1
|
Li J, Wang X. Functional roles of conserved lncRNAs and circRNAs in eukaryotes. Noncoding RNA Res 2024; 9:1271-1279. [PMID: 39036601 PMCID: PMC11260338 DOI: 10.1016/j.ncrna.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have emerged as critical regulators in essentially all biological processes across eukaryotes. They exert their functions through chromatin remodeling, transcriptional regulation, interacting with RNA-binding proteins (RBPs), serving as microRNA sponges, etc. Although non-coding RNAs are typically more species-specific than coding RNAs, a number of well-characterized lncRNA (such as XIST and NEAT1) and circRNA (such as CDR1as and ciRS-7) are evolutionarily conserved. The studies on conserved lncRNA and circRNAs across multiple species could facilitate a comprehensive understanding of their roles and mechanisms, thereby overcoming the limitations of single-species studies. In this review, we provide an overview of conserved lncRNAs and circRNAs, and summarize their conserved roles and mechanisms.
Collapse
Affiliation(s)
- Jingxin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, The RNA Institute, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, 230027, Anhui, China
| | - Xiaolin Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, The RNA Institute, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, 230027, Anhui, China
| |
Collapse
|
2
|
Kang Z, Wang C, Shao F, Deng H, Sun Y, Ren Z, Zhang W, Ding Z, Zhang J, Zang Y. The increase of long noncoding RNA Fendrr in hepatocytes contributes to liver fibrosis by promoting IL-6 production. J Biol Chem 2024; 300:107376. [PMID: 38762176 PMCID: PMC11190708 DOI: 10.1016/j.jbc.2024.107376] [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: 09/28/2023] [Revised: 04/14/2024] [Accepted: 05/07/2024] [Indexed: 05/20/2024] Open
Abstract
Liver fibrosis/cirrhosis is a pathological state caused by excessive extracellular matrix deposition. Sustained activation of hepatic stellate cells (HSC) is the predominant cause of liver fibrosis, but the detailed mechanism is far from clear. In this study, we found that long noncoding RNA Fendrr is exclusively increased in hepatocytes in the murine model of CCl4- and bile duct ligation-induced liver fibrosis, as well as in the biopsies of liver cirrhosis patients. In vivo, ectopic expression of Fendrr aggravated the severity of CCl4-induced liver fibrosis in mice. In contrast, inhibiting Fendrr blockaded the activation of HSC and ameliorated CCl4-induced liver fibrosis. Our mechanistic study showed that Fendrr binds to STAT2 and enhances its enrichment in the nucleus, which then promote the expression of interleukin 6 (IL-6), and, ultimately, activates HSC in a paracrine manner. Accordingly, disrupting the interaction between Fendrr and STAT2 by ectopic expression of a STAT2 mutant attenuated the profibrotic response inspired by Fendrr in the CCl4-induced liver fibrosis. Notably, the increase of Fendrr in patient fibrotic liver is positively correlated with the severity of fibrosis and the expression of IL-6. Meanwhile, hepatic IL-6 positively correlates with the extent of liver fibrosis and HSC activation as well, thus suggesting a causative role of Fendrr in HSC activation and liver fibrosis. In conclusion, these observations identify an important regulatory cross talk between hepatocyte Fendrr and HSC activation in the progression of liver fibrosis, which might represent a potential strategy for therapeutic intervention.
Collapse
Affiliation(s)
- Zhiqian Kang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, PR China
| | - Chenqi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, PR China
| | - Fang Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, PR China
| | - Hao Deng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, PR China
| | - Yanyan Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, PR China; State Key Laboratory for Organic Electronics and Information Displays (SKLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), School of Chemistry and Life Sciences, Nanjing University of Posts and Telecommunications, Nanjing, PR China
| | - Zhengrong Ren
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, PR China
| | - Wei Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, PR China
| | - Zhi Ding
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, PR China
| | - Junfeng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, PR China.
| | - Yuhui Zang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, PR China.
| |
Collapse
|
3
|
Liao YW, Yu CC, Hsieh CW, Chao SC, Hsieh PL. Aberrantly downregulated FENDRR by arecoline elevates ROS and myofibroblast activation via mitigating the miR-214/MFN2 axis. Int J Biol Macromol 2024; 264:130504. [PMID: 38442830 DOI: 10.1016/j.ijbiomac.2024.130504] [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: 10/21/2023] [Revised: 12/19/2023] [Accepted: 02/22/2024] [Indexed: 03/07/2024]
Abstract
Long non-coding RNA FENDRR possesses both anti-fibrotic and anti-cancer properties, but its significance in the development of premalignant oral submucous fibrosis (OSF) remains unclear. Here, we showed that FENDRR was downregulated in OSF specimens and fibrotic buccal mucosal fibroblasts (fBMFs), and overexpression of FENDRR mitigated various myofibroblasts hallmarks, and vice versa. In the course of investigating the mechanism underlying the implication of FENDRR in myofibroblast transdifferentiation, we found that FENDRR can directly bind to miR-214 and exhibit its suppressive effect on myofibroblast activation via titrating miR-214. Moreover, we showed that mitofusin 2 (MFN2), a protein that is crucial to the fusion of mitochondria, was a direct target of miR-214. Our data suggested that FENDRR was positively correlated with MFN2 and MFN2 was required for the inhibitory property of FENDRR pertaining to myofibroblast phenotypes. Additionally, our results showed that the FENDRR/miR-214 axis participated in the arecoline-induced reactive oxygen species (ROS) accumulation and myofibroblast transdifferentiation. Building on these results, we concluded that the aberrant downregulation of FENDRR in OSF may be associated with chronic exposure to arecoline, leading to upregulation of ROS and myofibroblast activation via the miR-214-mediated suppression of MFN2.
Collapse
Affiliation(s)
- Yi-Wen Liao
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung 402, Taiwan; Institute of Oral Sciences, Chung Shan Medical University, Taichung 402, Taiwan
| | - Cheng-Chia Yu
- Institute of Oral Sciences, Chung Shan Medical University, Taichung 402, Taiwan; School of Dentistry, Chung Shan Medical University, Taichung 402, Taiwan; Department of Dentistry, Chung Shan Medical University Hospital, Taichung 402, Taiwan
| | - Chang-Wei Hsieh
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
| | - Shih-Chi Chao
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung 402, Taiwan; Institute of Oral Sciences, Chung Shan Medical University, Taichung 402, Taiwan
| | - Pei-Ling Hsieh
- Department of Anatomy, School of Medicine, China Medical University, Taichung 404, Taiwan.
| |
Collapse
|
4
|
Zhang X, Shao R. LncRNA SNHG8 upregulates MUC5B to induce idiopathic pulmonary fibrosis progression by targeting miR-4701-5p. Heliyon 2024; 10:e23233. [PMID: 38163156 PMCID: PMC10756985 DOI: 10.1016/j.heliyon.2023.e23233] [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: 06/28/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) play a critical role in idiopathic pulmonary fibrosis (IPF); however, the underlying molecular mechanisms are unclear. Our study demonstrated that lncRNA small nucleolar RNA host gene 8 (SNHG8) was increased in bleomycin (BLM)-induced A549 cells. LncRNA SNHG8 overexpression further elevated fibrosis-related factors monocyte chemotactic protein 1 (MCP1), CC motif chemokine ligand 18 (CCL18), and α-smooth muscle actin (α-SMA), as well as increased collagen type I alpha-1 chain (COL1A1) and collagen type III alpha-1 chain (COL3A1). Meanwhile, lncRNA SNHG8 knockdown exhibited an opposite role in reducing BLM-induced pulmonary fibrosis. With regard to the mechanism, SNHG8 was then revealed to act as a competing endogenous RNA (ceRNA) for microRNA (miR)-4701-5p in regulating Mucin 5B (MUC5B) expression. Furthermore, the interactions between SNHG8 and miR-4701-5p, between miR-4701-5p and MUC5B, and between SNHG8 and MUC5B on the influence of fibrosis-related indicators were confirmed, respectively. In addition, SNHG8 overexpression enhanced the levels of transforming growth factor (TGF)-β1 and phosphorylation Smad2/3 (p-Smad2/3), which was suppressed by SNHG8 knockdown in BLM-induced A549 cells. Moreover, miR-4701-5p inhibitor-induced elevation of TGF-β1 and p-Smad2/3 was significantly suppressed by SNHG8 knockdown. In conclusion, SNHG8 knockdown attenuated pulmonary fibrosis progression by regulating miR-4701-5p/MUC5B axis, which might be associated with the modulation of TGF-β1/Smad2/3 signaling. These findings reveal that lncRNA SNHG8 may become a potential target for the treatment of IPF.
