expression compared with that of control mice by microarray analysis followed by quantitative RT-PCR. The initial profiling newly identified miRNA-5100, whose expression levels significantly decreased in kidneys in both LPS-AKI mice and IRI-AKI mice. Next, the administration of miRNA-5100-mimic conjugated with a nonviral vector, polyethylenimine nanoparticles (PEI-NPs), via the tail vein significantly induced miRNA-5100 overexpression in the kidney and prevented the development of IRI-AKI mice by inhibiting several apoptosis pathways in vivo. Furthermore, serum levels of miRNA-5100 in patients with AKI were identified as significantly lower than those of healthy subjects. ROC analysis showed that the serum expression level of miRNA-5100 can identify AKI (cut-off value 0.14, AUC 0.96, sensitivity 1.00, specificity 0.833, p<0.05). These results suggest that miRNA-5100 regulates AKI and may be useful as a novel diagnostic biomarker and therapeutic target for AKI.
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Affiliation(s)
- Akinori Aomatsu
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan; Division of Intensive Care Unit, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Shohei Kaneko
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Katsunori Yanai
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Hiroki Ishii
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Kiyonori Ito
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Keiji Hirai
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Susumu Ookawara
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Yasuma Kobayashi
- Department of Anesthesia, Saitama Children's Medical Center, Saitama, Japan
| | - Masamitsu Sanui
- Division of Intensive Care Unit, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Yoshiyuki Morishita
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan.
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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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9
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Elliot S, Catanuto P, Pereira-simon S, Xia X, Shahzeidi S, Roberts E, Ludlow J, Hamdan S, Daunert S, Parra J, Stone R, Pastar I, Tomic-Canic M, Glassberg MK. Urine-derived exosomes from individuals with IPF carry pro-fibrotic cargo. eLife 2022; 11:79543. [PMID: 36454035 PMCID: PMC9714968 DOI: 10.7554/elife.79543] [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] [Received: 04/17/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNA) and other components contained in extracellular vesicles may reflect the presence of a disease. Lung tissue, sputum, and sera of individuals with idiopathic pulmonary fibrosis (IPF) show alterations in miRNA expression. We designed this study to test whether urine and/or tissue derived exosomal miRNAs from individuals with IPF carry cargo that can promote fibrosis. METHODS Exosomes were isolated from urine (U-IPFexo), lung tissue myofibroblasts (MF-IPFexo), serum from individuals with IPF (n=16) and age/sex-matched controls without lung disease (n=10). We analyzed microRNA expression of isolated exosomes and their in vivo bio-distribution. We investigated the effect on ex vivo skin wound healing and in in vivo mouse lung models. RESULTS U-IPFexo or MF-IPFexo expressed miR-let-7d, miR-29a-5p, miR-181b-3p and miR-199a-3p consistent with previous reports of miRNA expression obtained from lung tissue/sera from patients with IPF. In vivo bio-distribution experiments detected bioluminescent exosomes in the lung of normal C57Bl6 mice within 5 min after intravenous infusion, followed by distribution to other organs irrespective of exosome source. Exosomes labeled with gold nanoparticles and imaged by transmission electron microscopy were visualized in alveolar epithelial type I and type II cells. Treatment of human and mouse lung punches obtained from control, non-fibrotic lungs with either U-IPFexo or MF-IPFexo produced a fibrotic phenotype. A fibrotic phenotype was also induced in a human ex vivo skin model and in in vivo lung models. CONCLUSIONS Our results provide evidence of a systemic feature of IPF whereby exosomes contain pro-fibrotic miRNAs when obtained from a fibrotic source and interfere with response to tissue injury as measured in skin and lung models. FUNDING This work was supported in part by Lester and Sue Smith Foundation and The Samrick Family Foundation and NIH grants R21 AG060338 (SE and MKG), U01 DK119085 (IP, RS, MTC).
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Affiliation(s)
- Sharon Elliot
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of MedicineMiamiUnited States
| | - Paola Catanuto
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of MedicineMiamiUnited States
| | - Simone Pereira-simon
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of MedicineMiamiUnited States
| | - Xiaomei Xia
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep, University of MiamiMiamiUnited States
| | | | - Evan Roberts
- Cancer Modeling Shared Resource Sylvester Comprehensive Cancer Center, University of MiamiMiamiUnited States
| | | | - Suzana Hamdan
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of MedicineMiamiUnited States,Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami Miller School of MedicineMiamiUnited States
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of MedicineMiamiUnited States,Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami Miller School of MedicineMiamiUnited States,Miami Clinical and Translational Science Institute, University of Miami Miller School of MedicineMiamiUnited States
| | - Jennifer Parra
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep, University of MiamiMiamiUnited States
| | - Rivka Stone
- Wound Healing and Regenerative Medicine Research Program, Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of MiamiMiamiUnited States
| | - Irena Pastar
- Wound Healing and Regenerative Medicine Research Program, Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of MiamiMiamiUnited States
| | - Marjana Tomic-Canic
- Wound Healing and Regenerative Medicine Research Program, Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of MiamiMiamiUnited States
| | - Marilyn K Glassberg
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of MedicineMiamiUnited States,Department of Medicine, Division of Pulmonary, Critical Care and Sleep, University of MiamiMiamiUnited States,Department of Medicine, Stritch School of Medicine, Loyola University ChicagoChicagoUnited States
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10
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Evaluation of microRNA expression in a sheep model for lung fibrosis. BMC Genomics 2021; 22:827. [PMID: 34789159 PMCID: PMC8596952 DOI: 10.1186/s12864-021-08073-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 09/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a chronic progressive fibroproliferative disorder that has one of the poorest prognoses amongst interstitial lung diseases. Recently, the finding of aberrant expression levels of miRNAs in IPF patients has drawn significant attention to the involvement of these molecules in the pathogenesis of this disease. Clarification of the differential expression of miRNAs in health and disease may identify novel therapeutic strategies that can be employed in the future to combat IPF. This study evaluates the miRNA expression profiles in a sheep model for lung fibrosis and compares them to the miRNA profiles of both IPF patients and the mouse bleomycin model for pulmonary fibrosis. Pathway enrichment analyses were performed on differentially expressed miRNAs to illustrate which biological mechanisms were associated with lung fibrosis. RESULTS We discovered 49 differentially expressed miRNAs in the sheep fibrosis model, in which 32 miRNAs were significantly down regulated, while 17 miRNAs were significantly upregulated due to bleomycin-induced lung injury. Moreover, the miRNA families miR-29, miR-26, miR-30, let-7, miR-21, miR-19, miR-17 and miR-199 were aberrantly expressed in both sheep and mouse models, with similar differential miRNAs expression observed in IPF cases. Importantly, 18 miRNAs were aberrantly expressed in both the sheep model and IPF patients, but not in mice. CONCLUSION Together with pathway enrichment analyses, these results show that the sheep model can potentially be used to characterize previously unrecognized biological pathways associated with lung fibrosis.
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11
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Niehof M, Reamon-Buettner SM, Danov O, Hansen T, Sewald K. A modified protocol for successful miRNA profiling in human precision-cut lung slices (PCLS). BMC Res Notes 2021; 14:255. [PMID: 34215333 PMCID: PMC8252208 DOI: 10.1186/s13104-021-05674-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
Objective Human precision cut lung slices (PCLS) are widely used as an ex vivo model system for drug discovery and development of new therapies. PCLS reflect the functional heterogeneity of lung tissue and possess relevant lung cell types. We thus determined the use of PCLS in studying non-coding RNAs notably miRNAs, which are important gene regulatory molecules. Since miRNAs play key role as mediators of respiratory diseases, they can serve as valuable prognostic or diagnostic biomarkers, and in therapeutic interventions, of lung diseases. A technical limitation though is the vast amount of agarose in PCLS which impedes (mi)RNA extraction by standard procedures. Here we modified our recently published protocol for RNA isolation from PCLS to enable miRNA readouts. Results The modified method relies on the separation of lysis and precipitation steps, and a clean-up procedure with specific magnetic beads. We obtained successfully quality miRNA amenable for downstream applications such as RTqPCR and whole transcriptome miRNA analysis. Comparison of miRNA profiles in PCLS with published data from human lung, identified all important miRNAs regulated in IPF, COPD, asthma or lung cancer. Therefore, this shows suitability of the method for analyzing miRNA targets and biomarkers in the valuable human PCLS model. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05674-w.
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Affiliation(s)
- Monika Niehof
- Department of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Nikolai-Fuchs-Str. 1, Hannover, 30625, Germany.
| | - Stella Marie Reamon-Buettner
- Department of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Nikolai-Fuchs-Str. 1, Hannover, 30625, Germany
| | - Olga Danov
- Department of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Nikolai-Fuchs-Str. 1, Hannover, 30625, Germany
| | - Tanja Hansen
- Department of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Nikolai-Fuchs-Str. 1, Hannover, 30625, Germany
| | - Katherina Sewald
- Department of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Nikolai-Fuchs-Str. 1, Hannover, 30625, Germany
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12
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MicroRNA Targets for Asthma Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1303:89-105. [PMID: 33788189 DOI: 10.1007/978-3-030-63046-1_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Asthma is a chronic inflammatory obstructive lung disease that is stratified into endotypes. Th2 high asthma is due to an imbalance of Th1/Th2 signaling leading to abnormally high levels of Th2 cytokines, IL-4, IL-5, and IL-13 and in some cases a reduction in type I interferons. Some asthmatics express Th2 low, Th1/Th17 high phenotypes with or without eosinophilia. Most asthmatics with Th2 high phenotype respond to beta-adrenergic agonists, muscarinic antagonists, and inhaled corticosteroids. However, 5-10% of asthmatics are not well controlled by these therapies despite significant advances in lung immunology and the pathogenesis of severe asthma. This problem is being addressed by developing novel classes of anti-inflammatory agents. Numerous studies have established efficacy of targeting pro-inflammatory microRNAs in mouse models of mild/moderate and severe asthma. Current approaches employ microRNA mimics and antagonists designed for use in vivo. Chemically modified oligonucleotides have enhanced stability in blood, increased cell permeability, and optimized target specificity. Delivery to lung tissue limits clinical applications, but it is a tractable problem. Future studies need to define the most effective microRNA targets and effective delivery systems. Successful oligonucleotide drug candidates must have adequate lung cell uptake, high target specificity, and efficacy with tolerable off-target effects.
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13
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Fortier SM, Penke LR, King D, Pham TX, Ligresti G, Peters-Golden M. Myofibroblast dedifferentiation proceeds via distinct transcriptomic and phenotypic transitions. JCI Insight 2021; 6:144799. [PMID: 33561015 PMCID: PMC8026183 DOI: 10.1172/jci.insight.144799] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/04/2021] [Indexed: 12/16/2022] Open
Abstract
Myofibroblasts are the major cellular source of collagen, and their accumulation - via differentiation from fibroblasts and resistance to apoptosis - is a hallmark of tissue fibrosis. Clearance of myofibroblasts by dedifferentiation and restoration of apoptosis sensitivity has the potential to reverse fibrosis. Prostaglandin E2 (PGE2) and mitogens such as FGF2 have each been shown to dedifferentiate myofibroblasts, but - to our knowledge - the resultant cellular phenotypes have neither been comprehensively characterized or compared. Here, we show that PGE2 elicited dedifferentiation of human lung myofibroblasts via cAMP/PKA, while FGF2 utilized MEK/ERK. The 2 mediators yielded transitional cells with distinct transcriptomes, with FGF2 promoting but PGE2 inhibiting proliferation and survival. The gene expression pattern in fibroblasts isolated from the lungs of mice undergoing resolution of experimental fibrosis resembled that of myofibroblasts treated with PGE2 in vitro. We conclude that myofibroblast dedifferentiation can proceed via distinct programs exemplified by treatment with PGE2 and FGF2, with dedifferentiation occurring in vivo most closely resembling the former.
