1
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Soni DK, Biswas R. Role of Non-Coding RNAs in Post-Transcriptional Regulation of Lung Diseases. Front Genet 2021; 12:767348. [PMID: 34819948 PMCID: PMC8606426 DOI: 10.3389/fgene.2021.767348] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/25/2021] [Indexed: 12/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs), notably microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), have recently gained increasing consideration because of their versatile role as key regulators of gene expression. They adopt diverse mechanisms to regulate transcription and translation, and thereby, the function of the protein, which is associated with several major biological processes. For example, proliferation, differentiation, apoptosis, and metabolic pathways demand fine-tuning for the precise development of a specific tissue or organ. The deregulation of ncRNA expression is concomitant with multiple diseases, including lung diseases. This review highlights recent advances in the post-transcriptional regulation of miRNAs and lncRNAs in lung diseases such as asthma, chronic obstructive pulmonary disease, cystic fibrosis, and idiopathic pulmonary fibrosis. Further, we also discuss the emerging role of ncRNAs as biomarkers as well as therapeutic targets for lung diseases. However, more investigations are required to explore miRNAs and lncRNAs interaction, and their function in the regulation of mRNA expression. Understanding these mechanisms might lead to early diagnosis and the development of novel therapeutics for lung diseases.
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Affiliation(s)
- Dharmendra Kumar Soni
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Roopa Biswas
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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2
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SFPQ rescues F508del-CFTR expression and function in cystic fibrosis bronchial epithelial cells. Sci Rep 2021; 11:16645. [PMID: 34404863 PMCID: PMC8371023 DOI: 10.1038/s41598-021-96141-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/05/2021] [Indexed: 01/19/2023] Open
Abstract
Cystic fibrosis (CF) occurs as a result of mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which lead to misfolding, trafficking defects, and impaired function of the CFTR protein. Splicing factor proline/glutamine-rich (SFPQ) is a multifunctional nuclear RNA-binding protein (RBP) implicated in the regulation of gene expression pathways and intracellular trafficking. Here, we investigated the role of SFPQ in the regulation of the expression and function of F508del-CFTR in CF lung epithelial cells. We find that the expression of SFPQ is reduced in F508del-CFTR CF epithelial cells compared to WT-CFTR control cells. Interestingly, the overexpression of SFPQ in CF cells increases the expression as well as rescues the function of F508del-CFTR. Further, comprehensive transcriptome analyses indicate that SFPQ plays a key role in activating the mutant F508del-CFTR by modulating several cellular signaling pathways. This is the first report on the role of SFPQ in the regulation of expression and function of F508del-CFTR in CF lung disease. Our findings provide new insights into SFPQ-mediated molecular mechanisms and point to possible novel epigenetic therapeutic targets for CF and related pulmonary diseases.
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3
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Hodos RA, Strub MD, Ramachandran S, Meleshkevitch EA, Boudko DY, Bridges RJ, Dudley JT, McCray PB. Integrative chemogenomic analysis identifies small molecules that partially rescue ΔF508-CFTR for cystic fibrosis. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2021; 10:500-510. [PMID: 33934548 PMCID: PMC8129714 DOI: 10.1002/psp4.12626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
Abstract
Rare diseases affect 10% of the first‐world population, yet over 95% lack even a single pharmaceutical treatment. In the present age of information, we need ways to leverage our vast data and knowledge to streamline therapeutic development and lessen this gap. Here, we develop and implement an innovative informatic approach to identify therapeutic molecules, using the Connectivity Map and LINCS L1000 databases and disease‐associated transcriptional signatures and pathways. We apply this to cystic fibrosis (CF), the most common genetic disease in people of northern European ancestry leading to chronic lung disease and reduced lifespan. We selected and tested 120 small molecules in a CF cell line, finding 8 with activity, and confirmed 3 in primary CF airway epithelia. Although chemically diverse, the transcriptional profiles of the hits suggest a common mechanism associated with the unfolded protein response and/or TNFα signaling. This study highlights the power of informatics to help identify new therapies and reveal mechanistic insights while moving beyond target‐centric drug discovery.