Collapse
Affiliation(s)
- Xiaoping Zhang
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450014, China
| | - Runxia Shao
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450014, China
| |
Collapse
|
5
|
Ali T, Rogala S, Krause NM, Bains JK, Melissari MT, Währisch S, Schwalbe H, Herrmann B, Grote P. Fendrr synergizes with Wnt signalling to regulate fibrosis related genes during lung development via its RNA:dsDNA triplex element. Nucleic Acids Res 2023; 51:6227-6237. [PMID: 37207329 PMCID: PMC10325902 DOI: 10.1093/nar/gkad395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023] Open
Abstract
Long non-coding RNAs are a very versatile class of molecules that can have important roles in regulating a cells function, including regulating other genes on the transcriptional level. One of these mechanisms is that RNA can directly interact with DNA thereby recruiting additional components such as proteins to these sites via an RNA:dsDNA triplex formation. We genetically deleted the triplex forming sequence (FendrrBox) from the lncRNA Fendrr in mice and found that this FendrrBox is partially required for Fendrr function in vivo. We found that the loss of the triplex forming site in developing lungs causes a dysregulation of gene programs associated with lung fibrosis. A set of these genes contain a triplex site directly at their promoter and are expressed in lung fibroblasts. We biophysically confirmed the formation of an RNA:dsDNA triplex with target promoters in vitro. We found that Fendrr with the Wnt signalling pathway regulates these genes, implicating that Fendrr synergizes with Wnt signalling in lung fibrosis.
Collapse
Affiliation(s)
- Tamer Ali
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590Frankfurt am Main, Hesse, Germany
- Faculty of Science, Benha University, Benha13518, Egypt
- Georg-Speyer-Haus, Paul-Ehrlich-Str. 42-44, 60596Frankfurt am Main, Hesse, Germany
| | - Sandra Rogala
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590Frankfurt am Main, Hesse, Germany
- Georg-Speyer-Haus, Paul-Ehrlich-Str. 42-44, 60596Frankfurt am Main, Hesse, Germany
| | - Nina M Krause
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Goethe University, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Hesse, Germany
| | - Jasleen Kaur Bains
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Goethe University, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Hesse, Germany
| | - Maria-Theodora Melissari
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590Frankfurt am Main, Hesse, Germany
| | - Sandra Währisch
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195Berlin, Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Goethe University, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Hesse, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195Berlin, Germany
| | - Phillip Grote
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590Frankfurt am Main, Hesse, Germany
- Georg-Speyer-Haus, Paul-Ehrlich-Str. 42-44, 60596Frankfurt am Main, Hesse, Germany
| |
Collapse
|
6
|
Karri K, Waxman DJ. Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis. RNA (NEW YORK, N.Y.) 2023; 29:977-1006. [PMID: 37015806 PMCID: PMC10275269 DOI: 10.1261/rna.079580.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
LncRNAs comprise a heterogeneous class of RNA-encoding genes typified by low expression, nuclear enrichment, high tissue-specificity, and functional diversity, but the vast majority remain uncharacterized. Here, we assembled the mouse liver noncoding transcriptome from >2000 bulk RNA-seq samples and discovered 48,261 liver-expressed lncRNAs, a majority novel. Using these lncRNAs as a single-cell transcriptomic reference set, we elucidated lncRNA dysregulation in mouse models of high fat diet-induced nonalcoholic steatohepatitis and carbon tetrachloride-induced liver fibrosis. Trajectory inference analysis revealed lncRNA zonation patterns across the liver lobule in each major liver cell population. Perturbations in lncRNA expression and zonation were common in several disease-associated liver cell types, including nonalcoholic steatohepatitis-associated macrophages, a hallmark of fatty liver disease progression, and collagen-producing myofibroblasts, a central feature of liver fibrosis. Single-cell-based gene regulatory network analysis using bigSCale2 linked individual lncRNAs to specific biological pathways, and network-essential regulatory lncRNAs with disease-associated functions were identified by their high network centrality metrics. For a subset of these lncRNAs, promoter sequences of the network-defined lncRNA target genes were significantly enriched for lncRNA triplex formation, providing independent mechanistic support for the lncRNA-target gene linkages predicted by the gene regulatory networks. These findings elucidate liver lncRNA cell-type specificities, spatial zonation patterns, associated regulatory networks, and temporal patterns of dysregulation during hepatic disease progression. A subset of the liver disease-associated regulatory lncRNAs identified have human orthologs and are promising candidates for biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Kritika Karri
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
| | - David J Waxman
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
| |
Collapse
|
7
|
Massaro M, Wu S, Baudo G, Liu H, Collum S, Lee H, Stigliano C, Segura-Ibarra V, Karmouty-Quintana H, Blanco E. Lipid nanoparticle-mediated mRNA delivery in lung fibrosis. Eur J Pharm Sci 2023; 183:106370. [PMID: 36642345 PMCID: PMC10898324 DOI: 10.1016/j.ejps.2023.106370] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/14/2022] [Accepted: 01/01/2023] [Indexed: 01/15/2023]
Abstract
mRNA delivery enables the specific synthesis of proteins with therapeutic potential, representing a powerful strategy in diseases lacking efficacious pharmacotherapies. Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease characterized by excessive extracellular matrix (ECM) deposition and subsequent alveolar remodeling. Alveolar epithelial type 2 cells (AEC2) and fibroblasts represent important targets in IPF given their role in initiating and driving aberrant wound healing responses that lead to excessive ECM deposition. Our objective was to examine a lipid nanoparticle (LNP)-based mRNA construct as a viable strategy to target alveolar epithelial cells and fibroblasts in IPF. mRNA-containing LNPs measuring ∼34 nm had high encapsulation efficiency, protected mRNA from degradation, and exhibited sustained release kinetics. eGFP mRNA LNP transfection in human primary cells proved dose- and time-dependent in vitro. In a bleomycin mouse model of lung fibrosis, luciferase mRNA LNPs administered intratracheally led to site-specific lung accumulation. Importantly, bioluminescence signal was detected in lungs as early as 2 h after delivery, with signal still evident at 48 h. Of note, LNPs were found associated with AEC2 and fibroblasts in vivo. Findings highlight the potential for pulmonary delivery of mRNA in IPF, opening therapeutic avenues aimed at halting and potentially reversing disease progression.