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Affiliation(s)
| | - Loka R. Penke
- Division of Pulmonary and Critical Care Medicine and
| | - Dana King
- BCRF Bioinformatics Core, University of Michigan, Ann Arbor, Michigan, USA
| | - Tho X. Pham
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Giovanni Ligresti
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
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14
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Tong J, Wu Z, Wang Y, Hao Q, Liu H, Cao F, Jiao Y. Astragaloside IV Synergizing with Ferulic Acid Ameliorates Pulmonary Fibrosis by TGF- β1/Smad3 Signaling. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:8845798. [PMID: 33763150 PMCID: PMC7946455 DOI: 10.1155/2021/8845798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/16/2021] [Accepted: 02/20/2021] [Indexed: 12/21/2022]
Abstract
OBJECTIVE The study aims to research the interventional effect and mechanism of astragaloside IV (Ast) synergizing with ferulic acid (FA) on idiopathic pulmonary fibrosis (IPF) induced by bleomycin in mice. METHODS The mice were randomly divided into seven groups with 10 mice in each group, namely, a sham operation group, a model group, a miRNA-29b (miR-29) group, a miR-29b negative control group (NC group), a FA group, an Ast group, and a combination group. A mouse model of pulmonary fibrosis was established by intratracheal instillation of bleomycin. Samples were collected after 28 days of continuous administration. Hematoxylin and eosin (HE) and Masson staining were used to observe pathological changes in the lung tissue, and the degree of fibrosis was evaluated using the hydroxyproline content. Changes in transforming growth factor-β1 (TGF-β1) and Smad3 in the lung were observed using immunohistochemistry. Enzyme-linked immunosorbent assay (ELISA) was used to detect the level of reactive oxygen species (ROS), malondialdehyde (MDA), and superoxide dismutase (SOD) in the serum. PCR was used to detect the expression of the miR-29b, TGF-β1, Smad3, and nuclear factor E2-related factor 2 (Nrf2) genes. Western blotting was used to detect the content of the TGF-β/Smad3 protein. RESULTS Ferulic acid combined with astragaloside IV reduced the degree of pulmonary fibrosis and the synthesis of hydroxyproline in lung tissue. The combination of the two also regulated the oxidative stress response , TGF-β1/Smad3 pathway and miR-29b in lung tissue. CONCLUSION Astragaloside IV combined with ferulic acid regulated the oxidative stress of lung tissues and TGF-β1/Smad3 signaling through miR-29b, thereby reducing the degree of pulmonary fibrosis. This provides a reference direction for the clinical treatment of IPF patients.
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Affiliation(s)
- Jiahuan Tong
- Beijing University of Chinese Medicine, No. 11 Bei San Huan Dong Lu, Chaoyang District, Beijing 100029, China
| | - Zhisong Wu
- Dongfang Hospital Affiliated to Beijing University of Chinese Medicine, No. 6 Fang Zhuang, Fengtai District, Beijing 100078, China
| | - Yuchen Wang
- Beijing University of Chinese Medicine, No. 11 Bei San Huan Dong Lu, Chaoyang District, Beijing 100029, China
| | - Qingxun Hao
- Beijing University of Chinese Medicine, No. 11 Bei San Huan Dong Lu, Chaoyang District, Beijing 100029, China
| | - Haoge Liu
- Beijing University of Chinese Medicine, No. 11 Bei San Huan Dong Lu, Chaoyang District, Beijing 100029, China
| | - Fang Cao
- Dongfang Hospital Affiliated to Beijing University of Chinese Medicine, No. 6 Fang Zhuang, Fengtai District, Beijing 100078, China
| | - Yang Jiao
- Dongfang Hospital Affiliated to Beijing University of Chinese Medicine, No. 6 Fang Zhuang, Fengtai District, Beijing 100078, China
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15
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Periera-Simon S, Xia X, Catanuto P, Coronado R, Kurtzberg J, Bellio M, Lee YS, Khan A, Smith R, Elliot SJ, Glassberg MK. Anti-fibrotic effects of different sources of MSC in bleomycin-induced lung fibrosis in C57BL6 male mice. Respirology 2021; 26:161-170. [PMID: 32851725 DOI: 10.1111/resp.13928] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 07/14/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND OBJECTIVE IPF is a fatal and debilitating lung disorder increasing in incidence worldwide. To date, two approved treatments only slow disease progression, have multiple side effects and do not provide a cure. MSC have promising therapeutic potential as a cell-based therapy for many lung disorders based on the anti-fibrotic properties of the MSC. METHODS Critical questions remain surrounding the optimal source, timing and efficacy of cell-based therapies. The present study examines the most effective sources of MSC. Human MSC were derived from adipose, WJ, chorionic membrane (CSC) and chorionic villi (CVC). MSC were injected into the ageing mouse model of BLM-induced lung fibrosis. RESULTS All sources decreased Aschroft and hydroxyproline levels when injected into BLM-treated mice at day 10 with the exception of CSC cells that did not change hydroxyproline levels. There were also decreases in mRNA expression of αv -integrin and TNFα in all sources except CSC. Only ASC- and WJ-derived cells reduced AKT and MMP-2 activation, while Cav-1 was increased by ASC treatment as previously reported. BLM-induced miR dysregulation of miR-29 and miR-199 was restored only by ASC treatment. CONCLUSION Our data suggest that sources of MSC may differ in the pathway(s) involved in repair.
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Affiliation(s)
- Simone Periera-Simon
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Xiaomei Xia
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Paola Catanuto
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Joanne Kurtzberg
- Marcus Center for Cellular Cures at Duke, Duke University School of Medicine, Durham, NC, USA
| | - Michael Bellio
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Yee-Shuan Lee
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Aisha Khan
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Robin Smith
- Department of Medicine, Rutgers University, New Brunswick, NJ, USA
| | - Sharon J Elliot
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Marilyn K Glassberg
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, The University of Arizona School of Medicine, Phoenix, AZ, USA
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16
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Bobba CM, Fei Q, Shukla V, Lee H, Patel P, Putman RK, Spitzer C, Tsai M, Wewers MD, Lee RJ, Christman JW, Ballinger MN, Ghadiali SN, Englert JA. Nanoparticle delivery of microRNA-146a regulates mechanotransduction in lung macrophages and mitigates injury during mechanical ventilation. Nat Commun 2021; 12:289. [PMID: 33436554 PMCID: PMC7804938 DOI: 10.1038/s41467-020-20449-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/03/2020] [Indexed: 12/15/2022] Open
Abstract
Mechanical ventilation generates injurious forces that exacerbate lung injury. These forces disrupt lung barrier integrity, trigger proinflammatory mediator release, and differentially regulate genes and non-coding oligonucleotides including microRNAs. In this study, we identify miR-146a as a mechanosensitive microRNA in alveolar macrophages that has therapeutic potential to mitigate lung injury during mechanical ventilation. We use humanized in-vitro systems, mouse models, and biospecimens from patients to elucidate the expression dynamics of miR-146a needed to decrease lung injury during mechanical ventilation. We find that the endogenous increase in miR-146a following injurious ventilation is not sufficient to prevent lung injury. However, when miR-146a is highly overexpressed using a nanoparticle delivery platform it is sufficient to prevent injury. These data indicate that the endogenous increase in microRNA-146a during mechanical ventilation is a compensatory response that partially limits injury and that nanoparticle delivery of miR-146a is an effective strategy for mitigating lung injury during mechanical ventilation.
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Affiliation(s)
- Christopher M Bobba
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
- Department of Biomedical Engineering, The Ohio State University, 140 West 19th Avenue, Columbus, OH, 43210, USA
- The Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
| | - Qinqin Fei
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
- Department of Biomedical Engineering, The Ohio State University, 140 West 19th Avenue, Columbus, OH, 43210, USA
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH, 43210, USA
| | - Vasudha Shukla
- Department of Biomedical Engineering, The Ohio State University, 140 West 19th Avenue, Columbus, OH, 43210, USA
- The Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
| | - Hyunwook Lee
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
- The Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
| | - Pragi Patel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
- The Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
| | - Rachel K Putman
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, 02115, USA
| | - Carleen Spitzer
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
| | - MuChun Tsai
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
| | - Mark D Wewers
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
- The Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
| | - Robert J Lee
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH, 43210, USA
| | - John W Christman
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
- The Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
| | - Megan N Ballinger
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
- The Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA
| | - Samir N Ghadiali
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA.
- Department of Biomedical Engineering, The Ohio State University, 140 West 19th Avenue, Columbus, OH, 43210, USA.
- The Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA.
| | - Joshua A Englert
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA.
- Department of Biomedical Engineering, The Ohio State University, 140 West 19th Avenue, Columbus, OH, 43210, USA.
- The Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, 473 West 12th Avenue, Columbus, OH, 43210, USA.
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17
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Zhu K, Xu A, Xia W, Li P, Han R, Wang E, Zhou S, Wang R. Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis. Int J Med Sci 2021; 18:3412-3424. [PMID: 34522168 PMCID: PMC8436110 DOI: 10.7150/ijms.61309] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/30/2021] [Indexed: 12/29/2022] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is one of the most aggressive forms of idiopathic interstitial pneumonia. Some miRNAs may be associated with IPF and may affect the occurrence and development of IPF in various pathways. Many miRNAs and genes that may be involved in the development of IPF have been discovered using chip and high throughput technologies. Methods: We analyzed one miRNA and four mRNA databases. We identified hub genes and pathways related to IPF using GO, KEGG enrichment analysis, gene set variation analysis (GSVA), PPI network construction, and hub gene analysis. A comprehensive analysis of differentially expressed miRNAs (DEMs), predicted miRNA target genes, and differentially expressed genes (DEGs) led to the creation of a miRNA-mRNA regulatory network in IPF. Results: We found 203 DEGs and 165 DEMs that were associated with IPF. The findings of enrichment analyses showed that these DEGs were mainly involved in antimicrobial humoral response, antimicrobial humoral immune response mediated by antimicrobial peptide, extracellular matrix organization, cell killing, and organ or tissue specific immune response. The VEGFA, CDH5, and WNT3A genes overlapped between hub genes and the miRNA-mRNA regulatory network. The miRNAs including miR-199b-5p, miR-140-5p, miR-199a-5p, miR-125A-5p, and miR-107 that we predicted would regulate the VEGFA, CDH5, and WNT3A genes, which were also associated with IPF or other fibrosis-related diseases. GSVA indicated that metabolic processes of UTP and IMP, immune response, regulation of Th2 cell cytokine production, and positive regulation of NK cell-mediated immunity are associated with the pathogenesis and treatment of IPF. These pathways also interact with VEGFA, CDH5, and WNT3A. Conclusion: These findings provide a new research direction for the diagnosis and treatment of IPF.
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Affiliation(s)
- Ke Zhu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Aiqun Xu
- Department of General Medicine, Hefei Second People's Hospital, Hefei 230001, China
| | - Wanli Xia
- Department of Thoracic Surgery, the first affiliated hospital of Anhui medical university, Hefei 230022, China
| | - Pulin Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Rui Han
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Enze Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Sijing Zhou
- Hefei Third Clinical College of Anhui Medical University, Hefei 230022, China.,Hefei Prevention and Treatment Center for Occupational Diseases, Hefei 230022, China
| | - Ran Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
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18
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Gaikwad AV, Eapen MS, McAlinden KD, Chia C, Larby J, Myers S, Dey S, Haug G, Markos J, Glanville AR, Sohal SS. Endothelial to mesenchymal transition (EndMT) and vascular remodeling in pulmonary hypertension and idiopathic pulmonary fibrosis. Expert Rev Respir Med 2020; 14:1027-1043. [PMID: 32659128 DOI: 10.1080/17476348.2020.1795832] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
INTRODUCTION Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and irreversible fibrotic disease associated with respiratory failure. The disease remains idiopathic, but repeated alveolar epithelium injury, disruption of alveolar-capillary integrity, abnormal vascular repair, and pulmonary vascular remodeling are considered possible pathogenic mechanisms. Also, the development of comorbidities such as pulmonary hypertension (PH) could further impact disease outcome, quality of life and survival rates in IPF. AREAS COVERED The current review provides a comprehensive literature survey of the mechanisms involved in the development and manifestations of IPF and their links to PH pathology. This review also provides the current understanding of molecular mechanisms that link the two pathologies and will specifically decipher the role of endothelial to mesenchymal transition (EndMT) along with the possible triggers of EndMT. The possibility of targeting EndMT as a therapeutic option in IPF is discussed. EXPERT OPINION With a steady increase in prevalence and mortality, IPF is no longer considered a rare disease. Thus, it is of utmost importance and urgency that the underlying profibrotic pathways and mechanisms are fully understood, to enable the development of novel therapeutic strategies.