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Affiliation(s)
- Rachel A Hodos
- Institute for Next Generation Healthcare, Mount Sinai School of Medicine, New York, NY, USA.,Courant Institute for Mathematical Sciences, New York University, New York, NY, USA
| | - Matthew D Strub
- Department of Pediatrics, University of Iowa, Carver College of Medicine, Iowa City, IA, USA.,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
| | | | - Ella A Meleshkevitch
- Department of Physiology and Biophysics, Rosalind Franklin University, North Chicago, IL, USA
| | - Dmitri Y Boudko
- Department of Physiology and Biophysics, Rosalind Franklin University, North Chicago, IL, USA
| | - Robert J Bridges
- Department of Physiology and Biophysics, Rosalind Franklin University, North Chicago, IL, USA
| | - Joel T Dudley
- Institute for Next Generation Healthcare, Mount Sinai School of Medicine, New York, NY, USA
| | - Paul B McCray
- Department of Pediatrics, University of Iowa, Carver College of Medicine, Iowa City, IA, USA.,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
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4
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Hodos RA, Strub MD, Ramachandran S, Li L, McCray PB, Dudley JT. Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and ΔF508-CFTR rescue. Sci Rep 2020; 10:20553. [PMID: 33239626 PMCID: PMC7689470 DOI: 10.1038/s41598-020-76347-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Cystic fibrosis (CF), caused by mutations to CFTR, leads to severe and progressive lung disease. The most common mutant, ΔF508-CFTR, undergoes proteasomal degradation, extinguishing its anion channel function. Numerous in vitro interventions have been identified to partially rescue ΔF508-CFTR function yet remain poorly understood. Improved understanding of both the altered state of CF cells and the mechanisms of existing rescue strategies could reveal novel therapeutic strategies. Toward this aim, we measured transcriptional profiles of established temperature, genetic, and chemical interventions that rescue ΔF508-CFTR and also re-analyzed public datasets characterizing transcription in human CF vs. non-CF samples from airway and whole blood. Meta-analysis yielded a core disease signature and two core rescue signatures. To interpret these through the lens of prior knowledge, we compiled a "CFTR Gene Set Library" from literature. The core disease signature revealed remarkably strong connections to genes with established effects on CFTR trafficking and function and suggested novel roles of EGR1 and SGK1 in the disease state. Our data also revealed an unexpected mechanistic link between several genetic rescue interventions and the unfolded protein response. Finally, we found that C18, an analog of the CFTR corrector compound Lumacaftor, induces almost no transcriptional perturbation despite its rescue activity.
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Affiliation(s)
- Rachel A Hodos
- Mount Sinai School of Medicine, Institute for Next Generation Healthcare, New York, NY, USA
- Courant Institute for Mathematical Sciences, New York University, New York, NY, USA
- BenevolentAI, Brooklyn, NY, USA
| | - Matthew D Strub
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
| | - Shyam Ramachandran
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Editas Medicine, Cambridge, MA, USA
| | - Li Li
- Mount Sinai School of Medicine, Institute for Next Generation Healthcare, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Paul B McCray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA.
| | - Joel T Dudley
- Mount Sinai School of Medicine, Institute for Next Generation Healthcare, New York, NY, USA.
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5
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Fabbri E, Tamanini A, Jakova T, Gasparello J, Manicardi A, Corradini R, Finotti A, Borgatti M, Lampronti I, Munari S, Dechecchi MC, Cabrini G, Gambari R. Treatment of human airway epithelial Calu-3 cells with a peptide-nucleic acid (PNA) targeting the microRNA miR-101-3p is associated with increased expression of the cystic fibrosis Transmembrane Conductance Regulator () gene. Eur J Med Chem 2020; 209:112876. [PMID: 33127171 DOI: 10.1016/j.ejmech.2020.112876] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023]
Abstract
Since the identification of microRNAs (miRNAs) involved in the regulation of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene, miRNAs known to down-regulate the expression of the CFTR and associated proteins have been investigated as potential therapeutic targets. Here we show that miR-101-3p, targeting the 3'-UTR sequence of the CFTR mRNA, can be selectively inhibited by a peptide nucleic acid (PNA) carrying a full complementary sequence. With respect to clinical relevance of microRNA targeting, it is expected that reduction in concentration of miRNAs (the anti-miRNA approach) could be associated with increasing amounts of target mRNAs. Consistently to this hypothesis, we report that PNA-mediated inhibition of miR-101-3p was accompanied by CFTR up-regulation. Next Generation Sequencing (NGS) was performed in order to verify the effects of the anti-miR-101-3p PNA on the Calu-3 miRNome. Upon inhibition of miR-101-3p we observed a fold change (FC) expression <2 of the majority of miRNAs (403/479, 84.13%), whereas we identified a list of dysregulated miRNAs, suggesting that specific miRNA inhibition (in our case miR-101-3p) might be accompanied by alteration of expression of other miRNAs, some of them known to be involved in Cystic Fibrosis (CF), such as miR-155-5p and miR-125b-5p.