Collapse
Affiliation(s)
- Matteo Massaro
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030 United States; College of Materials Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049 China
| | - Suhong Wu
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030 United States
| | - Gherardo Baudo
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030 United States; College of Materials Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049 China
| | - Haoran Liu
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030 United States
| | - Scott Collum
- Department of Biochemistry and Molecular Biology, Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Hyunho Lee
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030 United States
| | - Cinzia Stigliano
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030 United States
| | - Victor Segura-Ibarra
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030 United States
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Elvin Blanco
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030 United States; Department of Cardiology, Houston Methodist DeBakey Heart and Vascular Center, Houston Methodist Hospital, Houston, TX 77030 United States; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, United States.
| |
Collapse
|
8
|
Shrivastava AK, Sahu PK, Cecchi T, Shrestha L, Shah SK, Gupta A, Palikhey A, Joshi B, Gupta PP, Upadhyaya J, Paudel M, Koirala N. An emerging natural antioxidant therapy for COVID‐19 infection patients: Current and future directions. FOOD FRONTIERS 2023. [DOI: 10.1002/fft2.207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Amit Kumar Shrivastava
- Department of Pharmacology Universal College of Medical Sciences Bhairahawa Rupandehi Nepal
| | - Prafulla Kumar Sahu
- School of Pharmacy Centurion University of Technology and Management Bhubaneswar Odisha India
| | | | - Laxmi Shrestha
- Department of Pharmacology Universal College of Medical Sciences Bhairahawa Rupandehi Nepal
| | - Sanjay Kumar Shah
- Department of Reproductive MedicineJoint Inter‐national Research Laboratory of Reproduction and DevelopmentChongquing Medical University ChongqingPeople's Republic of China
| | - Anamika Gupta
- Sharjah Institute for Medical Sciences University of Sharjah Sharjah United Arab Emirates
| | - Anjan Palikhey
- Department of Pharmacology Universal College of Medical Sciences Bhairahawa Rupandehi Nepal
| | - Bishal Joshi
- Department of Physiology, Universal College of Medical Sciences Bhairahawa Rupandehi Nepal
| | - Pramodkumar P. Gupta
- School of Biotechnology and Bioinformatics D. Y. Patil Deemed to be University, CBD Belapur Navi Mumbai India
| | - Jitendra Upadhyaya
- Institute of Agriculture and Animal Science Tribhuvan University Chitwan Nepal
| | - Mahendra Paudel
- Department of Agri‐Botany and Ecology Institute of Agriculture and Animal Science Tribhuvan University Mahendranagar Nepal
| | - Niranjan Koirala
- Natural Products Research FacilityGandaki Province Academy of Science and Technology Pokhara, Gandaki Province Nepal
| |
Collapse
|
9
|
Zhang T, Zhang M, Yang L, Gao L, Sun W. Potential targeted therapy based on deep insight into the relationship between the pulmonary microbiota and immune regulation in lung fibrosis. Front Immunol 2023; 14:1032355. [PMID: 36761779 PMCID: PMC9904240 DOI: 10.3389/fimmu.2023.1032355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Pulmonary fibrosis is an irreversible disease, and its mechanism is unclear. The lung is a vital organ connecting the respiratory tract and the outside world. The changes in lung microbiota affect the progress of lung fibrosis. The latest research showed that lung microbiota differs in healthy people, including idiopathic pulmonary fibrosis (IPF) and acute exacerbation-idiopathic pulmonary fibrosis (AE-IPF). How to regulate the lung microbiota and whether the potential regulatory mechanism can become a necessary targeted treatment of IPF are unclear. Some studies showed that immune response and lung microbiota balance and maintain lung homeostasis. However, unbalanced lung homeostasis stimulates the immune response. The subsequent biological effects are closely related to lung fibrosis. Core fucosylation (CF), a significant protein functional modification, affects the lung microbiota. CF regulates immune protein modifications by regulating key inflammatory factors and signaling pathways generated after immune response. The treatment of immune regulation, such as antibiotic treatment, vitamin D supplementation, and exosome micro-RNAs, has achieved an initial effect in clearing the inflammatory storm induced by an immune response. Based on the above, the highlight of this review is clarifying the relationship between pulmonary microbiota and immune regulation and identifying the correlation between the two, the impact on pulmonary fibrosis, and potential therapeutic targets.
Collapse
Affiliation(s)
- Tao Zhang
- School of Medicine, Nankai University, Tianjin, China
| | - Min Zhang
- Department of Geriatric Endocrinology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, China
| | - Liqing Yang
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, Chengdu, China
| | - Lingyun Gao
- Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences, Chengdu, China,Medical College, University of Electronic Science and Technology, Chengdu, China,Guanghan People's Hospital, Guanghan, China,*Correspondence: Wei Sun, ; Lingyun Gao,
| | - Wei Sun
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, Chengdu, China,Medical College, University of Electronic Science and Technology, Chengdu, China,*Correspondence: Wei Sun, ; Lingyun Gao,
| |
Collapse
|
10
|
Tirelli C, Pesenti C, Miozzo M, Mondoni M, Fontana L, Centanni S. The Genetic and Epigenetic Footprint in Idiopathic Pulmonary Fibrosis and Familial Pulmonary Fibrosis: A State-of-the-Art Review. Diagnostics (Basel) 2022; 12:diagnostics12123107. [PMID: 36553114 PMCID: PMC9777399 DOI: 10.3390/diagnostics12123107] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a rare disease of the lung with a largely unknown etiology and a poor prognosis. Intriguingly, forms of familial pulmonary fibrosis (FPF) have long been known and linked to specific genetic mutations. There is little evidence of the possible role of genetics in the etiology of sporadic IPF. We carried out a non-systematic, narrative literature review aimed at describing the main known genetic and epigenetic mechanisms that are involved in the pathogenesis and prognosis of IPF and FPF. In this review, we highlighted the mutations in classical genes associated with FPF, including those encoding for telomerases (TERT, TERC, PARN, RTEL1), which are also found in about 10-20% of cases of sporadic IPF. In addition to the Mendelian forms, mutations in the genes encoding for the surfactant proteins (SFTPC, SFTPA1, SFTPA2, ABCA3) and polymorphisms of genes for the mucin MUC5B and the Toll-interacting protein TOLLIP are other pathways favoring the fibrogenesis that have been thoroughly explored. Moreover, great attention has been paid to the main epigenetic alterations (DNA methylation, histone modification and non-coding RNA gene silencing) that are emerging to play a role in fibrogenesis. Finally, a gaze on the shared mechanisms between cancer and fibrogenesis, and future perspectives on the genetics of pulmonary fibrosis have been analyzed.