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Affiliation(s)
- Archana Vijay Gaikwad
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania , Launceston, Australia
| | - Mathew Suji Eapen
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania , Launceston, Australia
| | - Kielan D McAlinden
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania , Launceston, Australia
| | - Collin Chia
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania , Launceston, Australia.,Department of Respiratory Medicine, Launceston General Hospital , Launceston, Australia
| | - Josie Larby
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania , Launceston, Australia.,Department of Respiratory Medicine, Launceston General Hospital , Launceston, Australia
| | - Stephen Myers
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania , Launceston, Australia
| | - Surajit Dey
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania , Launceston, Australia
| | - Greg Haug
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania , Launceston, Australia.,Department of Respiratory Medicine, Launceston General Hospital , Launceston, Australia
| | - James Markos
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania , Launceston, Australia.,Department of Respiratory Medicine, Launceston General Hospital , Launceston, Australia
| | - Allan R Glanville
- Lung Transplant Unit, Department of Thoracic Medicine, St Vincent's Hospital , Sydney, Australia
| | - Sukhwinder Singh Sohal
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania , Launceston, Australia
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19
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Wu G, Xie B, Lu C, Chen C, Zhou J, Deng Z. microRNA-30a attenuates TGF-β1-induced activation of pulmonary fibroblast cell by targeting FAP-α. J Cell Mol Med 2020; 24:3745-3750. [PMID: 31991519 PMCID: PMC7131934 DOI: 10.1111/jcmm.15020] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/20/2019] [Accepted: 12/16/2019] [Indexed: 01/14/2023] Open
Abstract
Idiopathic interstitial pulmonary fibrosis is a common diffuse interstitial lung disease and has poor prognosis. And one of the pathological features of it is persistent fibroblast activation. It was reported that microRNA‐30a was down‐regulated in bronchoalveolar lavage fluid from idiopathic pulmonary fibrosis patients. But whether miR‐30a is involved in fibroblast activation and its specific mechanism is unclear. In this study, we aimed to investigate the role of miR‐30a in fibroblast activation induced by TGF‐β1. We found miR‐30a could targetedly suppress FAP‐α expression. In MRC5 cells, miR‐30a was not only involved in regulating the expression of FAP‐α, col1a and α‐SMA induced by TGF‐β1 but also had a role in cell proliferation with or without TGF‐β1 treatment via regulating FAP‐α expression. Thus, the results indicated that miR‐30a alleviated fibroblast activation by regulating the expression of FAP‐α.
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Affiliation(s)
- Geting Wu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Bin Xie
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Can Lu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Chen Chen
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
| | - Jianhua Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
| | - Zhenghao Deng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
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20
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Idiopathic Pulmonary Fibrosis: Pathogenesis and the Emerging Role of Long Non-Coding RNAs. Int J Mol Sci 2020; 21:ijms21020524. [PMID: 31947693 PMCID: PMC7013390 DOI: 10.3390/ijms21020524] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/16/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive chronic disease characterized by excessing scarring of the lungs leading to irreversible decline in lung function. The aetiology and pathogenesis of the disease are still unclear, although lung fibroblast and epithelial cell activation, as well as the secretion of fibrotic and inflammatory mediators, have been strongly associated with the development and progression of IPF. Significantly, long non-coding RNAs (lncRNAs) are emerging as modulators of multiple biological processes, although their function and mechanism of action in IPF is poorly understood. LncRNAs have been shown to be important regulators of several diseases and their aberrant expression has been linked to the pathophysiology of fibrosis including IPF. This review will provide an overview of this emerging role of lncRNAs in the development of IPF.
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21
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MicroRNA-31/184 is involved in transforming growth factor-β-induced apoptosis in A549 human alveolar adenocarcinoma cells. Life Sci 2019; 242:117205. [PMID: 31874165 DOI: 10.1016/j.lfs.2019.117205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/04/2019] [Accepted: 12/17/2019] [Indexed: 12/25/2022]
Abstract
AIMS TGF-β-induced alveolar epithelial cells apoptosis were involved in idiopathic pulmonary fibrosis (IPF). This study aimed to explore potential targets and mechanisms of IPF. MAIN METHODS mRNA and microRNA arrays were used to analyze differentially expressed genes and miRNAs. Several essential targets of TGF-β-SMADs and TGF-β-PI3K-AKT pathways were detected. KEY FINDINGS miR-31 and miR-184 expression levels were positively correlated with smad6 and smad2/akt expression levels in IPF patients. TGF-β could induce miR-31 and suppress miR-184 levels in A549 cells. miR-31 was confirmed to bind to the smad6-3'UTR and functionally suppress its expression. Down-regulated SMAD6 enhanced SMAD2/SMAD4 dimer formation and translocation due to its failure to prevent SMAD2 phosphorylation. In contrast, anti-fibrotic functions of miR-184 were abolished due to TGF-β directly suppressing miR-184 levels in A549 cells. When A549 was stimulated by TGF-β combined with or without miR-31 inhibitor/miR-184 mimic, it was showed that depleted miR-31 and/or increased miR-184 significantly ameliorated TGF-β-induced viability of A549 cells, as well as inhibited the expression of profibrotic factors, MMP7 and RUNX2. SIGNIFICANCE Inhibiting miR-31 and/or promoting miR-184 protect against TGF-β-induced fibrogenesis by respectively repressing the TGF-β-SMAD2 and TGF-β-PI3K-AKT signaling pathways, implying that miR-31/184 are potential targets and suggesting a new management strategy for IPF.
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22
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Moimas S, Salton F, Kosmider B, Ring N, Volpe MC, Bahmed K, Braga L, Rehman M, Vodret S, Graziani ML, Wolfson MR, Marchetti N, Rogers TJ, Giacca M, Criner GJ, Zacchigna S, Confalonieri M. miR-200 family members reduce senescence and restore idiopathic pulmonary fibrosis type II alveolar epithelial cell transdifferentiation. ERJ Open Res 2019; 5:00138-2019. [PMID: 31857992 PMCID: PMC6911923 DOI: 10.1183/23120541.00138-2019] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 09/23/2019] [Indexed: 12/12/2022] Open
Abstract
Rationale Alveolar type II (ATII) cells act as adult stem cells contributing to alveolar type I (ATI) cell renewal and play a major role in idiopathic pulmonary fibrosis (IPF), as supported by familial cases harbouring mutations in genes specifically expressed by these cells. During IPF, ATII cells lose their regenerative potential and aberrantly express pathways contributing to epithelial–mesenchymal transition (EMT). The microRNA miR-200 family is downregulated in IPF, but its effect on human IPF ATII cells remains unproven. We wanted to 1) evaluate the characteristics and transdifferentiating ability of IPF ATII cells, and 2) test whether miR-200 family members can rescue the regenerative potential of fibrotic ATII cells. Methods ATII cells were isolated from control or IPF lungs and cultured in conditions promoting their transdifferentiation into ATI cells. Cells were either phenotypically monitored over time or transfected with miR-200 family members to evaluate the microRNA effect on the expression of transdifferentiation, senescence and EMT markers. Results IPF ATII cells show a senescent phenotype (p16 and p21), overexpression of EMT (ZEB1/2) and impaired expression of ATI cell markers (AQP5 and HOPX) after 6 days of culture in differentiating medium. Transfection with certain miR-200 family members (particularly miR-200b-3p and miR-200c-3p) reduced senescence marker expression and restored the ability to transdifferentiate into ATI cells. Conclusions We demonstrated that ATII cells from IPF patients express senescence and EMT markers, and display a reduced ability to transdifferentiate into ATI cells. Transfection with certain miR-200 family members rescues this phenotype, reducing senescence and restoring transdifferentiation marker expression. Idiopathic pulmonary fibrosis alveolar epithelial type II cells show senescence and EMT features, but miR-200b and miR-200c can restore the ability of type II cells to transdifferentiate in vitro into type I alveolar epithelial cellshttp://bit.ly/359tlit
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Affiliation(s)
- Silvia Moimas
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.,These authors contributed equally to this work (co-first authors)
| | - Francesco Salton
- Pulmonology Dept, University Hospital of Cattinara, Trieste, Italy.,These authors contributed equally to this work (co-first authors)
| | - Beata Kosmider
- Center for Inflammation, Translational and Clinical Lung Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.,Dept of Thoracic Medicine and Surgery, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.,Dept of Physiology, Temple University, Philadelphia, PA, USA.,These authors contributed equally to this work (co-first authors)
| | - Nadja Ring
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Maria C Volpe
- Pulmonology Dept, University Hospital of Cattinara, Trieste, Italy.,Dept of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Karim Bahmed
- Center for Inflammation, Translational and Clinical Lung Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.,Dept of Thoracic Medicine and Surgery, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Luca Braga
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Michael Rehman
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Simone Vodret
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | | | - Marla R Wolfson
- Center for Inflammation, Translational and Clinical Lung Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.,Dept of Thoracic Medicine and Surgery, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.,Dept of Physiology, Temple University, Philadelphia, PA, USA.,CENTRe: Collaborative for Environmental and Neonatal Therapeutics, Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Nathaniel Marchetti
- Dept of Thoracic Medicine and Surgery, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Thomas J Rogers
- Center for Inflammation, Translational and Clinical Lung Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.,Dept of Thoracic Medicine and Surgery, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Mauro Giacca
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.,Dept of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Gerard J Criner
- Dept of Thoracic Medicine and Surgery, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.,These authors contributed equally to this work (co-last authors)
| | - Serena Zacchigna
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.,Dept of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,These authors contributed equally to this work (co-last authors)
| | - Marco Confalonieri
- Pulmonology Dept, University Hospital of Cattinara, Trieste, Italy.,Dept of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,These authors contributed equally to this work (co-last authors)
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23
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Elliot S, Periera-Simon S, Xia X, Catanuto P, Rubio G, Shahzeidi S, El Salem F, Shapiro J, Briegel K, Korach KS, Glassberg MK. MicroRNA let-7 Downregulates Ligand-Independent Estrogen Receptor-mediated Male-Predominant Pulmonary Fibrosis. Am J Respir Crit Care Med 2019; 200:1246-1257. [PMID: 31291549 PMCID: PMC6857483 DOI: 10.1164/rccm.201903-0508oc] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/10/2019] [Indexed: 12/26/2022] Open
Abstract
Rationale: The relevance of hormones in idiopathic pulmonary fibrosis (IPF), a predominantly male lung disease, is unknown.Objectives: To determine whether the ER (estrogen receptor) facilitates the development of pulmonary fibrosis and is mediated in part through microRNA regulation of ERα and ERα-activated profibrotic pathways.Methods: ER expression in male lung tissue and myofibroblasts from control subjects (n = 6) and patients with IPF (n = 6), aging bleomycin (BLM)-treated mice (n = 7), and BLM-treated AF2ERKI mice (n = 7) was determined. MicroRNAs that regulate ER and fibrotic pathways were assessed. Transfections with a reporter plasmid containing the 3' untranslated region of the gene encoding ERα (ESR1) with and without miRNA let-7 mimics or inhibitors or an estrogen response element-driven reporter construct (ERE) construct were conducted.Measurements and Main Results: ERα expression increased in IPF lung tissue, myofibroblasts, or BLM mice. In vitro treatment with let-7 mimic transfections in human myofibroblasts reduced ERα expression and associated fibrotic pathways. AF2ERKI mice developed BLM-induced lung fibrosis, suggesting a role for growth factors in stimulating ER and fibrosis. IGF-1 (insulin-like growth factor 1) expression was increased and induced a fourfold increase of an ERE construct.Conclusions: Our data show 1) a critical role for ER and let-7 in lung fibrosis, and 2) that IGF may stimulate ER in an E2-independent manner. These results underscore the role of sex steroid hormones and their receptors in diseases that demonstrate a sex prevalence, such as IPF.