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Affiliation(s)
- Enrica Fabbri
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy
| | - Anna Tamanini
- Laboratory of Molecular Pathology, Department of Pathology and Diagnostics, University Hospital of Verona, Italy
| | - Tiziana Jakova
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Section of Clinical Biochemistry, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy
| | - Alex Manicardi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Section of Clinical Biochemistry, Italy; Department of Organic and Macromolecular Chemistry, University of Ghent, Belgium
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Section of Clinical Biochemistry, Italy
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy
| | - Ilaria Lampronti
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy
| | - Silvia Munari
- Laboratory of Molecular Pathology, Department of Pathology and Diagnostics, University Hospital of Verona, Italy
| | | | - Giulio Cabrini
- Department of Neurosciences, Biomedicine and Movement, University of Verona, Verona, Italy; Research Center for Innovative Therapies of Cystic Fibrosis, University of Ferrara, Italy
| | - Roberto Gambari
- Research Center for Innovative Therapies of Cystic Fibrosis, University of Ferrara, Italy.
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6
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Anasagasti A, Lara-López A, Milla-Navarro S, Escudero-Arrarás L, Rodríguez-Hidalgo M, Zabaleta N, González Aseguinolaza G, de la Villa P, Ruiz-Ederra J. Inhibition of MicroRNA 6937 Delays Photoreceptor and Vision Loss in a Mouse Model of Retinitis Pigmentosa. Pharmaceutics 2020; 12:pharmaceutics12100913. [PMID: 32987664 PMCID: PMC7598722 DOI: 10.3390/pharmaceutics12100913] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) are a group of rare retinal conditions, including retinitis pigmentosa (RP), caused by monogenic mutations in 1 out of more than 250 genes. Despite recent advancements in gene therapy, there is still a lack of an effective treatment for this group of retinal conditions. MicroRNAs (miRNAs) are a class of highly conserved small non-coding RNAs that inhibit gene expression. Control of miRNAs-mediated protein expression has been described as a widely used mechanism for post-transcriptional regulation in many physiological and pathological processes in different organs, including the retina. Our main purpose was to test the hypothesis that modulation of a group of miRNAs can protect photoreceptor cells from death in the rd10 mouse model of retinitis pigmentosa. For this, we incorporated modulators of three miRNAs in adeno-associated viruses (AAVs), which were administered through sub-retinal injections. The results obtained indicate that inhibition of the miR-6937-5p slows down the visual deterioration of rd10 mice, reflected by an increased electroretinogram (ERG) wave response under scotopic conditions and significant preservation of the outer nuclear layer thickness. This work contributes to broadening our knowledge on the molecular mechanisms underlying retinitis pigmentosa and supports the development of novel therapeutic approaches for RP based on miRNA modulation.
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Affiliation(s)
- Ander Anasagasti
- Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, 20014 San Sebastian, Spain; (A.A.); (A.L.-L.); (L.E.-A.); (M.R.-H.)