Collapse
Affiliation(s)
- Claudio Tirelli
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
- Correspondence:
| | - Chiara Pesenti
- Medical Genetics Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Monica Miozzo
- Medical Genetics Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Michele Mondoni
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Laura Fontana
- Medical Genetics Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Stefano Centanni
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| |
Collapse
|
11
|
Zhang J, Wang H, Chen H, Li H, Xu P, Liu B, Zhang Q, Lv C, Song X. ATF3 -activated accelerating effect of LINC00941/lncIAPF on fibroblast-to-myofibroblast differentiation by blocking autophagy depending on ELAVL1/HuR in pulmonary fibrosis. Autophagy 2022; 18:2636-2655. [PMID: 35427207 PMCID: PMC9629064 DOI: 10.1080/15548627.2022.2046448] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by lung scarring and has no effective treatment. Fibroblast-to-myofibroblast differentiation and myofibroblast proliferation and migration are major clinical manifestations of this disease; hence, blocking these processes is a practical treatment strategy. Here, highly upregulated LINC00941/lncIAPF was found to accelerate pulmonary fibrosis by promoting fibroblast-to-myofibroblast differentiation and myofibroblast proliferation and migration. Assay for transposase-accessible chromatin using sequencing and chromatin immunoprecipitation experiments elucidated that histone 3 lysine 27 acetylation (H3K27ac) activated the chromosome region opening in the LINC00941 promoter. As a consequence, the transcription factor ATF3 (activating transcription factor 3) bound to this region, and LINC00941 transcription was enhanced. RNA affinity isolation, RNA immunoprecipitation (RIP), RNase-RIP, half-life analysis, and ubiquitination experiments unveiled that LINC00941 formed a RNA-protein complex with ELAVL1/HuR (ELAV like RNA binding protein 1) to exert its pro-fibrotic function. Dual-fluorescence mRFP-GFP-MAP1LC3/LC3 (microtubule associated protein 1 light chain 3) adenovirus monitoring technology, human autophagy RT2 profiler PCR array, and autophagic flux revealed that the LINC00941-ELAVL1 axis inhibited autophagosome fusion with a lysosome. ELAVL1 RIP-seq, RIP-PCR, mRNA stability, and rescue experiments showed that the LINC00941-ELAVL1 complex inhibited autophagy by controlling the stability of the target genes EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit), STAT1 (signal transducer and activators of transcription 1) and FOXK1 (forkhead box K1). Finally, the therapeutic effect of LINC00941 was confirmed in a mouse model and patients with IPF. This work provides a therapeutic target and a new effective therapeutic strategy related to autophagy for IPF.Abbreviations: ACTA2/a-SMA: actin alpha 2, smooth muscle; ATF3: activating transcription factor 3; ATG: autophagy related; Baf-A1: bafilomycin A1; BLM: bleomycin; CDKN: cyclin dependent kinase inhibitor; CLN3: CLN3 lysosomal/endosomal transmembrane protein, battenin; COL1A: collagen type I alpha; COL3A: collagen type III alpha; CXCR4: C-X-C motif chemokine receptor 4; DRAM2: DNA damage regulated autophagy modulator 2; ELAVL1/HuR: ELAV like RNA binding protein 1; EZH2: enhancer of zeste 2 polycomb repressive complex 2 subunit; FADD: Fas associated via death domain; FAP/FAPα: fibroblast activation protein alpha; FOXK1: forkhead box K1; FVC: forced vital capacity; GABARAP: GABA type A receptor-associated protein; GABARAPL2: GABA type A receptor associated protein like 2; IGF1: insulin like growth factor 1; IPF: idiopathic pulmonary fibrosis; LAMP: lysosomal associated membrane protein; lncRNA: long noncoding RNA; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NPC1: NPC intracellular cholesterol transporter 1; RGS: regulator of G protein signaling; RPLP0: ribosomal protein lateral stalk subunit P0; ROC: receiver operating characteristic; S100A4: S100 calcium binding protein A4; SQSTM1/p62: sequestosome 1; STAT1: signal transducers and activators of transcription 1; TGFB1/TGF-β1: transforming growth factor beta 1; TNF: tumor necrosis factor; UIP: usual interstitial pneumonia; ULK1: unc-51 like autophagy activating kinase 1; VIM: vimentin.
Collapse
Affiliation(s)
- Jinjin Zhang
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, Shandong, China,Medical Research Center, Binzhou Medical University, Yantai, Shandong, China
| | - Haixia Wang
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, Shandong, China,Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China
| | - Hongbin Chen
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Hongbo Li
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China
| | - Pan Xu
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China
| | - Bo Liu
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China
| | - Qian Zhang
- Department of Pathology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China
| | - Changjun Lv
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China,Changjun Lv Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University
| | - Xiaodong Song
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, Shandong, China,Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China,CONTACT Xiaodong Song Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai264003, Shandong, China
| |
Collapse
|
12
|
Zheng J, Wang J, Qin X, Li K, Gao Q, Yang M, Liu H, Li S, Chang X, Sun Y. LncRNA HOTAIRM1 Involved in Nano NiO-Induced Pulmonary Fibrosis via Regulating PRKCB DNA Methylation-Mediated JNK/c-Jun Pathway. Toxicol Sci 2022; 190:64-78. [PMID: 36066426 DOI: 10.1093/toxsci/kfac092] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Nickel oxide nanoparticles (Nano NiO) lead to pulmonary fibrosis, and the mechanisms are associated with epigenetics. This study aimed to clarify the regulatory relationship among long noncoding RNA HOXA transcript antisense RNA myeloid-specific 1 (HOTAIRM1), DNA methylation and expression of protein kinase C beta (PRKCB), and JNK/c-Jun pathway in Nano NiO-induced pulmonary fibrosis. Therefore, we constructed the rat pulmonary fibrosis model by intratracheal instillation of Nano NiO twice a week for 9 weeks and established the collagen deposition model by treating BEAS-2B cells with Nano NiO for 24 h. Here, the DNA methylation pattern was analyzed by whole-genome bisulfite sequencing in rat fibrotic lung tissues. Then, we integrated mRNA transcriptome data and found 93 DNA methylation genes with transcriptional significance. Meanwhile, the data showed that Nano NiO caused the down-regulation of lncRNA HOTAIRM1, the hypomethylation, and up-regulation of PRKCB2, JNK/c-Jun pathway activation, and collagen deposition (the up-regulated Col-I and α-SMA) both in vivo and in vitro. DNMTs inhibitor 5-AZDC attenuated Nano NiO-induced PRKCB2 expression, JNK/c-Jun pathway activation, and collagen deposition, but overexpression of PRKCB2 aggravated the changes mentioned indicators in Nano NiO-induced BEAS-2B cells. Furthermore, JNK/c-Jun pathway inhibitor (SP600125) alleviated Nano NiO-induced excessive collagen formation. Additionally, overexpression of HOTAIRM1 restrained the PRKCB hypomethylation, the activation of JNK/c-Jun pathway, and collagen formation induced by Nano NiO in BEAS-2B cells. In conclusion, these findings demonstrated that HOTAIRM1 could arrest Nano NiO-induced pulmonary fibrosis by suppressing the PRKCB DNA methylation-mediated JNK/c-Jun pathway.
Collapse
Affiliation(s)
- Jinfa Zheng
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jinyu Wang
- Institute of Anthropotomy and Histoembryology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xin Qin
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Kun Li
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qing Gao
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Mengmeng Yang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Han Liu
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Sheng Li
- Department of Public Health, The First People's Hospital of Lanzhou City, Lanzhou 730050, China
| | - Xuhong Chang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yingbiao Sun
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| |
Collapse
|
13
|
Saito S, Deskin B, Rehan M, Yadav S, Matsunaga Y, Lasky JA, Thannickal VJ. Novel mediators of idiopathic pulmonary fibrosis. Clin Sci (Lond) 2022; 136:1229-1240. [PMID: 36043396 DOI: 10.1042/cs20210878] [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: 04/15/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022]
Abstract
Fibrosis involving the lung may occur in many settings, including in association with known environmental agents, connective tissue diseases, and exposure to drugs or radiation therapy. The most common form is referred to as 'idiopathic' since a causal agent or specific association has not been determined; the strongest risk factor for idiopathic pulmonary fibrosis is aging. Emerging studies indicate that targeting certain components of aging biology may be effective in mitigating age-associated fibrosis. While transforming growth factor-β1 (TGF-β1) is a central mediator of fibrosis in almost all contexts, and across multiple organs, it is not feasible to target this canonical pathway at the ligand-receptor level due to the pleiotropic nature of its actions; importantly, its homeostatic roles as a tumor-suppressor and immune-modulator make this an imprudent strategy. However, defining targets downstream of its receptor(s) that mediate fibrogenesis, while relatively dispenable for tumor- and immune-suppressive functions may aid in developing safer and more effective therapies. In this review, we explore molecular targets that, although TGF-β1 induced/activated, may be relatively more selective in mediating tissue fibrosis. Additionally, we explore epigenetic mechanisms with global effects on the fibrogenic process, as well as metabolic pathways that regulate aging and fibrosis.