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Affiliation(s)
| | | | - Xiaomei Xia
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, and
| | | | | | - Shahriar Shahzeidi
- Division of Pediatric Pulmonology, Department of Pediatrics, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
| | - Fadi El Salem
- Icahn School of Medicine at Mount Sinai, New York, New York; and
| | - Josh Shapiro
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, and
| | | | - Kenneth S. Korach
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Marilyn K. Glassberg
- Department of Surgery
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, and
- Division of Pediatric Pulmonology, Department of Pediatrics, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
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24
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Sai L, Yu G, Bo C, Zhang Y, Du Z, Li C, Zhang Z, Jia Q, Shao H, Peng C. Profiling long non-coding RNA changes in silica-induced pulmonary fibrosis in rat. Toxicol Lett 2019; 310:7-13. [PMID: 30978436 DOI: 10.1016/j.toxlet.2019.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/23/2019] [Accepted: 04/01/2019] [Indexed: 12/15/2022]
Abstract
Silicosis is a kind of chronic and incurable lung fibrotic disease with pathogenesis and molecular mechanisms largely unknown. Mounting evidence suggests that long non-coding RNAs (lncRNAs) are involved in the pathogenesis of silicosis. However, how many lncRNAs involved in the pulmonary fibrosis remains to be elucidated. In this study, Wistar rats were exposed to silicon dioxide by an improved tracheal intubation method. Rats in the control group were treated with normal saline solution. Results showed that 28 days after exposure, there were significant differences in body weight and lung coefficient of rats treated with silica compared with control rats. The formation of lung fibrosis in silica-induced rats was confirmed by histologic examination. We then investigated the lncRNAs expression changes in lung tissues of silica-exposed rats and compared that with the rats in the control group using microarray. The results indicated that silica exposure leads to altered expression profile in 682 lncRNAs (300 upregulated and 382 downregulated). Seventy-three ceRNA pairs were acquired by predicted analysis. Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology analyses were used to predict the biological pathway and functional classification of lncRNAs. The results showed that silica exposure affected 13 lncRNAs pathways. The functional classification mainly involved in protein binding, cell shape and extracellular exosome. This study indicated that alteration of lncRNAs may play a role in silica-induced pulmonary fibrosis through regulation of expressions of functional genes in lungs of rat. Our results provide more insights into the mechanism of silicosis.
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Affiliation(s)
- Linlin Sai
- Shandong Academy of Occupational Health and Occupational Medicine, Ji'nan, Shandong, China
| | - Gongchang Yu
- Shandong Academy of Occupational Health and Occupational Medicine, Ji'nan, Shandong, China
| | - Cunxiang Bo
- Shandong Academy of Occupational Health and Occupational Medicine, Ji'nan, Shandong, China
| | - Yu Zhang
- Shandong Academy of Occupational Health and Occupational Medicine, Ji'nan, Shandong, China
| | - Zhongjun Du
- Shandong Academy of Occupational Health and Occupational Medicine, Ji'nan, Shandong, China
| | - Chao Li
- Shandong Academy of Occupational Health and Occupational Medicine, Ji'nan, Shandong, China
| | - Zhenling Zhang
- Shandong Academy of Occupational Health and Occupational Medicine, Ji'nan, Shandong, China
| | - Qiang Jia
- Shandong Academy of Occupational Health and Occupational Medicine, Ji'nan, Shandong, China.
| | - Hua Shao
- Shandong Academy of Occupational Health and Occupational Medicine, Ji'nan, Shandong, China.
| | - Cheng Peng
- Shandong Academy of Occupational Health and Occupational Medicine, Ji'nan, Shandong, China; The University of Queensland, Queensland Alliance for Environmental Health Sciences (QAEHS), Brisbane, Queensland, Australia
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25
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Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts: A Next-Generation Sequencing and Bioinformatics Study. J Clin Med 2019; 8:jcm8030308. [PMID: 30841487 PMCID: PMC6462954 DOI: 10.3390/jcm8030308] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 02/18/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and fatal interstitial lung disease. Therapeutic options for IPF remain limited. Nintedanib, a tyrosine kinase inhibitor approved for IPF treatment, is known to inhibit fibroblasts proliferation, migration and transformation to myofibroblasts. However, how nintedanib changes gene regulations in IPF has never been systematically investigated. We conducted a next-generation sequencing and bioinformatics study to evaluate the changes of mRNA and miRNA profiles in IPF fibroblasts treated with 2 µM and 4 µM nintedanib, compared to those without treatment. We identified 157 upregulated and 151 downregulated genes and used STRING and DAVID databases for analysis of protein⁻protein interactions, biological pathways, and molecular functions. We found strong protein⁻protein interactions within these dysregulated genes, mostly involved in the pathways of cell cycle and mitotic cell cycle. We also discovered 13 potential miRNA⁻mRNA interactions associated with nintedanib treatment. After validation using miRDB, TargetScan, and RT-qPCR, we identified 4 downregulated genes (DDX11, E2F1, NPTX1, and PLXNA4) which might be repressed by the upregulated hsa-miR-486-3p. According to the proposed functions of DDX11, E2F1, and PLXNA4 reported in previous studies, these gene expression changes together might contribute to decreased proliferation of fibroblasts and decreased angiogenesis in the microenvironment of IPF. Our findings need further studies to confirm.
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26
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Moro A, Driscoll TP, Boraas LC, Armero W, Kasper DM, Baeyens N, Jouy C, Mallikarjun V, Swift J, Ahn SJ, Lee D, Zhang J, Gu M, Gerstein M, Schwartz M, Nicoli S. MicroRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis. Nat Cell Biol 2019; 21:348-358. [PMID: 30742093 PMCID: PMC6528464 DOI: 10.1038/s41556-019-0272-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 01/02/2019] [Indexed: 12/13/2022]
Abstract
Vertebrate tissues exhibit mechanical homeostasis, showing stable stiffness and tension over time and recovery after changes in mechanical stress. However, the regulatory pathways that mediate these effects are unknown. A comprehensive identification of Argonaute-2(AGO2)-associated microRNAs and mRNAs in endothelial cells identified a network of 122 microRNA families that target 73 mRNAs encoding cytoskeletal, contractile, adhesive and extracellular matrix (CAM) proteins. These microRNAs increased in cells plated on stiff vs. soft substrates, consistent with homeostasis, and suppressed targets via microRNA recognition elements (MREs) within the 3’UTRs of CAM mRNAs. Inhibition of DROSHA or AGO2, or disruption of MREs within individual target mRNAs such as Connective Tissue Growth Factor (CTGF), induced hyper-adhesive, hyper-contractile phenotypes in endothelial and fibroblast cells in vitro, and increased tissue stiffness, contractility and extracellular matrix (ECM) deposition in the zebrafish fin-fold in vivo. Thus, a network of microRNAs buffers CAM expression to mediate tissue mechanical homeostasis.
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Affiliation(s)
- Albertomaria Moro
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA
| | - Tristan P Driscoll
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA
| | - Liana C Boraas
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA
| | - William Armero
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA
| | - Dionna M Kasper
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA
| | - Nicolas Baeyens
- Laboratoire de Physiologie et Pharmacologie, Faculty of Medicine, Université Libre De Bruxelles, Brussels, Belgium.,Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Charlene Jouy
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK
| | - Venkatesh Mallikarjun
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK.,Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Joe Swift
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK.,Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Sang Joon Ahn
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA
| | - Donghoon Lee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jing Zhang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Mengting Gu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Computer Science, Yale University, New Haven, CT, USA
| | - Martin Schwartz
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA. .,Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, UK. .,Departments of Cell Biology and Biomedical Engineering, Yale University, New Haven, CT, USA.
| | - Stefania Nicoli
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA. .,Department of Genetics, Yale University School of Medicine, New Haven, CT, USA. .,Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
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27
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Ebrahimpour A, Shrestha S, Bonnen MD, Eissa NT, Raghu G, Ghebre YT. Nicotine Modulates Growth Factors and MicroRNA to Promote Inflammatory and Fibrotic Processes. J Pharmacol Exp Ther 2019; 368:169-178. [PMID: 30446578 PMCID: PMC6323623 DOI: 10.1124/jpet.118.252650] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 11/01/2018] [Indexed: 02/06/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal disease that destroys the structure and function of the lungs. Risk factors include advanced age and genetic predisposition. However, tobacco use is the chief modifiable risk factor. The prevalence of tobacco use in IPF reaches up to 80%. Although tobacco smoke contains over 5000 chemicals, nicotine is a major component. Nicotine is a bioactive molecule that acts upon nicotinic acetylcholine receptors expressed on neuronal and non-neuronal cells including endothelial cells. Accordingly, it has a pleiotropic effect on cell proliferation and angiogenesis. The angiogenic effect is partly mediated by stimulation of growth factors including fibroblast, platelet-derived, and vascular endothelial growth factors. Nintedanib, a Food and Drug Administration-approved drug for IPF, works by inhibiting receptors for these growth factors, suggesting a pathobiologic role of the growth factors in IPF and a potential mechanism by which tobacco use may exacerbate the disease process; additionally, nicotine downregulates anti-inflammatory microRNAs (miRs) in lung cells. Here, we profiled the expression of miRs in lung tissues explanted from a lung injury model and examined the effect of nicotine on one of the identified miRs (miR-24) and its downstream targets. Our data show that miR-24 is downregulated during lung injury and is suppressed by nicotine. We also found that nicotine upregulates the expression of inflammatory cytokines targeted by miR-24. Finally, nicotine stimulated growth factors, fibroblast proliferation, collagen release, and expression of myofibroblast markers. Taken together, nicotine, alone or as a component of tobacco smoke, may accelerate the disease process in IPF through stimulation of growth factors and downregulation of anti-inflammatory miRs.
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Affiliation(s)
- Afshin Ebrahimpour
- Departments of Radiation Oncology (A.E., S.S., M.D.B., Y.T.G.) and Medicine, Section on Pulmonary and Critical Care Medicine (N.T.E., Y.T.G.), Baylor College of Medicine, Houston, Texas; and Division of Pulmonary and Critical Care Medicine, Center for Interstitial Lung Disease, University of Washington, Seattle, Washington (G.R.)
| | - Samana Shrestha
- Departments of Radiation Oncology (A.E., S.S., M.D.B., Y.T.G.) and Medicine, Section on Pulmonary and Critical Care Medicine (N.T.E., Y.T.G.), Baylor College of Medicine, Houston, Texas; and Division of Pulmonary and Critical Care Medicine, Center for Interstitial Lung Disease, University of Washington, Seattle, Washington (G.R.)
| | - Mark D Bonnen
- Departments of Radiation Oncology (A.E., S.S., M.D.B., Y.T.G.) and Medicine, Section on Pulmonary and Critical Care Medicine (N.T.E., Y.T.G.), Baylor College of Medicine, Houston, Texas; and Division of Pulmonary and Critical Care Medicine, Center for Interstitial Lung Disease, University of Washington, Seattle, Washington (G.R.)
| | - N Tony Eissa
- Departments of Radiation Oncology (A.E., S.S., M.D.B., Y.T.G.) and Medicine, Section on Pulmonary and Critical Care Medicine (N.T.E., Y.T.G.), Baylor College of Medicine, Houston, Texas; and Division of Pulmonary and Critical Care Medicine, Center for Interstitial Lung Disease, University of Washington, Seattle, Washington (G.R.)
| | - Ganesh Raghu
- Departments of Radiation Oncology (A.E., S.S., M.D.B., Y.T.G.) and Medicine, Section on Pulmonary and Critical Care Medicine (N.T.E., Y.T.G.), Baylor College of Medicine, Houston, Texas; and Division of Pulmonary and Critical Care Medicine, Center for Interstitial Lung Disease, University of Washington, Seattle, Washington (G.R.)
| | - Yohannes T Ghebre
- Departments of Radiation Oncology (A.E., S.S., M.D.B., Y.T.G.) and Medicine, Section on Pulmonary and Critical Care Medicine (N.T.E., Y.T.G.), Baylor College of Medicine, Houston, Texas; and Division of Pulmonary and Critical Care Medicine, Center for Interstitial Lung Disease, University of Washington, Seattle, Washington (G.R.)