- Viralgen Vector Core, 20009 San Sebastián, Spain
| | - Araceli Lara-López
- Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, 20014 San Sebastian, Spain; (A.A.); (A.L.-L.); (L.E.-A.); (M.R.-H.)
| | - Santiago Milla-Navarro
- Visual Neurophysiology, IRYCIS, University of Alcala, 28801 Madrid, Spain; (S.M.-N.); (P.d.l.V.)
| | - Leire Escudero-Arrarás
- Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, 20014 San Sebastian, Spain; (A.A.); (A.L.-L.); (L.E.-A.); (M.R.-H.)
| | - María Rodríguez-Hidalgo
- Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, 20014 San Sebastian, Spain; (A.A.); (A.L.-L.); (L.E.-A.); (M.R.-H.)
| | - Nerea Zabaleta
- Gene Therapy and Regulation of Gene Expression Program, CIMA, FIMA, University of Navarra, Navarra Institute for Health Research (IdisNA), 31008 Pamplona, Spain; (N.Z.); (G.G.A.)
| | - Gloria González Aseguinolaza
- Gene Therapy and Regulation of Gene Expression Program, CIMA, FIMA, University of Navarra, Navarra Institute for Health Research (IdisNA), 31008 Pamplona, Spain; (N.Z.); (G.G.A.)
| | - Pedro de la Villa
- Visual Neurophysiology, IRYCIS, University of Alcala, 28801 Madrid, Spain; (S.M.-N.); (P.d.l.V.)
- RETICS OFTARED, 28040 Madrid, Spain
| | - Javier Ruiz-Ederra
- Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, 20014 San Sebastian, Spain; (A.A.); (A.L.-L.); (L.E.-A.); (M.R.-H.)
- RETICS OFTARED, 28040 Madrid, Spain
- Correspondence: ; Tel.: +34-943-006128
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7
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Rezaei S, Mahjoubin-Tehran M, Aghaee-Bakhtiari SH, Jalili A, Movahedpour A, Khan H, Moghoofei M, Shojaei Z, R Hamblin M, Mirzaei H. Autophagy-related MicroRNAs in chronic lung diseases and lung cancer. Crit Rev Oncol Hematol 2020; 153:103063. [DOI: 10.1016/j.critrevonc.2020.103063] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 06/11/2020] [Accepted: 07/12/2020] [Indexed: 12/24/2022] Open
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8
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Anasagasti A, Ezquerra-Inchausti M, Barandika O, Muñoz-Culla M, Caffarel MM, Otaegui D, López de Munain A, Ruiz-Ederra J. Expression Profiling Analysis Reveals Key MicroRNA-mRNA Interactions in Early Retinal Degeneration in Retinitis Pigmentosa. Invest Ophthalmol Vis Sci 2019; 59:2381-2392. [PMID: 29847644 PMCID: PMC5939684 DOI: 10.1167/iovs.18-24091] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose The aim of this study was to identify differentially expressed microRNAs (miRNAs) that might play an important role in the etiology of retinal degeneration in a genetic mouse model of retinitis pigmentosa (rd10 mice) at initial stages of the disease. Methods miRNAs–mRNA interaction networks were generated for analysis of biological pathways involved in retinal degeneration. Results Of more than 1900 miRNAs analyzed, we selected 19 miRNAs on the basis of (1) a significant differential expression in rd10 retinas compared with control samples and (2) an inverse expression relationship with predicted mRNA targets involved in biological pathways relevant to retinal biology and/or degeneration. Seven of the selected miRNAs have been associated with retinal dystrophies, whereas, to our knowledge, nine have not been previously linked to any disease. Conclusions This study contributes to our understanding of the etiology and progression of retinal degeneration.