Collapse
Affiliation(s)
- Shigeki Saito
- Section of Pulmonary Diseases, Critical Care and Environmental Medicine, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
| | - Brian Deskin
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
| | - Mohammad Rehan
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
| | - Santosh Yadav
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
| | - Yasuka Matsunaga
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
| | - Joseph A Lasky
- Section of Pulmonary Diseases, Critical Care and Environmental Medicine, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
| | - Victor J Thannickal
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, U.S.A, and the Southeast Louisiana Veterans Health Care System, New Orleans, LA, U.S.A
| |
Collapse
|
14
|
Ilieva M, Uchida S. Long Non-Coding RNAs in Cardiac and Pulmonary Fibroblasts and Fibrosis. Noncoding RNA 2022; 8:ncrna8040053. [PMID: 35893236 PMCID: PMC9326574 DOI: 10.3390/ncrna8040053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022] Open
Abstract
The cardiopulmonary system delivers oxygen throughout the body via blood circulation. It is an essential part of the body to sustain the lives of organisms. The integral parts of the cardiopulmonary system—the heart and lungs—are constantly exposed to damaging agents (e.g., dust, viruses), and can be greatly affected by injuries caused by dysfunction in tissues (e.g., myocardial infarction). When damaged, mesenchymal cells, such as fibroblasts, are activated to become myofibroblasts to initiate fibrosis as part of a regenerative mechanism. In diseased states, the excess accumulation of extracellular matrices secreted by myofibroblasts results in further dysfunction in the damaged organs. These fibrotic tissues cannot easily be removed. Thus, there is a growing interest in understanding the fibrotic process, as well as finding biomolecules that can be targets for slowing down or potentially stopping fibrosis. Among these biomolecules, the interest in studying long non-coding RNAs (lncRNAs; any non-protein-coding RNAs longer than 200 nucleotides) has intensified in recent years. In this commentary, we summarize the current status of lncRNA research in the cardiopulmonary system by focusing on cardiac and pulmonary fibrosis.
Collapse
|
15
|
Exosomes Derived from Mesenchymal Stem Cells Ameliorate the Progression of Atherosclerosis in ApoE -/- Mice via FENDRR. Cardiovasc Toxicol 2022; 22:528-544. [PMID: 35344140 DOI: 10.1007/s12012-022-09736-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/16/2022] [Indexed: 01/12/2023]
Abstract
Exosomes (EXO) are extracellular vesicles with lipid bilayer membrane structure containing noncoding RNA, DNA, and other molecules which mediate biological functions. The importance of EXO derived from mesenchymal stem cells (MSCs) has been underlined in cardiovascular diseases. However, the functional role of long non-coding RNA (lncRNA) released by MSCs-EXO on atherosclerosis (AS) was unknown. We aimed to investigate the effects of lncRNA fetal-lethal non-coding developmental regulatory RNA (FENDRR) released from MSC-derived EXO on AS. The accumulation of oxidized low-density lipoprotein (oxLDL) caused AS in mice and damage to human vascular endothelial cells (HUV-EC-C). MSC-EXO restored HUV-EC-C activity and alleviated arterial injury. LncRNA microarrays revealed that FENDRR was delivered to cells and tissues by MSC-EXO. FENDRR bound to microRNA (miR)-28 to regulate TEA domain transcription factor 1 (TEAD1) expression. Moreover, FENDRR knockdown exacerbated cell injury and arterial injury in mice. miR-28 inhibitor reversed the effects of FENDRR silencing and reduced atherosclerotic plaque formation. While loss of TEAD1 mitigated the effect of miR-28 inhibitor and accentuated HUV-EC-C injury in vitro and AS symptoms in vivo. Our results demonstrated that MSC-EXO secreted FENDRR to treat AS. FENDRR competed with TEAD1 to bind to miR-28, thereby reducing HUV-EC-C injury and atherosclerotic plaque formation.
Collapse
|
16
|
Zhao X, Wang C, Liu M, Meng F, Liu K. LncRNA FENDRR Servers as a Possible Marker of Essential Hypertension and Regulates Human Umbilical Vein Endothelial Cells Dysfunction via miR-423-5p/Nox4 Axis. Int J Gen Med 2022; 15:2529-2540. [PMID: 35282648 PMCID: PMC8906997 DOI: 10.2147/ijgm.s338147] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/05/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Essential hypertension (EH) is an intricate non-communicable infirmity and lncRNAs are validated as essential mediators in EH. The study aimed to propose the expression pattern of FENDRR and miR-423-5p, substantiate the potential mechanism of FENDRR/miR-423-5p/Nox4 axis in EH. Patients and Methods The expression of FENDRR and miR-423-5p was evaluated by qRT-PCR and the clinical significance was explored by the ROC curve. Pearson correlation indicated the relationship between FENDRR and miR-423-5p. The function of FENDRR and miR-423-5p on HUVECs was clarified by CCK-8 assay, Transwell assay, and flow cytometry. Western blot was used to assess the relative protein expression of Nox4. Results FENDRR was highly expressed and miR-423-5p was lowly expressed in EH patients and a negative correlation between them was determined. FENDRR might serve as a predictive diagnosis in differentiating EH patients. Knockdown of FENDRR or overexpression of miR-423-5p showed expansionary effects in cell proliferation, cell migration, and inhibiting cell apoptosis. Meanwhile, miR-423-5p was determined as a target of FENDRR and mediated the function of FENDRR on HUVECs. Moreover, Nox4 is a down-streaming target gene of miR-423-5p. The protein expression of Nox4 was regulated by the alternation of miR-423-5p expression. Conclusion FENDRR played an energetic role in EH and contributed to HUVECs dysfunction by restricting cell proliferation, suppressing cell migration, and accelerating cell apoptosis by manipulating the miR-423-5p/Nox4 axis.
Collapse
Affiliation(s)
- Xiaojian Zhao
- Department of Hypertension, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Chen Wang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Min Liu
- Department of Hypertension, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Fansen Meng
- Department of Hypertension, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Kai Liu
- Department of Hypertension, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
- Correspondence: Kai Liu, Department of Hypertension, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, 450003, People’s Republic of China, Tel/Fax +86-371-65964376, Email
| |
Collapse
|
17
|
Pushparaj S, Zhu Z, Huang C, More S, Liang Y, Lin K, Vaddadi K, Liu L. Regulation of influenza A virus infection by Lnc-PINK1-2:5. J Cell Mol Med 2022; 26:2285-2298. [PMID: 35201667 PMCID: PMC8995437 DOI: 10.1111/jcmm.17249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/14/2022] [Accepted: 02/08/2022] [Indexed: 12/13/2022] Open
Abstract
Influenza virus causes approximately 291,000 to 646,000 human deaths worldwide annually. It is also a disease of zoonotic importance, affecting animals such as pigs, horses, and birds. Even though vaccination is being used to prevent influenza virus infection, there are limited options available to treat the disease. Long noncoding RNAs (lncRNAs) are RNA molecules with more than 200 nucleotides that do not translate into proteins. They play important roles in the physiological and pathological processes. In this study, we identified a novel transcript, Lnc‐PINK1‐2:5 that was upregulated by influenza virus. This lncRNA was predominantly located in the nucleus and was not affected by type I interferons. Overexpression of Lnc‐PINK1‐2:5 reduced the influenza viral mRNA and protein levels in cells as well as titres in culture media. Knockdown of Lnc‐PINK1‐2:5 using CRISPR interference enhanced the virus replication. Antiviral activity of Lnc‐PINK1‐2:5 was independent of influenza virus strains. RNA sequencing analysis revealed that Lnc‐PINK1‐2:5 upregulated thioredoxin interacting protein (TXNIP) during influenza virus infection. Overexpression of TXNIP reduced influenza virus infection, suggesting that TXNIP is an antiviral gene. Knockdown of TXNIP abolished the Lnc‐PINK1‐2:5‐mediated increase in influenza virus infection. In conclusion, the newly identified Lnc‐PINK1‐2:5 isoform is an anti‐influenza lncRNA acting through the upregulation of TXNIP gene expression.