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28
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Sandbo N. Mechanisms of Fibrosis in IPF. Respir Med 2019. [DOI: 10.1007/978-3-319-99975-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Future Directions for IPF Research. Respir Med 2019. [DOI: 10.1007/978-3-319-99975-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Systems Analysis of Transcriptomic and Proteomic Profiles Identifies Novel Regulation of Fibrotic Programs by miRNAs in Pulmonary Fibrosis Fibroblasts. Genes (Basel) 2018; 9:genes9120588. [PMID: 30501089 PMCID: PMC6316743 DOI: 10.3390/genes9120588] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/23/2018] [Accepted: 11/23/2018] [Indexed: 01/10/2023] Open
Abstract
Fibroblasts/myofibroblasts are the key effector cells responsible for excessive extracellular matrix (ECM) deposition and fibrosis progression in both idiopathic pulmonary fibrosis (IPF) and systemic sclerosis (SSc) patient lungs, thus it is critical to understand the transcriptomic and proteomic programs underlying their fibrogenic activity. We conducted the first integrative analysis of the fibrotic programming in these cells at the levels of gene and microRNA (miRNA) expression, as well as deposited ECM protein to gain insights into how fibrotic transcriptional programs culminate in aberrant ECM protein production/deposition. We identified messenger RNA (mRNA), miRNA, and deposited matrisome protein signatures for IPF and SSc fibroblasts obtained from lung transplants using next-generation sequencing and mass spectrometry. SSc and IPF fibroblast transcriptional signatures were remarkably similar, with enrichment of WNT, TGF-β, and ECM genes. miRNA-seq identified differentially regulated miRNAs, including downregulation of miR-29b-3p, miR-138-5p and miR-146b-5p in disease fibroblasts and transfection of their mimics decreased expression of distinct sets of fibrotic signature genes as assessed using a Nanostring fibrosis panel. Finally, proteomic analyses uncovered a distinct "fibrotic" matrisome profile deposited by IPF and SSc fibroblasts compared to controls that highlights the dysregulated ECM production underlying their fibrogenic activities. Our comprehensive analyses of mRNA, miRNA, and matrisome proteomic profiles in IPF and SSc lung fibroblasts revealed robust fibrotic signatures at both the gene and protein expression levels and identified novel fibrogenesis-associated miRNAs whose aberrant downregulation in disease fibroblasts likely contributes to their fibrotic and ECM gene expression.
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Vella S, Conaldi PG, Cova E, Meloni F, Liotta R, Cuzzocrea S, Martino L, Bertani A, Luca A, Vitulo P. Lung resident mesenchymal cells isolated from patients with the Bronchiolitis Obliterans Syndrome display a deregulated epigenetic profile. Sci Rep 2018; 8:11167. [PMID: 30042393 PMCID: PMC6057887 DOI: 10.1038/s41598-018-29504-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 07/09/2018] [Indexed: 12/13/2022] Open
Abstract
Bronchiolitis Obliterans Syndrome is the major determinant of the graft function loss after lung transplantation, but its pathogenesis is still incompletely understood and currently available therapeutic strategies are poorly effective. A deeper understanding of its pathogenic mechanisms is crucial for the development of new strategies to prevent and treat this devastating complication. In this study, we focused on the mesenchymal stromal cells, recently recognized as BOS key effectors, and our primary aim was to identify their epigenetic determinants, such as histone modifications and non-coding RNA regulation, which could contribute to their differentiation in myofibroblasts. Interestingly, we identified a deregulated expression of histone deacetylases and methyltransferases, and a microRNA-epigenetic regulatory network, which could represent novel targets for anti-fibrotic therapy. We validated our results in vitro, in a cell model of fibrogenesis, confirming the epigenetic involvement in this process and paving the way for a new application for epigenetic drugs.
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Affiliation(s)
- Serena Vella
- Department of Laboratory Medicine and Advanced Biotechnologies, IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), Palermo, Italy.
- Anemocyte S.r.l, Gerenzano, Italy.
| | - Pier Giulio Conaldi
- Department of Laboratory Medicine and Advanced Biotechnologies, IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), Palermo, Italy
| | - Emanuela Cova
- Department of Respiratory Diseases, IRCCS San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Federica Meloni
- Department of Respiratory Diseases, IRCCS San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Rosa Liotta
- Department of Diagnostic and Therapeutic Services, Pathology Service, IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), Palermo, Italy
| | - Salvatore Cuzzocrea
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Lavinia Martino
- Department for the Treatment and Study of Cardiothoracic Diseases and Cardiothoracic Transplantation, IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), Palermo, Italy
| | - Alessandro Bertani
- Department for the Treatment and Study of Cardiothoracic Diseases and Cardiothoracic Transplantation, IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), Palermo, Italy
| | - Angelo Luca
- Department of Diagnostic and Therapeutic Services, Radiology Service, IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), Palermo, Italy
| | - Patrizio Vitulo
- Department for the Treatment and Study of Cardiothoracic Diseases and Cardiothoracic Transplantation, IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), Palermo, Italy
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Lipoxin A 4 Attenuates Bronchopulmonary Dysplasia via Upregulation of Let-7c and Downregulation of TGF-β 1 Signaling Pathway. Inflammation 2018; 40:2094-2108. [PMID: 28819748 DOI: 10.1007/s10753-017-0649-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Transforming growth factor-β (TGF-β) superfamily members are key regulators for lung development and progress of bronchopulmonary dysplasia (BPD). The mechanisms by which lipoxin A4 (LXA4) attenuates development of BPD have not been clarified. Neonatal murine BPD models were inducted by hyperoxia treatment. Neonatal mice were exposed to room air or 85% O2 hyperoxia with or without treatment with 5S,6R-methyl-LXA4 or anti-TGF-β antibodies. Mouse lung epithelial cells (MLE-12 cells) and mouse embryonic fibroblasts (NIH/3T3 cells) were cultured in room air or 85% O2 followed by treatment of LXA4, anti-TGF-β antibodies, and let-7c mimic/anti-microRNA transfections. Treatment with 5S,6R-methyl-LXA4 and anti-TGF-β antibodies both attenuated the mice alveolar simplification induced by hyperoxia. Hyperoxia treatment significantly altered pulmonary basal mRNA and protein expressions of several important extracellular matrix (ECM) and ECM remodeling proteins including fibronectin, α-smooth muscle actin (α-SMA), tissue inhibitor of metalloproteinase-1 (TIMP-1), elastin, tenascin C, collagen I, and matrix metalloproteinase-1 (MMP-1). 5S,6R-methyl-LXA4 and anti-TGF-β antibodies suppressed the mRNA and protein expressions of TGF-β1 and TGF-βR1 but not TGF-βR2 in the lungs exposed to hyperoxia. Treatment with LXA4 and anti-TGF-β antibodies alleviated hyperoxia-induced injury of the NIH/3T3 cells identified by morphologic observation and flow cytometry, and expressions of ECM, ECM remodeling proteins, and TGF-β1 signaling pathway, but reversed by transfection with let-7c anti-miRNA. LXA4 upregulated the let-7c expression in MLE-12 cells, transfection with let-7c anti-miRNA, inhibited the LXA4-induced let-7c expression in MLE-12 cells exposed to hyperoxia and reduced the relative luciferase activity of let-7c binding with let-7c binding sites of the TGF-βR1 3' UTR. Treatment with 5S,6R-methyl-LXA4 and anti-TGF-β antibodies significantly improved histology, ECM, and ECM remodeling proteins in the lungs isolated from the murine BPD model induced by hyperoxia. The LXA4-imparted protective effects on hyperoxia-induced lung injury are mediated by upregulation of let-7c and inhibition of TGF-β1 and subsequent downregulation of TGF-β1 signaling pathway.
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Vukmirovic M, Kaminski N. Impact of Transcriptomics on Our Understanding of Pulmonary Fibrosis. Front Med (Lausanne) 2018; 5:87. [PMID: 29670881 PMCID: PMC5894436 DOI: 10.3389/fmed.2018.00087] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 03/20/2018] [Indexed: 12/22/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a lethal fibrotic lung disease characterized by aberrant remodeling of the lung parenchyma with extensive changes to the phenotypes of all lung resident cells. The introduction of transcriptomics, genome scale profiling of thousands of RNA transcripts, caused a significant inversion in IPF research. Instead of generating hypotheses based on animal models of disease, or biological plausibility, with limited validation in humans, investigators were able to generate hypotheses based on unbiased molecular analysis of human samples and then use animal models of disease to test their hypotheses. In this review, we describe the insights made from transcriptomic analysis of human IPF samples. We describe how transcriptomic studies led to identification of novel genes and pathways involved in the human IPF lung such as: matrix metalloproteinases, WNT pathway, epithelial genes, role of microRNAs among others, as well as conceptual insights such as the involvement of developmental pathways and deep shifts in epithelial and fibroblast phenotypes. The impact of lung and transcriptomic studies on disease classification, endotype discovery, and reproducible biomarkers is also described in detail. Despite these impressive achievements, the impact of transcriptomic studies has been limited because they analyzed bulk tissue and did not address the cellular and spatial heterogeneity of the IPF lung. We discuss new emerging technologies and applications, such as single-cell RNAseq and microenvironment analysis that may address cellular and spatial heterogeneity. We end by making the point that most current tissue collections and resources are not amenable to analysis using the novel technologies. To take advantage of the new opportunities, we need new efforts of sample collections, this time focused on access to all the microenvironments and cells in the IPF lung.
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Affiliation(s)
- Milica Vukmirovic
- Section of Pulmonary, Critical Care and Sleep Medicine, Precision Pulmonary Medicine Center (P2MED), Yale University School of Medicine, New Haven, CT, United States
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Precision Pulmonary Medicine Center (P2MED), Yale University School of Medicine, New Haven, CT, United States
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34
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Fibrosis: Lessons from OMICS analyses of the human lung. Matrix Biol 2018; 68-69:422-434. [PMID: 29567123 DOI: 10.1016/j.matbio.2018.03.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 12/30/2022]
Abstract
In recent decades there has been a significant shift in our understanding of idiopathic pulmonary fibrosis (IPF), a progressive and lethal disorder. While initially much of the mechanistic understanding was derived from hypotheses generated from animal models of disease, in recent decades new insights derived from humans with IPF have taken precedence. This is mainly because of the establishment of large collections of IPF lung tissues and patient cohorts, and the emergence of high throughput profiling technologies collectively termed 'omics' technologies based on their shared suffix. In this review we describe impacts of 'omics' analyses of human IPF samples on our understanding of the disease. In particular, we discuss the results of genomics and transcriptomics studies, as well as proteomics, epigenomics and metabolomics. We then describe how these findings can be integrated in a modified paradigm of human idiopathic pulmonary fibrosis, that introduces the 'hallmarks of aging' as a central theme in the IPF lung. This allows resolution of all the disparate cellular and molecular features in IPF, from the central role of epithelial cells, through the dramatic phenotypic alterations observed in fibroblasts and the numerous aberrations that inflammatory cells exhibit. We end with reiterating a call for renewed efforts to collect and analyze carefully characterized human tissues, in ways that would facilitate implementation of novel technologies for high resolution single cell omics profiling.