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Affiliation(s)
- Ander Anasagasti
- Neuroscience Area, Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, San Sebastian, Spain
| | - Maitane Ezquerra-Inchausti
- Neuroscience Area, Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, San Sebastian, Spain.,RETICS OFTARED, National Institute of Health Carlos III, Ministry of Economy and Competitiveness, Spain
| | - Olatz Barandika
- Neuroscience Area, Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, San Sebastian, Spain
| | - Maider Muñoz-Culla
- Neuroscience Area, Multiple Sclerosis Group, Biodonostia Health Research Institute, San Sebastian, Spain.,Spanish Network on Multiple Sclerosis (Red Española de Esclerosis Múltiple)
| | - María M Caffarel
- Oncology Area, Biodonostia Health Research Institute, San Sebastian, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - David Otaegui
- Neuroscience Area, Multiple Sclerosis Group, Biodonostia Health Research Institute, San Sebastian, Spain.,Spanish Network on Multiple Sclerosis (Red Española de Esclerosis Múltiple)
| | - Adolfo López de Munain
- Neuroscience Area, Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, San Sebastian, Spain.,Department of Neurology, Donostia University Hospital, San Sebastian, Spain.,Centro de Investigaciones Biomédicas en Red Sobre Enfermedades Neurodegenerativas, Instituto Carlos III, Ministerio de Economía y Competitividad, Spain.,Department of Neuroscience, University of the Basque Country, San Sebastian, Spain
| | - Javier Ruiz-Ederra
- Neuroscience Area, Sensorial Neurodegeneration Group, Biodonostia Health Research Institute, San Sebastian, Spain.,RETICS OFTARED, National Institute of Health Carlos III, Ministry of Economy and Competitiveness, Spain
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9
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Stolzenburg LR, Harris A. The role of microRNAs in chronic respiratory disease: recent insights. Biol Chem 2018; 399:219-234. [PMID: 29148977 DOI: 10.1515/hsz-2017-0249] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/24/2017] [Indexed: 01/16/2023]
Abstract
Chronic respiratory diseases encompass a group of diverse conditions affecting the airways, which all impair lung function over time. They include cystic fibrosis (CF), idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD) and asthma, which together affect hundreds of millions of people worldwide. MicroRNAs (miRNAs), a class of small non-coding RNAs involved in post-transcriptional gene repression, are now recognized as major regulators in the development and progression of chronic lung disease. Alterations in miRNA abundance occur in lung tissue, inflammatory cells, and freely circulating in blood and are thought to function both as drivers and modifiers of disease. Their importance in lung pathology has prompted the development of miRNA-based therapies and biomarker tools. Here, we review the current literature on miRNA expression and function in chronic respiratory disease and highlight further research that is needed to propel miRNA treatments for lung disorders towards the clinic.
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Affiliation(s)
- Lindsay R Stolzenburg
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44016, USA
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10
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Zhang Y, Sun Q, Li X, Ma X, Li Y, Jiao Z, Yang XD. Apigenin suppresses mouse peritoneal fibrosis by down-regulating miR34a expression. Biomed Pharmacother 2018; 106:373-380. [DOI: 10.1016/j.biopha.2018.06.138] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/20/2018] [Accepted: 06/25/2018] [Indexed: 12/18/2022] Open
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11
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Abstract
Non-coding RNAs (ncRNAs) are an abundant class of RNAs that include small ncRNAs, long non-coding RNAs (lncRNA) and pseudogenes. The human ncRNA atlas includes thousands of these specialised RNA molecules that are further subcategorised based on their size or function. Two of the more well-known and widely studied ncRNA species are microRNAs (miRNAs) and lncRNAs. These are regulatory RNAs and their altered expression has been implicated in the pathogenesis of a variety of human diseases. Failure to express a functional cystic fibrosis (CF) transmembrane receptor (CFTR) chloride ion channel in epithelial cells underpins CF. Secondary to the CFTR defect, it is known that other pathways can be altered and these may contribute to the pathophysiology of CF lung disease in particular. For example, quantitative alterations in expression of some ncRNAs are associated with CF. In recent years, there has been a series of published studies exploring ncRNA expression and function in CF. The majority have focussed principally on miRNAs, with just a handful of reports to date on lncRNAs. The present study reviews what is currently known about ncRNA expression and function in CF, and discusses the possibility of applying this knowledge to the clinical management of CF in the near future.
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Affiliation(s)
- Arlene M.A. Glasgow
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Chiara De Santi
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Catherine M. Greene
- Lung Biology Group, Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
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12
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Fernandez Fernandez E, De Santi C, De Rose V, Greene CM. CFTR dysfunction in cystic fibrosis and chronic obstructive pulmonary disease. Expert Rev Respir Med 2018; 12:483-492. [PMID: 29750581 DOI: 10.1080/17476348.2018.1475235] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Obstructive lung diseases such as cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are causes of high morbidity and mortality worldwide. CF is a multiorgan genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and is characterized by progressive chronic obstructive lung disease. Most cases of COPD are a result of noxious particles, mainly cigarette smoke but also other environmental pollutants. Areas covered: Although the pathogenesis and pathophysiology of CF and COPD differ, they do share key phenotypic features and because of these similarities there is great interest in exploring common mechanisms and/or factors affected by CFTR mutations and environmental insults involved in COPD. Various molecular, cellular and clinical studies have confirmed that CFTR protein dysfunction is common in both the CF and COPD airways. This review provides an update of our understanding of the role of dysfunctional CFTR in both respiratory diseases. Expert commentary: Drugs developed for people with CF to improve mutant CFTR function and enhance CFTR ion channel activity might also be beneficial in patients with COPD. A move toward personalized therapy using, for example, microRNA modulators in conjunction with CFTR potentiators or correctors, could enhance treatment of both diseases.