Collapse
Affiliation(s)
- Samuel Pushparaj
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Zhengyu Zhu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Chaoqun Huang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Sunil More
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Yurong Liang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Kong Lin
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Kishore Vaddadi
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lin Liu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.,The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| |
Collapse
|
18
|
Joshi R, Batie MR, Fan Q, Varisco BM. Mouse lung organoid responses to reduced, increased, and cyclic stretch. Am J Physiol Lung Cell Mol Physiol 2022; 322:L162-L173. [PMID: 34851724 PMCID: PMC8794016 DOI: 10.1152/ajplung.00310.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 01/03/2023] Open
Abstract
Most lung development occurs in the context of cyclic stretch. Alteration of the mechanical microenvironment is a common feature of many pulmonary diseases, with congenital diaphragmatic hernia (CDH) and fetal tracheal occlusion (FETO, a therapy for CDH) being extreme examples with changes in lung structure, cell differentiation, and function. To address limitations in cell culture and in vivo mechanotransductive models, we developed two mouse lung organoid (mLO) mechanotransductive models using postnatal day 5 (PND5) mouse lung CD326-positive cells and fibroblasts subjected to increased, decreased, and cyclic strain. In the first model, mLOs were exposed to forskolin (FSK) and/or disrupted (DIS) and evaluated at 20 h. mLO cross-sectional area changed by +59%, +24%, and -68% in FSK, control, and DIS mLOs, respectively. FSK-treated organoids had twice as many proliferating cells as other organoids. In the second model, 20 h of 10.25% biaxial cyclic strain increased the mRNAs of lung mesenchymal cell lineages compared with static stretch and no stretch. Cyclic stretch increased TGF-β and integrin-mediated signaling, with upstream analysis indicating roles for histone deacetylases, microRNAs, and long noncoding RNAs. Cyclic stretch mLOs increased αSMA-positive and αSMA-PDGFRα-double-positive cells compared with no stretch and static stretch mLOs. In this PND5 mLO mechanotransductive model, cell proliferation is increased by static stretch, and cyclic stretch induces mesenchymal gene expression changes important in postnatal lung development.
Collapse
Affiliation(s)
- Rashika Joshi
- Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Matthew R Batie
- Biomedical Engineering, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Qiang Fan
- Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Brian M Varisco
- Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- College of Medicine, University of Cincinnati, Cincinnati, Ohio
| |
Collapse
|
19
|
Li S, Zhang H, Chang J, Li D, Cao P. Iron overload and mitochondrial dysfunction orchestrate pulmonary fibrosis. Eur J Pharmacol 2021; 912:174613. [PMID: 34740581 DOI: 10.1016/j.ejphar.2021.174613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 09/06/2021] [Accepted: 09/11/2021] [Indexed: 12/26/2022]
Abstract
Pulmonary fibrosis (PF) is a chronic, progressive heterogeneous disease of lung tissues with poor lung function caused by scar tissue. Due to our limited understanding of its mechanism, there is currently no treatment strategy that can prevent the development of PF. In recent years, iron accumulation and mitochondrial damage have been reported to participate in PF, and drugs that reduce iron content and improve mitochondrial function have shown significant efficacy in animal experimental models. Excessive iron leads to mitochondrial impairment, which may be the key cause that results in the dysfunction of various kinds of pulmonary cells and further promotes PF. As an emerging research hotspot, there are few targeted effective therapeutic strategies at present due to limited mechanistic understanding. In this review, the roles of iron homeostasis imbalance and mitochondrial damage in PF are summarized and discussed, highlighting a promising direction for finding truly effective therapeutics for PF.
Collapse
Affiliation(s)
- Shuxin Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China
| | - Hongmin Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China
| | - Jing Chang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China
| | - Dongming Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China.
| | - Pengxiu Cao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China.
| |
Collapse
|
20
|
Wang T, Wang W, Li W, Duan H, Xu C, Tian X, Zhang D. Genome-wide DNA methylation analysis of pulmonary function in middle and old-aged Chinese monozygotic twins. Respir Res 2021; 22:300. [PMID: 34809630 PMCID: PMC8609861 DOI: 10.1186/s12931-021-01896-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/12/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Previous studies have determined the epigenetic association between DNA methylation and pulmonary function among various ethnics, whereas this association is largely unknown in Chinese adults. Thus, we aimed to explore epigenetic relationships between genome-wide DNA methylation levels and pulmonary function among middle-aged Chinese monozygotic twins. METHODS The monozygotic twin sample was drawn from the Qingdao Twin Registry. Pulmonary function was measured by three parameters including forced expiratory volume the first second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio. Linear mixed effect model was used to regress the methylation level of CpG sites on pulmonary function. After that, we applied Genomic Regions Enrichment of Annotations Tool (GREAT) to predict the genomic regions enrichment, and used comb-p python library to detect differentially methylated regions (DMRs). Gene expression analysis was conducted to validate the results of differentially methylated analyses. RESULTS We identified 112 CpG sites with the level of P < 1 × 10-4 which were annotated to 40 genes. We identified 12 common enriched pathways of three pulmonary function parameters. We detected 39 DMRs located at 23 genes, of which PRDM1 was related to decreased pulmonary function, and MPL, LTB4R2, and EPHB3 were related to increased pulmonary function. The gene expression analyses validated DIP2C, ASB2, SLC6A5, and GAS6 related to decreased pulmonary function. CONCLUSION Our DNA methylation sequencing analysis on identical twins provides new references for the epigenetic regulation on pulmonary function. Several CpG sites, genes, biological pathways and DMRs are considered as possible crucial to pulmonary function.
Collapse
Affiliation(s)
- Tong Wang
- Department of Epidemiology and Health Statistics, the College of Public Health of Qingdao University, NO. 308 Ning Xia Street, Qingdao, 266071, Shandong Province, People's Republic of China
| | - Weijing Wang
- Department of Epidemiology and Health Statistics, the College of Public Health of Qingdao University, NO. 308 Ning Xia Street, Qingdao, 266071, Shandong Province, People's Republic of China
| | - Weilong Li
- Population Research Unit, Faculty of Social Sciences, University of Helsinki, Helsinki, Finland
| | - Haiping Duan
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong Province, People's Republic of China.,Qingdao Institute of Preventive Medicine, Qingdao, Shandong Province, People's Republic of China
| | - Chunsheng Xu
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong Province, People's Republic of China.,Qingdao Institute of Preventive Medicine, Qingdao, Shandong Province, People's Republic of China
| | - Xiaocao Tian
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong Province, People's Republic of China.,Qingdao Institute of Preventive Medicine, Qingdao, Shandong Province, People's Republic of China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, the College of Public Health of Qingdao University, NO. 308 Ning Xia Street, Qingdao, 266071, Shandong Province, People's Republic of China.
| |
Collapse
|
21
|
Konigsberg IR, Borie R, Walts AD, Cardwell J, Rojas M, Metzger F, Hauck SM, Fingerlin TE, Yang IV, Schwartz DA. Molecular Signatures of Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2021; 65:430-441. [PMID: 34038697 PMCID: PMC8525208 DOI: 10.1165/rcmb.2020-0546oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 05/24/2021] [Indexed: 11/24/2022] Open
Abstract
Molecular patterns and pathways in idiopathic pulmonary fibrosis (IPF) have been extensively investigated, but few studies have assimilated multiomic platforms to provide an integrative understanding of molecular patterns that are relevant in IPF. Herein, we combine the coding and noncoding transcriptomes, DNA methylomes, and proteomes from IPF and healthy lung tissue to identify molecules and pathways associated with this disease. RNA sequencing, Illumina MethylationEPIC array, and liquid chromatography-mass spectrometry proteomic data were collected on lung tissue from 24 subjects with IPF and 14 control subjects. Significant differential features were identified by using linear models adjusting for age and sex, inflation, and bias when appropriate. Data Integration Analysis for Biomarker Discovery Using a Latent Component Method for Omics Studies was used for integrative multiomic analysis. We identified 4,643 differentially expressed transcripts aligning to 3,439 genes, 998 differentially abundant proteins, 2,500 differentially methylated regions, and 1,269 differentially expressed long noncoding RNAs (lncRNAs) that were significant after correcting for multiple tests (false discovery rate < 0.05). Unsupervised hierarchical clustering using 20 coding mRNA, protein, methylation, and lncRNA features with the highest loadings on the top latent variable from the four data sets demonstrates perfect separation of IPF and control lungs. Our analysis confirmed previously validated molecules and pathways known to be dysregulated in disease and implicated novel molecular features as potential drivers and modifiers of disease. For example, 4 proteins, 18 differentially methylated regions, and 10 lncRNAs were found to have strong correlations (|r| > 0.8) with MMP7 (matrix metalloproteinase 7). Therefore, by using a system biology approach, we have identified novel molecular relationships in IPF.