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35
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Rubio GA, Elliot SJ, Wikramanayake TC, Xia X, Pereira-Simon S, Thaller SR, Glinos GD, Jozic I, Hirt P, Pastar I, Tomic-Canic M, Glassberg MK. Mesenchymal stromal cells prevent bleomycin-induced lung and skin fibrosis in aged mice and restore wound healing. J Cell Physiol 2018; 233:5503-5512. [PMID: 29271488 DOI: 10.1002/jcp.26418] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/19/2017] [Indexed: 02/06/2023]
Abstract
Fibrosis can develop in nearly any tissue leading to a wide range of chronic fibrotic diseases. However, current treatment options are limited. In this study, we utilized an established aged mouse model of bleomycin-induced lung fibrosis (BLM) to test our hypothesis that fibrosis may develop simultaneously in multiple organs by evaluating skin fibrosis and wound healing. Fibrosis was induced in lung in aged (18-22-month-old) C57BL/6 male mice by intratracheal BLM administration. Allogeneic adipose-derived mesenchymal stromal cells (ASCs) or saline were injected intravenously 24 hr after BLM administration. Full thickness 8-mm punch wounds were performed 7 days later to study potential systemic anti-fibrotic and wound healing effects of intravenously delivered ASCs. Mice developed lung and skin fibrosis as well as delayed wound closure. Moreover, we observed similar changes in the expression of known pro-fibrotic factors in both lung and skin wound tissue, including miR-199 and protein expression of its corresponding target, caveolin-1, as well as phosphorylation of protein kinase B. Importantly, ASC-treated mice exhibited attenuation of BLM-induced lung and skin fibrosis and accelerated wound healing, suggesting that ASCs may prime injured tissues and prevent end-organ fibrosis.
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Affiliation(s)
- Gustavo A Rubio
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
| | - Sharon J Elliot
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
| | - Tongyu C Wikramanayake
- Wound Healing and Regenerative Medicine Research Program, Department of Dermatology and Cutaneous Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
| | - Xiaomei Xia
- Department of Medicine, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
| | - Simone Pereira-Simon
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
| | - Seth R Thaller
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
| | - George D Glinos
- Wound Healing and Regenerative Medicine Research Program, Department of Dermatology and Cutaneous Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
| | - Ivan Jozic
- Wound Healing and Regenerative Medicine Research Program, Department of Dermatology and Cutaneous Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
| | - Penelope Hirt
- Wound Healing and Regenerative Medicine Research Program, Department of Dermatology and Cutaneous Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
| | - Irena Pastar
- Wound Healing and Regenerative Medicine Research Program, Department of Dermatology and Cutaneous Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
| | - Marjana Tomic-Canic
- Wound Healing and Regenerative Medicine Research Program, Department of Dermatology and Cutaneous Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
| | - Marilyn K Glassberg
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida.,Department of Medicine, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
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36
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MiR-185/AKT and miR-29a/collagen 1a pathways are activated in IPF BAL cells. Oncotarget 2018; 7:74569-74581. [PMID: 27769060 PMCID: PMC5342687 DOI: 10.18632/oncotarget.12740] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/04/2016] [Indexed: 12/29/2022] Open
Abstract
MicroRNA signatures of BAL cells and alveolar macrophages are currently lacking in IPF. Here we sought to investigate the expression of fibrosis-related microRNAs in the cellular component of the BAL in IPF. We thus focused on microRNAs previously associated with fibrosis (miR-29a, miR-29b, miR-29c, let-7d, and miR-21) and rapid IPF progression (miR-185, miR-210, miR-302c-3p miR-376c and miR-423-5p). Among the tested microRNAs miR-29a and miR-185 were found significantly downregulated in IPF while miR-302c-3p and miR-376c were not expressed by BAL cells. Importantly, the downregulation of miR-29a inversely correlated with the significantly increased levels of COL1A1 mRNA in IPF BAL cells. Collagen 1 a was found mainly overexpressed in alveolar macrophages and not other cell types of the BAL by immunofluorescence. In view of the downregulation of miR-185, we tested the response of THP-1 macrophages to profibrotic cytokine TGFb and observed the downregulation of miR-185. Conversely, proinflammatory stimulation lead to miR-185 upregulation. Upon examination of the mRNA levels of known miR-185 targets AKT1, DNMT1 and HMGA2, no significant correlations were observed in the BAL cells. However, increased levels of total AKT and AKTser473 phosphorylation were observed in the IPF BAL cells. Furthermore, miR-185 inhibition in THP-1 macrophages resulted in significant increase of AKTser473 phosphorylation. Our study highlights the importance of BAL microRNA signatures in IPF and identifies significant differences in miR-185/AKT and miR-29a/collagen axes in the BAL cells of IPF patients.
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37
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Yang L, Liu L, Ying H, Yu Y, Zhang D, Deng H, Zhang H, Chai J. Acute downregulation of miR-155 leads to a reduced collagen synthesis through attenuating macrophages inflammatory factor secretion by targeting SHIP1. J Mol Histol 2018; 49:165-174. [PMID: 29330743 DOI: 10.1007/s10735-018-9756-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/08/2018] [Indexed: 12/15/2022]
Abstract
Fibrosis, tightly associated with fibroblasts collagen synthesis, is related closely with inflammatory response. Our previously study found that acute downregulation of miR-155 at wound sites leads to a reduced fibrosis, however its particular mechanism is unclear. Herein, we aimed to explore the mechanism of miR-155 in reducing fibrosis. We first found that down-regulation of miR-155 inhibited macrophages transforming growth factor-β1 (TGF-β1) and IL-1β secretion. Next, we found that co-cultured with macrophages increased the proliferation and collagen synthesis of fibroblasts, and downregulation of miR-155 in macrophages could effectively attenuate the accelerative effects. We further identified SH2 domain containing inositol-5-phosphatase 1 (SHIP1) as a direct target of miR-155 in macrophages, and the expression of SHIP1 was negatively correlated with the level of miR-155. We further confirmed that PI3K/Akt pathway was involved in this process. Last, we found that downregulation of miR-155 leads to a reduced fibrosis in sever burn rat. Taken together, these results indicate that down-regulation of miR-155 leads to a reduced fibroblasts proliferation and collagen synthesis through attenuating macrophages TGF-β1 and IL-1β secretion by targeting SHIP1 via PI3K/Akt pathway, suggesting its potential therapeutic effects on the treatment of skin fibrosis.
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Affiliation(s)
- Longlong Yang
- Department of Burn & Plastic Surgery, Burns Institute, the First Affiliated Hospital to PLA General Hospital, 51 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Lingying Liu
- Department of Burn & Plastic Surgery, Burns Institute, the First Affiliated Hospital to PLA General Hospital, 51 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Huinan Ying
- Department of Burn & Plastic Surgery, Burns Institute, the First Affiliated Hospital to PLA General Hospital, 51 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Yonghui Yu
- Department of Burn & Plastic Surgery, Burns Institute, the First Affiliated Hospital to PLA General Hospital, 51 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Donghai Zhang
- Department of Burn & Plastic Surgery, Burns Institute, the First Affiliated Hospital to PLA General Hospital, 51 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Huping Deng
- Department of Burn & Plastic Surgery, Burns Institute, the First Affiliated Hospital to PLA General Hospital, 51 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Haijun Zhang
- Department of Burn & Plastic Surgery, Burns Institute, the First Affiliated Hospital to PLA General Hospital, 51 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Jiake Chai
- Department of Burn & Plastic Surgery, Burns Institute, the First Affiliated Hospital to PLA General Hospital, 51 Fucheng Road, Haidian District, Beijing, 100048, China.
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38
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Yu G, Tzouvelekis A, Wang R, Herazo-Maya JD, Ibarra GH, Srivastava A, de Castro JPW, DeIuliis G, Ahangari F, Woolard T, Aurelien N, e Drigo RA, Gan Y, Graham M, Liu X, Homer RJ, Scanlan TS, Mannam P, Lee PJ, Herzog EL, Bianco AC, Kaminski N. Thyroid hormone inhibits lung fibrosis in mice by improving epithelial mitochondrial function. Nat Med 2018; 24:39-49. [PMID: 29200204 PMCID: PMC5760280 DOI: 10.1038/nm.4447] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 10/23/2017] [Indexed: 12/15/2022]
Abstract
Thyroid hormone (TH) is critical for the maintenance of cellular homeostasis during stress responses, but its role in lung fibrosis is unknown. Here we found that the activity and expression of iodothyronine deiodinase 2 (DIO2), an enzyme that activates TH, were higher in lungs from patients with idiopathic pulmonary fibrosis than in control individuals and were correlated with disease severity. We also found that Dio2-knockout mice exhibited enhanced bleomycin-induced lung fibrosis. Aerosolized TH delivery increased survival and resolved fibrosis in two models of pulmonary fibrosis in mice (intratracheal bleomycin and inducible TGF-β1). Sobetirome, a TH mimetic, also blunted bleomycin-induced lung fibrosis. After bleomycin-induced injury, TH promoted mitochondrial biogenesis, improved mitochondrial bioenergetics and attenuated mitochondria-regulated apoptosis in alveolar epithelial cells both in vivo and in vitro. TH did not blunt fibrosis in Ppargc1a- or Pink1-knockout mice, suggesting dependence on these pathways. We conclude that the antifibrotic properties of TH are associated with protection of alveolar epithelial cells and restoration of mitochondrial function and that TH may thus represent a potential therapy for pulmonary fibrosis.
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Affiliation(s)
- Guoying Yu
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Argyris Tzouvelekis
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
- Division of Immunology, Biomedical Sciences Research Center
“Alexander Fleming”, Athens, Greece
| | - Rong Wang
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Jose D. Herazo-Maya
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Gabriel H. Ibarra
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Anup Srivastava
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Joao Pedro Werneck de Castro
- Division of Endocrinology/Metabolism, Rush University Medical
Center, Chicago IL
- Biophysics Institute, Federal University of Rio de Janeiro, RJ,
Brazil
| | - Giuseppe DeIuliis
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Farida Ahangari
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Tony Woolard
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Nachelle Aurelien
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Rafael Arrojo e Drigo
- The Salk Institute for Biological Studies, Molecular and Cell
biology laboratory, La Jolla, CA
| | - Ye Gan
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Morven Graham
- CCMI Electron Microscopy Core Facility, Yale University School of
Medicine, New Haven, CT
| | - Xinran Liu
- CCMI Electron Microscopy Core Facility, Yale University School of
Medicine, New Haven, CT
| | - Robert J. Homer
- Department of Pathology, Yale University School of Medicine, New
Haven, C
- Pathology and Laboratory Medicine Service, VA CT HealthCare System,
West Haven, CT
| | - Thomas S. Scanlan
- Department of Physiology and Pharmacology, Oregon Health and Science
University, Portland, Oregon, USA
| | - Praveen Mannam
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Patty J. Lee
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Erica L. Herzog
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Antonio C. Bianco
- Division of Endocrinology/Metabolism, Rush University Medical
Center, Chicago IL
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Department
of Internal Medicine, Yale School of Medicine, New Haven, CT
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39
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Balderas-Martínez YI, Rinaldi F, Contreras G, Solano-Lira H, Sánchez-Pérez M, Collado-Vides J, Selman M, Pardo A. Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3748307. [PMID: 28605770 PMCID: PMC5467562 DOI: 10.1093/database/bax030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 03/25/2017] [Indexed: 12/24/2022]
Abstract
MicroRNAs (miRNAs) are small and non-coding RNA molecules that inhibit gene expression posttranscriptionally. They play important roles in several biological processes, and in recent years there has been an interest in studying how they are related to the pathogenesis of diseases. Although there are already some databases that contain information for miRNAs and their relation with illnesses, their curation represents a significant challenge due to the amount of information that is being generated every day. In particular, respiratory diseases are poorly documented in databases, despite the fact that they are of increasing concern regarding morbidity, mortality and economic impacts. In this work, we present the results that we obtained in the BioCreative Interactive Track (IAT), using a semiautomatic approach for improving biocuration of miRNAs related to diseases. Our procedures will be useful to complement databases that contain this type of information. We adapted the OntoGene text mining pipeline and the ODIN curation system in a full-text corpus of scientific publications concerning one specific respiratory disease: idiopathic pulmonary fibrosis, the most common and aggressive of the idiopathic interstitial cases of pneumonia. We curated 823 miRNA text snippets and found a total of 246 miRNAs related to this disease based on our semiautomatic approach with the system OntoGene/ODIN. The biocuration throughput improved by a factor of 12 compared with traditional manual biocuration. A significant advantage of our semiautomatic pipeline is that it can be applied to obtain the miRNAs of all the respiratory diseases and offers the possibility to be used for other illnesses. Database URL http://odin.ccg.unam.mx/ODIN/bc2015-miRNA/.