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Affiliation(s)
- Elena Fernandez Fernandez
- a Lung Biology Group, Department of Clinical Microbiology , RCSI Education & Research Centre, Beaumont Hospital , Dublin 9 , Ireland
| | - Chiara De Santi
- a Lung Biology Group, Department of Clinical Microbiology , RCSI Education & Research Centre, Beaumont Hospital , Dublin 9 , Ireland
| | - Virginia De Rose
- b Department of Clinical and Biological Sciences , University of Torino , Torino , Italy
| | - Catherine M Greene
- a Lung Biology Group, Department of Clinical Microbiology , RCSI Education & Research Centre, Beaumont Hospital , Dublin 9 , Ireland
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13
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Aslani S, Sobhani S, Gharibdoost F, Jamshidi A, Mahmoudi M. Epigenetics and pathogenesis of systemic sclerosis; the ins and outs. Hum Immunol 2018; 79:178-187. [PMID: 29330110 DOI: 10.1016/j.humimm.2018.01.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/25/2017] [Accepted: 01/08/2018] [Indexed: 12/22/2022]
Abstract
The pathogenesis of many diseases is influenced by environmental factors which can affect human genome and be inherited from generation to generation. Adverse environmental stimuli are recognized through the epigenetic regulatory complex, leading to gene expression alteration, which in turn culminates in disease outcomes. Three epigenetic regulatory mechanisms modulate the manifestation of a gene, namely DNA methylation, histone changes, and microRNAs. Both epigenetics and genetics have been implicated in the pathogenesis of systemic sclerosis (SSc) disease. Genetic inheritance rate of SSc is low and the concordance rate in both monozygotic (MZ) and dizygotic (DZ) twins is little, implying other possible pathways in SSc pathogenesis scenario. Here, we provide an extensive overview of the studies regarding different epigenetic events which may offer insights into the pathology of SSc. Furthermore, epigenetic-based interventions to treat SSc patients were discussed.
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Affiliation(s)
- Saeed Aslani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Soheila Sobhani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Farhad Gharibdoost
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmadreza Jamshidi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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14
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Narożna B, Langwiński W, Szczepankiewicz A. Non-Coding RNAs in Pediatric Airway Diseases. Genes (Basel) 2017; 8:genes8120348. [PMID: 29186897 PMCID: PMC5748666 DOI: 10.3390/genes8120348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/18/2017] [Accepted: 11/21/2017] [Indexed: 12/18/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are involved in the regulation of numerous biological processes and pathways and therefore have been extensively studied in human diseases. Previous reports have shown that non-coding RNAs play a crucial role in the pathogenesis and aberrant regulation of respiratory diseases. The altered expression of microRNAs (miRNAs) and long non-coding RNAs in blood and also locally in sputum or exhaled breath condensate influences lung function, immune response, and disease phenotype and may be used for the development of biomarkers specific for airway disease. In this review, we provide an overview of the recent works studying the non-coding RNAs in airway diseases, with a particular focus on chronic respiratory diseases of childhood. We have chosen the most common chronic respiratory condition—asthma—and the most severe, chronic disease of the airways—cystic fibrosis. Study of the altered expression of non-coding RNAs in these diseases may be key to better understanding their pathogenesis and improving diagnosis, while also holding promise for the development of therapeutic strategies using the regulatory potential of non-coding RNAs.
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Affiliation(s)
- Beata Narożna
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, 60-512 Poznan, Poland.
| | - Wojciech Langwiński
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, 60-512 Poznan, Poland.
| | - Aleksandra Szczepankiewicz
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, 60-512 Poznan, Poland.