Collapse
Affiliation(s)
- Iain R. Konigsberg
- Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado
| | - Raphael Borie
- Department of Medicine, Bichat Hospital, Paris, France
| | - Avram D. Walts
- Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado
| | - Jonathan Cardwell
- Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado
| | - Mauricio Rojas
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Fabian Metzger
- Research Unit for Protein Science, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany; and
| | - Stefanie M. Hauck
- Research Unit for Protein Science, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany; and
| | - Tasha E. Fingerlin
- Department of Immunology and Genomic Medicine and Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado
| | - Ivana V. Yang
- Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado
| | - David A. Schwartz
- Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado
| |
Collapse
|
22
|
Long Noncoding RNA FENDRR Inhibits Lung Fibroblast Proliferation via a Reduction of β-Catenin. Int J Mol Sci 2021; 22:ijms22168536. [PMID: 34445242 PMCID: PMC8395204 DOI: 10.3390/ijms22168536] [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: 07/10/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 02/06/2023] Open
Abstract
Idiopathic Pulmonary Fibrosis (IPF) is a chronic, progressive, and usually lethal lung disease and it has been widely accepted that fibroblast proliferation is one of the key characteristics of IPF. Long noncoding RNAs (lncRNAs) play vital roles in the pathogenesis of many diseases. In this study, we investigated the role of lncRNA FENDRR on fibroblast proliferation. Human lung fibroblasts stably overexpressing FENDRR showed a reduced cell proliferation compared to those expressing the control vector. On the other hand, FENDRR silencing increased fibroblast proliferation. FENDRR bound serine-arginine rich splicing factor 9 (SRSF9) and inhibited the phosphorylation of p70 ribosomal S6 kinase 1 (PS6K), a downstream protein of the mammalian target of rapamycin (mTOR) signaling. Silencing SRSF9 reduced fibroblast proliferation. FENDRR reduced β-catenin protein, but not mRNA levels. The reduction of β-catenin protein levels in lung fibroblasts by gene silencing or chemical inhibitor decreased fibroblast proliferation. Adenovirus-mediated FENDRR transfer to the lungs of mice reduced asbestos-induced fibrotic lesions and collagen deposition. RNA sequencing of lung tissues identified 7 cell proliferation-related genes that were up-regulated by asbestos but reversed by FENDRR. In conclusion, FENDRR inhibits fibroblast proliferation and functions as an anti-fibrotic lncRNA.
Collapse
|
23
|
Podolanczuk AJ, Wong AW, Saito S, Lasky JA, Ryerson CJ, Eickelberg O. Update in Interstitial Lung Disease 2020. Am J Respir Crit Care Med 2021; 203:1343-1352. [PMID: 33835899 DOI: 10.1164/rccm.202103-0559up] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Anna J Podolanczuk
- Division of Pulmonary and Critical Care, Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Alyson W Wong
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Shigeki Saito
- Section of Pulmonary Disease, Critical Care and Environmental Medicine, Department of Medicine, Tulane University, New Orleans, Louisiana; and
| | - Joseph A Lasky
- Section of Pulmonary Disease, Critical Care and Environmental Medicine, Department of Medicine, Tulane University, New Orleans, Louisiana; and
| | - Christopher J Ryerson
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Oliver Eickelberg
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| |
Collapse
|
24
|
Fukushima K, Akira S. Novel insights into the pathogenesis of lung fibrosis: the RBM7-NEAT1-CXCL12-SatM axis at fibrosis onset. Int Immunol 2021; 33:659-663. [PMID: 34165514 DOI: 10.1093/intimm/dxab034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022] Open
Abstract
Fibrosis is a life-threatening disorder with significant morbidity and mortality and is caused by excessive formation of connective tissue that can affect several important organs. Fibrosis in organ tissues is caused by an abnormal wound-healing process from repeated injuries. In our recent study using a mouse model of bleomycin-induced lung fibrosis, we examined the role of RNA-binding protein 7 (RBM7) on the development of lung fibrosis. RBM7 is upregulated in the injured lung epithelium and disturbs normal epithelial cell repair and regeneration by promoting apoptosis of damaged epithelial cells. RBM7 causes the decay of nuclear-enriched abundant transcript 1 (NEAT1), which results in apoptosis of lung epithelial cells. These apoptotic cells then produce C-X-C motif chemokine ligand 12 (CXCL12), which leads to the recruitment of a fibrosis-promoting monocyte population called segregated-nucleus-containing atypical monocytes (SatM) to the damaged area, followed by the initiation and promotion of lung fibrosis. Here, we review recent insights into the crosstalk between lung parenchymal cells and hematopoietic cells during the development of pulmonary fibrosis.
Collapse
Affiliation(s)
- Kiyoharu Fukushima
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan.,Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan.,Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan.,Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| |
Collapse
|
25
|
LncRNA CTD-2528L19.6 prevents the progression of IPF by alleviating fibroblast activation. Cell Death Dis 2021; 12:600. [PMID: 34112765 PMCID: PMC8192779 DOI: 10.1038/s41419-021-03884-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 12/15/2022]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as critical factors for regulating multiple biological processes during organ fibrosis. However, the mechanism of lncRNAs in idiopathic pulmonary fibrosis (IPF) remains incompletely understood. In the present study, two sets of lncRNAs were defined: IPF pathogenic lncRNAs and IPF progression lncRNAs. IPF pathogenic and progression lncRNAs-mRNAs co-expression networks were constructed to identify essential lncRNAs. Network analysis revealed a key lncRNA CTD-2528L19.6, which was up-regulated in early-stage IPF compared to normal lung tissue, and subsequently down-regulated during advanced-stage IPF. CTD-2528L19.6 was indicated to regulate fibroblast activation in IPF progression by mediating the expression of fibrosis related genes LRRC8C, DDIT4, THBS1, S100A8 and TLR7 et al. Further studies showed that silencing of CTD-2528L19.6 increases the expression of Fn1 and Collagen I both at mRNA and protein levels, promoted the transition of fibroblasts into myofibroblasts and accelerated the migration and proliferation of MRC-5 cells. In contrast, CTD-2528L19.6 overexpression alleviated fibroblast activation in MRC-5 cells induced by TGF-β1. LncRNA CTD-2528L19.6 inhibited fibroblast activation through regulating the expression of LRRC8C in vitro assays. Our results suggest that CTD-2528L19.6 may prevent the progression of IPF from early-stage and alleviate fibroblast activation during the advanced-stage of IPF. Thus, exploring the regulatory effect of lncRNA CTD-2528L19.6 may provide new sights for the prevention and treatment of IPF.
Collapse
|
26
|
Ye Z, Hu Y. TGF‑β1: Gentlemanly orchestrator in idiopathic pulmonary fibrosis (Review). Int J Mol Med 2021; 48:132. [PMID: 34013369 PMCID: PMC8136122 DOI: 10.3892/ijmm.2021.4965] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/29/2021] [Indexed: 01/09/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a worldwide disease characterized by the chronic and irreversible decline of lung function. Currently, there is no drug to successfully treat the disease except for lung transplantation. Numerous studies have been devoted to the study of the fibrotic process of IPF and findings showed that transforming growth factor-β1 (TGF-β1) plays a central role in the development of IPF. TGF-β1 promotes the fibrotic process of IPF through various signaling pathways, including the Smad, MAPK, and ERK signaling pathways. There are intersections between these signaling pathways, which provide new targets for researchers to study new drugs. In addition, TGF-β1 can affect the fibrosis process of IPF by affecting oxidative stress, epigenetics and other aspects. Most of the processes involved in TGF-β1 promote IPF, but TGF-β1 can also inhibit it. This review discusses the role of TGF-β1 in IPF.