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Affiliation(s)
- Yalbi Itzel Balderas-Martínez
- Facultad de Ciencias, Departamento Biología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n, Coyoacán, CP 04510, Ciudad de México, CDMX, México.,CONACYT-INER Ismael Cosío Villegas, Departamento Investigación, Calzada de Tlalpan 4502 Sección XVI, Tlalpan, CP Ciudad de México, CDMX, México
| | - Fabio Rinaldi
- Swiss Institute of Bioinformatics and Institute of Computational Linguistics, University of Zurich, Andreasstrasse 15, CH-8050 Zurich, Switzerland.,Center for Genomics Sciences, Computational Genomics Program, Universidad Nacional Autónoma de México, Av. Universidad s/n, Chamilpa, CP 62210, Cuernavaca, Morelos, México
| | - Gabriela Contreras
- Center for Genomics Sciences, Computational Genomics Program, Universidad Nacional Autónoma de México, Av. Universidad s/n, Chamilpa, CP 62210, Cuernavaca, Morelos, México
| | - Hilda Solano-Lira
- Center for Genomics Sciences, Computational Genomics Program, Universidad Nacional Autónoma de México, Av. Universidad s/n, Chamilpa, CP 62210, Cuernavaca, Morelos, México
| | - Mishael Sánchez-Pérez
- Center for Genomics Sciences, Computational Genomics Program, Universidad Nacional Autónoma de México, Av. Universidad s/n, Chamilpa, CP 62210, Cuernavaca, Morelos, México
| | - Julio Collado-Vides
- Center for Genomics Sciences, Computational Genomics Program, Universidad Nacional Autónoma de México, Av. Universidad s/n, Chamilpa, CP 62210, Cuernavaca, Morelos, México
| | - Moisés Selman
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Dirección de Investigación Calzada de Tlalpan 4502 Sección XVI, Tlalpan, CP Ciudad de México, CDMX, México
| | - Annie Pardo
- Facultad de Ciencias, Departamento Biología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n, Coyoacán, CP 04510, Ciudad de México, CDMX, México
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40
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Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive lung disease characterized by progressive lung scarring and the histological picture of usual interstitial pneumonia (UIP). It is associated with increasing cough and dyspnoea and impaired quality of life. IPF affects ∼3 million people worldwide, with incidence increasing dramatically with age. The diagnostic approach includes the exclusion of other interstitial lung diseases or overlapping conditions and depends on the identification of the UIP pattern, usually with high-resolution CT; lung biopsy might be required in some patients. The UIP pattern is predominantly bilateral, peripheral and with a basal distribution of reticular changes associated with traction bronchiectasis and clusters of subpleural cystic airspaces. The biological processes underlying IPF are thought to reflect an aberrant reparative response to repetitive alveolar epithelial injury in a genetically susceptible ageing individual, although many questions remain on how to define susceptibility. Substantial progress has been made in the understanding of the clinical management of IPF, with the availability of two pharmacotherapeutic agents, pirfenidone and nintedanib, that decrease physiological progression and likely improve progression-free survival. Current efforts are directed at identifying IPF early, potentially relying on combinations of biomarkers that include circulating factors, demographics and imaging data.
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Ascher K, Elliot SJ, Rubio GA, Glassberg MK. Lung Diseases of the Elderly: Cellular Mechanisms. Clin Geriatr Med 2017; 33:473-490. [PMID: 28991645 DOI: 10.1016/j.cger.2017.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Natural lung aging is characterized by molecular and cellular changes in multiple lung cell populations. These changes include shorter telomeres, increased expression of cellular senescence markers, increased DNA damage, oxidative stress, apoptosis, and stem cell exhaustion. Aging, combined with the loss of protective repair processes, correlates with the development and incidence of chronic respiratory diseases, including idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease. Ultimately, it is the interplay of age-related changes in biology and the subsequent responses to environmental exposures that largely define the physiology and clinical course of the aging lung.
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Affiliation(s)
- Kori Ascher
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Miami Leonard M. Miller School of Medicine, 1600 Northwest 10th Avenue RMSB 7056 (D-60), Miami, FL 33136, USA
| | - Sharon J Elliot
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
| | - Gustavo A Rubio
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
| | - Marilyn K Glassberg
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Miami Leonard M. Miller School of Medicine, 1600 Northwest 10th Avenue RMSB 7056 (D-60), Miami, FL 33136, USA; DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA; Division of Pediatric Pulmonology, Department of Pediatrics, University of Miami Leonard M. Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA.
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42
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Cui H, Banerjee S, Xie N, Ge J, Liu RM, Matalon S, Thannickal VJ, Liu G. MicroRNA-27a-3p Is a Negative Regulator of Lung Fibrosis by Targeting Myofibroblast Differentiation. Am J Respir Cell Mol Biol 2017; 54:843-52. [PMID: 26600197 DOI: 10.1165/rcmb.2015-0205oc] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Although microRNAs (miRs) have been well recognized to play an important role in the pathogenesis of organ fibrosis, there is a lack of evidence as to whether miRs directly regulate the differentiation of myofibroblasts, the putative effector cells during pathological fibrogenesis. In this study, we found that levels of miR-27a-3p were up-regulated in transforming growth factor-β1-treated human lung fibroblasts in a Smad2/3-dependent manner and in fibroblasts isolated from lungs of mice with experimental pulmonary fibrosis. However, both basal and transforming growth factor-β1-induced expression of miR-27a-3p were reduced in lung fibroblasts from patients with idiopathic pulmonary fibrosis compared with that from normal control subjects. Overexpression of miR-27a-3p inhibited, whereas knockdown of miR-27a-3p enhanced, the differentiation of lung fibroblasts into myofibroblasts. We found that miR-27a-3p directly targeted the phenotypic marker of myofibroblasts, α-smooth muscle actin, and two key Smad transcription factors, Smad2 and Smad4. More importantly, we found that therapeutic expression of miR-27a-3p in mouse lungs through lentiviral delivery diminished bleomycin-induced lung fibrosis. In conclusion, our data suggest that miR-27a-3p functions via a negative-feedback mechanism in inhibiting lung fibrosis. This study also indicates that targeting miR-27a-3p is a novel therapeutic approach to treat fibrotic organ disorders, including lung fibrosis.
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Affiliation(s)
- Huachun Cui
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Sami Banerjee
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Na Xie
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Jing Ge
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Rui-Ming Liu
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Sadis Matalon
- 2 Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Victor J Thannickal
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Gang Liu
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
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43
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Cui H, Ge J, Xie N, Banerjee S, Zhou Y, Antony VB, Thannickal VJ, Liu G. miR-34a Inhibits Lung Fibrosis by Inducing Lung Fibroblast Senescence. Am J Respir Cell Mol Biol 2017; 56:168-178. [PMID: 27635790 DOI: 10.1165/rcmb.2016-0163oc] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Cellular senescence has been implicated in diverse pathologies. However, there is conflicting evidence regarding the role of this process in tissue fibrosis. Although dysregulation of microRNAs is a key mechanism in the pathogenesis of lung fibrosis, it is unclear whether microRNAs function by regulating cellular senescence in the disease. In this study, we found that miR-34a demonstrated greater expression in the lungs of patients with idiopathic pulmonary fibrosis and in mice with experimental pulmonary fibrosis, with its primary localization in lung fibroblasts. More importantly, miR-34a was up-regulated significantly in both human and mouse lung myofibroblasts. We found that mice with miR-34a ablation developed more severe pulmonary fibrosis than did wild-type animals after fibrotic lung injury. Mechanistically, we found that miR-34a induced a senescent phenotype in lung fibroblasts because this microRNA increased senescence-associated β-galactosidase activity, enhanced expression of senescence markers, and decreased cell proliferative capacities. Consistently, we found that primary lung fibroblasts from fibrotic lungs of miR-34a-deficient mice had a diminished senescent phenotype and enhanced resistance to apoptosis as compared with those from wild-type animals. We also identified multiple miR-34a targets that likely mediated its activities in inducing senescence in lung fibroblasts. In conclusion, our data suggest that miR-34a functions through a negative feedback mechanism to restrain fibrotic response in the lungs by promoting senescence of pulmonary fibroblasts.
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Affiliation(s)
- Huachun Cui
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Jing Ge
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and.,2 Department of Geriatrics and Institute of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Na Xie
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Sami Banerjee
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Yong Zhou
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Veena B Antony
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Victor J Thannickal
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Gang Liu
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama; and
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44
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Huleihel L, Scarritt ME, Badylak SF. The Influence of Extracellular RNA on Cell Behavior in Health, Disease and Regeneration. CURRENT PATHOBIOLOGY REPORTS 2017; 5:13-22. [PMID: 28944104 PMCID: PMC5604481 DOI: 10.1007/s40139-017-0121-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW An overview of the role of extracellular RNAs (exRNA) in the regulation of homeostasis, disease progression, and regeneration is provided herein. Several exRNAs have been identified as potential biomarkers for disease and disease progression. In addition, the potential of exRNAs as a therapeutic modality is discussed. RECENT FINDINGS Fibrotic diseases of the lung, liver, and heart, among other organs share a number of identical exRNAs which play key roles in disease pathogenesis. Though regeneration is limited to only a few tissues in humans, small RNAs (e.g. microRNA) have been shown to be involved in the regenerative process of tissues such as liver and bone. The regulation of healing versus disease appears to be balanced by small RNAs. Because small RNAs are critical to health, they are being investigated as drug targets in multiple ongoing clinical trials. Preclinical studies suggest that promoting or blocking specific small RNAs can provide a novel therapeutic approach. SUMMARY exRNA can be utilized for both detection and treatment of disease. Natural and synthetic RNA carriers are being investigated as delivery methods for small RNA molecules. Current and future investigations are likely to lead to expanded applications for exRNAs.
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Affiliation(s)
- Luai Huleihel
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Michelle E. Scarritt
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Stephen F. Badylak
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15219, USA
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45
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Ameis D, Khoshgoo N, Iwasiow BM, Snarr P, Keijzer R. MicroRNAs in Lung Development and Disease. Paediatr Respir Rev 2017; 22:38-43. [PMID: 28237418 DOI: 10.1016/j.prrv.2016.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 12/05/2016] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) are small (∼22 nucleotides), non-coding RNA molecules that regulate gene expression post-transcriptionally by inhibiting target mRNAs. Research into the roles of miRNAs in lung development and disease is at the early stages. In this review, we discuss the role of miRNAs in pediatric respiratory disease, including cystic fibrosis, asthma, and bronchopulmonary dysplasia.
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Affiliation(s)
- Dustin Ameis
- Departments of Surgery, Pediatrics and Child Health and Physiology and Pathophysiology, University of Manitoba, and The Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Naghmeh Khoshgoo
- Departments of Surgery, Pediatrics and Child Health and Physiology and Pathophysiology, University of Manitoba, and The Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Barbara M Iwasiow
- Departments of Surgery, Pediatrics and Child Health and Physiology and Pathophysiology, University of Manitoba, and The Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Phillip Snarr
- Departments of Surgery, Pediatrics and Child Health and Physiology and Pathophysiology, University of Manitoba, and The Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Richard Keijzer
- Departments of Surgery, Pediatrics and Child Health and Physiology and Pathophysiology, University of Manitoba, and The Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.