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15
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Biswas R, Kumar P, Pollard HB. Regulation of mRNA turnover in cystic fibrosis lung disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27863009 DOI: 10.1002/wrna.1408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/13/2016] [Accepted: 10/16/2016] [Indexed: 01/07/2023]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease due to mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, F508del-CFTR being the most frequent mutation. The CF lung is characterized by a hyperinflammatory phenotype and is regulated by multiple factors that coordinate its pathophysiology. In CF the expression of CFTR as well as proinflammatory genes are regulated at the level of messenger RNA (mRNA) stability, which subsequently affect translation. These mechanisms are mediated by inflammatory RNA-binding proteins as well as small endogenous noncoding microRNAs, in coordination with cellular signaling pathways. These regulatory factors exhibit altered expression and function in vivo in the CF lung, and play a key role in the pathophysiology of CF lung disease. In this review, we have described the role of mRNA stability and associated regulatory mechanisms in CF lung disease. WIREs RNA 2017, 8:e1408. doi: 10.1002/wrna.1408 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Roopa Biswas
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Parameet Kumar
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Harvey B Pollard
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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16
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Kim N, Duncan GA, Hanes J, Suk JS. Barriers to inhaled gene therapy of obstructive lung diseases: A review. J Control Release 2016; 240:465-488. [PMID: 27196742 DOI: 10.1016/j.jconrel.2016.05.031] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 12/29/2022]
Abstract
Knowledge of genetic origins of obstructive lung diseases has made inhaled gene therapy an attractive alternative to the current standards of care that are limited to managing disease symptoms. Initial lung gene therapy clinical trials occurred in the early 1990s following the discovery of the genetic defect responsible for cystic fibrosis (CF), a monogenic disorder. However, despite over two decades of intensive effort, gene therapy has yet to help patients with CF or any other obstructive lung disease. The slow progress is due in part to poor understanding of the biological barriers to inhaled gene therapy. Encouragingly, clinical trials have shown that inhaled gene therapy with various viral vectors and non-viral gene vectors is well tolerated by patients, and continued research has provided valuable lessons and resources that may lead to future success of this therapeutic strategy. In this review, we first introduce representative obstructive lung diseases and examine limitations of currently available therapeutic options. We then review key components for successful execution of inhaled gene therapy, including gene delivery systems, primary physiological barriers and strategies to overcome them, and advances in preclinical disease models with which the most promising systems may be identified for human clinical trials.
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Affiliation(s)
- Namho Kim
- The Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Gregg A Duncan
- The Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Justin Hanes
- The Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Environmental and Health Sciences, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neurosurgery, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jung Soo Suk
- The Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
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17
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McKiernan PJ, Greene CM. High-throughput profiling for discovery of non-coding RNA biomarkers of lung disease. Expert Rev Mol Diagn 2015; 16:173-85. [PMID: 26581119 DOI: 10.1586/14737159.2016.1122526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In respiratory medicine there is a need for clinical biomarkers for diagnosis, prognosis and assessment of response to therapy. Noncoding RNA (ncRNA) is expressed in all human cells; two major classes--long ncRNA and microRNA--are detectable extracellularly in the circulation and other biofluids. Altered ncRNA expression is associated with lung disease; collectively this indicates that ncRNA represents a potential biomarker class. This article presents and compares existing platforms for detection and quantification of ncRNA, specifically hybridization, qRT-PCR and RNA sequencing, and outlines methods for data interpretation and normalization. Each approach has merits and shortcomings, which can affect the choice of method when embarking on a biomarker study. Biomarker properties and pre-analytical considerations for ncRNA profiling are also presented. Since a variety of profiling approaches are available, careful study and experimental design are important. Finally, challenges and goals for reliable, standardized high-throughput ncRNA profiling in biofluids as lung disease biomarkers are reviewed.
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Affiliation(s)
- Paul J McKiernan
- a Respiratory Research, Department of Medicine, The Royal College of Surgeons in Ireland, Education and Research Centre , Beaumont Hospital , Dublin , Ireland
| | - Catherine M Greene
- a Respiratory Research, Department of Medicine, The Royal College of Surgeons in Ireland, Education and Research Centre , Beaumont Hospital , Dublin , Ireland
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