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46
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Pociask DA, Robinson KM, Chen K, McHugh KJ, Clay ME, Huang GT, Benos PV, Janssen-Heininger YMW, Kolls JK, Anathy V, Alcorn JF. Epigenetic and Transcriptomic Regulation of Lung Repair during Recovery from Influenza Infection. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:851-863. [PMID: 28193481 DOI: 10.1016/j.ajpath.2016.12.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/07/2016] [Accepted: 12/21/2016] [Indexed: 11/28/2022]
Abstract
Seasonal and pandemic influenza is a cause of morbidity and mortality worldwide. Most people infected with influenza virus display mild-to-moderate disease phenotypes and recover within a few weeks. Influenza is known to cause persistent alveolitis in animal models; however, little is known about the molecular pathways involved in this phenotype. We challenged C57BL/6 mice with influenza A/PR/8/34 and examined lung pathologic processes and inflammation, as well as transcriptomic and epigenetic changes at 21 to 60 days after infection. Influenza induced persistent parenchymal lung inflammation, alveolar epithelial metaplasia, and epithelial endoplasmic reticulum stress that were evident after the clearance of virus and resolution of morbidity. Influenza infection induced robust changes in the lung transcriptome, including a significant impact on inflammatory and extracellular matrix protein expression. Despite the robust changes in lung gene expression, preceding influenza (21 days) did not exacerbate secondary Staphylococcus aureus infection. Finally, we examined the impact of influenza on miRNA expression in the lung and found an increase in miR-155. miR-155 knockout mice recovered from influenza infection faster than controls and had decreased lung inflammation and endoplasmic reticulum stress. These data illuminate the dynamic molecular changes in the lung in the weeks after influenza infection and characterize the repair process, identifying a novel role for miR-155.
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Affiliation(s)
- Derek A Pociask
- Department of Pulmonary Critical Care and Environmental Medicine, Tulane University School of Medicine, New Orleans, Louisiana; Richard K. Mellon Foundation Institute, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania
| | - Keven M Robinson
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Kong Chen
- Richard K. Mellon Foundation Institute, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania
| | - Kevin J McHugh
- Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania
| | - Michelle E Clay
- Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania
| | - Grace T Huang
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania; PhD Program in Computational Biology, Carnegie Mellon University and University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Jay K Kolls
- Richard K. Mellon Foundation Institute, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania
| | - Vikas Anathy
- Department of Pathology, University of Vermont, Burlington, Vermont
| | - John F Alcorn
- Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania.
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47
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Rosenbloom J, Macarak E, Piera-Velazquez S, Jimenez SA. Human Fibrotic Diseases: Current Challenges in Fibrosis Research. Methods Mol Biol 2017; 1627:1-23. [PMID: 28836191 DOI: 10.1007/978-1-4939-7113-8_1] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Human fibrotic diseases constitute a major health problem worldwide owing to the large number of affected individuals, the incomplete knowledge of the fibrotic process pathogenesis, the marked heterogeneity in their etiology and clinical manifestations, the absence of appropriate and fully validated biomarkers, and, most importantly, the current void of effective disease-modifying therapeutic agents. The fibrotic disorders encompass a wide spectrum of clinical entities including systemic fibrotic diseases such as systemic sclerosis (SSc), sclerodermatous graft vs. host disease, and nephrogenic systemic fibrosis, as well as numerous organ-specific disorders including radiation-induced fibrosis and cardiac, pulmonary, liver, and kidney fibrosis. Although their causative mechanisms are quite diverse and in several instances have remained elusive, these diseases share the common feature of an uncontrolled and progressive accumulation of fibrotic tissue in affected organs causing their dysfunction and ultimate failure. Despite the remarkable heterogeneity in the etiologic mechanisms responsible for the development of fibrotic diseases and in their clinical manifestations, numerous studies have identified activated myofibroblasts as the common cellular element ultimately responsible for the replacement of normal tissues with nonfunctional fibrotic tissue. Critical signaling cascades, initiated primarily by transforming growth factor-β (TGF-β), but also involving numerous cytokines and signaling molecules which stimulate profibrotic reactions in myofibroblasts, offer potential therapeutic targets. Here, we briefly review the current knowledge of the molecular mechanisms involved in the development of tissue fibrosis and point out some of the most important challenges to research in the fibrotic diseases and to the development of effective therapeutic approaches for this often fatal group of disorders. Efforts to further clarify the complex pathogenetic mechanisms of the fibrotic process should be encouraged to attain the elusive goal of developing effective therapies for these serious, untreatable, and often fatal disorders.
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Affiliation(s)
- Joel Rosenbloom
- The Joan and Joel Rosenbloom Center for Fibrotic Diseases and The Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Edward Macarak
- The Joan and Joel Rosenbloom Center for Fibrotic Diseases and The Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sonsoles Piera-Velazquez
- The Joan and Joel Rosenbloom Center for Fibrotic Diseases and The Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sergio A Jimenez
- The Joan and Joel Rosenbloom Center for Fibrotic Diseases and The Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA.
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48
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Plantier L, Renaud H, Respaud R, Marchand-Adam S, Crestani B. Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways. Int J Mol Sci 2016; 17:ijms17122091. [PMID: 27983601 PMCID: PMC5187891 DOI: 10.3390/ijms17122091] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 12/21/2022] Open
Abstract
Heritable profibrotic differentiation of lung fibroblasts is a key mechanism of idiopathic pulmonary fibrosis (IPF). Its mechanisms are yet to be fully understood. In this study, individual data from four independent microarray studies comparing the transcriptome of fibroblasts cultured in vitro from normal (total n = 20) and IPF (total n = 20) human lung were compiled for meta-analysis following normalization to z-scores. One hundred and thirteen transcripts were upregulated and 115 were downregulated in IPF fibroblasts using the Significance Analysis of Microrrays algorithm with a false discovery rate of 5%. Downregulated genes were highly enriched for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classes related to inflammation and immunity such as Defense response to virus, Influenza A, tumor necrosis factor (TNF) mediated signaling pathway, interferon-inducible absent in melanoma2 (AIM2) inflammasome as well as Apoptosis. Although upregulated genes were not enriched for any functional class, select factors known to play key roles in lung fibrogenesis were overexpressed in IPF fibroblasts, most notably connective tissue growth factor (CTGF) and serum response factor (SRF), supporting their role as drivers of IPF. The full data table is available as a supplement.
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Affiliation(s)
- Laurent Plantier
- Centre d'Étude des Pathologies Respiratoires-CEPR, Institut National de la Santé et de la Recherche Médicale-INSERM, Unité Mixte de Recherche-UMR1100, Labex Mabimprove, 37000 Tours, France.
- Université François Rabelais, 37000 Tours, France.
- Centre Hospitalier Régional Universitaire-CHRU de Tours, Hôpital Bretonneau, Service de Pneumologie et Explorations Fonctionnelles Respiratoires, 37000 Tours, France.
| | - Hélène Renaud
- Institut National de la Santé et de la Recherche Médicale-INSERM, Unité Mixte de Recherche-UMR1152, Labex Inflamex, 75018 Paris, France.
| | - Renaud Respaud
- Centre d'Étude des Pathologies Respiratoires-CEPR, Institut National de la Santé et de la Recherche Médicale-INSERM, Unité Mixte de Recherche-UMR1100, Labex Mabimprove, 37000 Tours, France.
- Université François Rabelais, 37000 Tours, France.
- Centre Hospitalier Régional Universitaire-CHRU de Tours, Hôpital Trousseau, Service de Pharmacie, 37170 Chambray-les-Tours, France.
| | - Sylvain Marchand-Adam
- Centre d'Étude des Pathologies Respiratoires-CEPR, Institut National de la Santé et de la Recherche Médicale-INSERM, Unité Mixte de Recherche-UMR1100, Labex Mabimprove, 37000 Tours, France.
- Université François Rabelais, 37000 Tours, France.
- Centre Hospitalier Régional Universitaire-CHRU de Tours, Hôpital Bretonneau, Service de Pneumologie et Explorations Fonctionnelles Respiratoires, 37000 Tours, France.
| | - Bruno Crestani
- Institut National de la Santé et de la Recherche Médicale-INSERM, Unité Mixte de Recherche-UMR1152, Labex Inflamex, 75018 Paris, France.
- Université Paris Diderot, PRES Sorbonne Paris Cité, 75018 Paris, France.
- AP-HP, Hôpital Bichat, Service de Pneumologie A, DHU FIRE, 75018 Paris, France.
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49
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Zou XZ, Liu T, Gong ZC, Hu CP, Zhang Z. MicroRNAs-mediated epithelial-mesenchymal transition in fibrotic diseases. Eur J Pharmacol 2016; 796:190-206. [PMID: 27916556 DOI: 10.1016/j.ejphar.2016.12.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/24/2016] [Accepted: 12/01/2016] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs), a large family of small and highly conserved non-coding RNAs, regulate gene expression through translational repression or mRNA degradation. Aberrant expression of miRNAs underlies a spectrum of diseases including organ fibrosis. Recent evidence suggests that miRNAs contribute to organ fibrosis through mediating epithelial-mesenchymal transition (EMT). Alleviation of EMT has been proposed as a promising strategy against fibrotic diseases given the key role of EMT in fibrosis. miRNAs impact the expression of specific ligands, receptors, and signaling pathways, thus modulating EMT and consequently influencing fibrosis. This review summarizes the current knowledge concerning how miRNAs regulate EMT and highlights the specific roles that miRNAs-regulated EMT plays in fibrotic diseases as diverse as pulmonary fibrosis, hepatic fibrosis, renal fibrosis and cardiac fibrosis. It is desirable that a more comprehensive understanding of the functions of miRNAs-regulated EMT will facilitate the development of novel diagnostic and therapeutic strategies for various debilitating organ fibrosis.
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Affiliation(s)
- Xiao-Zhou Zou
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, China
| | - Ting Liu
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, China
| | - Zhi-Cheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Chang-Ping Hu
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, China; Hunan Provincial Key Laboratory of Cardiovascular Research, Central South University, Changsha, Hunan 410078, China.
| | - Zheng Zhang
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410078, China; Hunan Provincial Key Laboratory of Cardiovascular Research, Central South University, Changsha, Hunan 410078, China.
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50
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Selman M, López-Otín C, Pardo A. Age-driven developmental drift in the pathogenesis of idiopathic pulmonary fibrosis. Eur Respir J 2016; 48:538-52. [DOI: 10.1183/13993003.00398-2016] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/13/2016] [Indexed: 12/21/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and usually lethal disease of unknown aetiology. A growing body of evidence supports that IPF represents an epithelial-driven process characterised by aberrant epithelial cell behaviour, fibroblast/myofibroblast activation and excessive accumulation of extracellular matrix with the subsequent destruction of the lung architecture. The mechanisms involved in the abnormal hyper-activation of the epithelium are unclear, but we propose that recapitulation of pathways and processes critical to embryological development associated with a tissue specific age-related stochastic epigenetic drift may be implicated. These pathways may also contribute to the distinctive behaviour of IPF fibroblasts. Genomic and epigenomic studies have revealed that wingless/Int, sonic hedgehog and other developmental signalling pathways are reactivated and deregulated in IPF. Moreover, some of these pathways cross-talk with transforming growth factor-β activating a profibrotic feedback loop. The expression pattern of microRNAs is also dysregulated in IPF and exhibits a similar expression profile to embryonic lungs. In addition, senescence, a process usually associated with ageing, which occurs early in alveolar epithelial cells of IPF lungs, likely represents a conserved programmed developmental mechanism. Here, we review the major developmental pathways that get twisted in IPF, and discuss the connection with ageing and potential therapeutic approaches.
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