Collapse
Affiliation(s)
- Zhimin Ye
- Department of Pathology, Basic Medical School, Central South University, Changsha, Hunan 410006, P.R. China
| | - Yongbin Hu
- Department of Pathology, Basic Medical School, Central South University, Changsha, Hunan 410006, P.R. China
| |
Collapse
|
27
|
Szafranski P, Gambin T, Karolak JA, Popek E, Stankiewicz P. Lung-specific distant enhancer cis regulates expression of FOXF1 and lncRNA FENDRR. Hum Mutat 2021; 42:694-698. [PMID: 33739555 DOI: 10.1002/humu.24198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/22/2021] [Accepted: 03/14/2021] [Indexed: 12/21/2022]
Abstract
The FOXF1 gene, causative for a neonatal lethal lung developmental disorder alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), maps 1.7 kb away from the long noncoding RNA gene FENDRR on the opposite strand, suggesting they may be coregulated. Using RNA sequencing in lung tissue from ACDMPV patients with heterozygous deletions of the FOXF1 distant enhancer located 286 kb upstream, leaving FOXF1 and FENDRR intact, we have found that the FENDRR and FOXF1 expressions were reduced by approximately 75% and 50%, respectively, and were monoallelic from the intact chromosome 16q24.1. In contrast, ACDMPV patients with FOXF1 SNVs had biallelic FENDRR expression reduced by 66%-82%. Corroboratively, depletion of FOXF1 by small interfering RNA in lung fibroblasts resulted in a 50% decrease of FENDRR expression. These data indicate that FENDRR expression in the lungs is regulated both in cis by the FOXF1 distant enhancer and in trans by FOXF1. Our findings are compatible with the involvement of FENDRR in FOXF1-related disorders, including ACDMPV.
Collapse
Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Justyna A Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznań University of Medical Sciences, Poznań, Poland
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
28
|
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: 36] [Impact Index Per Article: 12.0] [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.
Collapse
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
| | | |
Collapse
|
29
|
Zhang S, Chen H, Yue D, Blackwell TS, Lv C, Song X. Long non-coding RNAs: Promising new targets in pulmonary fibrosis. J Gene Med 2021; 23:e3318. [PMID: 33533071 PMCID: PMC7988597 DOI: 10.1002/jgm.3318] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/09/2021] [Accepted: 01/15/2021] [Indexed: 12/11/2022] Open
Abstract
Pulmonary fibrosis is characterized by progressive and irreversible scarring in the lungs with poor prognosis and treatment. It is caused by various factors, including environmental and occupational exposures, and some rheumatic immune diseases. Even the rapid global spread of the COVID‐19 pandemic can also cause pulmonary fibrosis with a high probability. Functions attributed to long non‐coding RNAs (lncRNAs) make them highly attractive diagnostic and therapeutic targets in fibroproliferative diseases. Therefore, an understanding of the specific mechanisms by which lncRNAs regulate pulmonary fibrotic pathogenesis is urgently needed to identify new possibilities for therapy. In this review, we focus on the molecular mechanisms and implications of lncRNAs targeted protein‐coding and non‐coding genes during pulmonary fibrogenesis, and systematically analyze the communication of lncRNAs with various types of RNAs, including microRNA, circular RNA and mRNA. Finally, we propose the potential approach of lncRNA‐based diagnosis and therapy for pulmonary fibrosis. We hope that understanding these interactions between protein‐coding and non‐coding genes will contribute to the development of lncRNA‐based clinical applications for pulmonary fibrosis.
Collapse
Affiliation(s)
- Songzi Zhang
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, China.,Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou Medical University, Binzhou, China
| | - Hongbin Chen
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, China
| | - Dayong Yue
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, China
| | | | - Changjun Lv
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, China.,Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou Medical University, Binzhou, China
| | - Xiaodong Song
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, China.,Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou Medical University, Binzhou, China
| |
Collapse
|
30
|
Szafranski P, Stankiewicz P. Long Non-Coding RNA FENDRR: Gene Structure, Expression, and Biological Relevance. Genes (Basel) 2021; 12:177. [PMID: 33513839 PMCID: PMC7911649 DOI: 10.3390/genes12020177] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/13/2022] Open
Abstract
The FOXF1 Adjacent Noncoding Developmental Regulatory RNA (Fendrr) plays an important role in the control of gene expression in mammals. It is transcribed in the opposite direction to the neighboring Foxf1 gene with which it shares a region containing promoters. In humans, FENDRR is located on chromosome 16q24.1, and is positively regulated both by the FOXF1 distant lung-specific cis-acting enhancer and by trans-acting FOXF1. Fendrr has been shown to function as a competing endogenous RNA, sponging microRNAs and protein factors that control stability of mRNAs, and as an epigenetic modifier of chromatin structure around gene promoters and other regulatory sites, targeting them with histone methyltrasferase complexes. In mice, Fendrr is essential for development of the heart, lungs, and gastrointestinal system; its homozygous loss causes embryonic or perinatal lethality. Importantly, deregulation of FENDRR expression has been causatively linked also to tumorigenesis, resistance to chemotherapy, fibrosis, and inflammatory diseases. Here, we review the current knowledge on the FENDRR structure, expression, and involvement in development and tissue maintenance.
Collapse
Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA;
| | | |
Collapse
|
31
|
Omote N, Sauler M. Non-coding RNAs as Regulators of Cellular Senescence in Idiopathic Pulmonary Fibrosis and Chronic Obstructive Pulmonary Disease. Front Med (Lausanne) 2020; 7:603047. [PMID: 33425948 PMCID: PMC7785852 DOI: 10.3389/fmed.2020.603047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022] Open
Abstract
Cellular senescence is a cell fate implicated in the pathogenesis of idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD). Cellular senescence occurs in response to cellular stressors such as oxidative stress, DNA damage, telomere shortening, and mitochondrial dysfunction. Whether these stresses induce cellular senescence or an alternative cell fate depends on the type and magnitude of cellular stress, but also on intrinsic factors regulating the cellular stress response. Non-coding RNAs, including both microRNAs and long non-coding RNAs, are key regulators of cellular stress responses and susceptibility to cellular senescence. In this review, we will discuss cellular mechanisms that contribute to senescence in IPF and COPD and highlight recent advances in our understanding of how these processes are influenced by non-coding RNAs. We will also discuss the potential therapeutic role for targeting non-coding RNAs to treat these chronic lung diseases.
Collapse
Affiliation(s)
- Norihito Omote
- Pulmonary, Critical Care and Sleep Medicine Section, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Maor Sauler
- Pulmonary, Critical Care and Sleep Medicine Section, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| |
Collapse
|
32
|
Agarwal M, Goheen M, Jia S, Ling S, White ES, Kim KK. Type I Collagen Signaling Regulates Opposing Fibrotic Pathways through α 2β 1 Integrin. Am J Respir Cell Mol Biol 2020; 63:613-622. [PMID: 32692932 DOI: 10.1165/rcmb.2020-0150oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Fibrosis is characterized by fibroblast activation, leading to matrix remodeling culminating in a stiff, type I collagen-rich fibrotic matrix. Alveolar epithelial cell (AEC) apoptosis is also a major feature of fibrogenesis, and AEC apoptosis is sufficient to initiate a robust lung fibrotic response. TGF-β (transforming growth factor-β) is a major driver of fibrosis and can induce both AEC apoptosis and fibroblast activation. We and others have previously shown that changes in extracellular matrix stiffness and composition can regulate the cellular response to TGF-β. In the present study, we find that type I collagen signaling promotes TGF-β-mediated fibroblast activation and inhibits TGF-β-induced AEC death. Fibroblasts cultured on type I collagen or fibrotic decellularized lung matrix had augmented activation in response to TGF-β, whereas AECs on cultured on type I collagen or fibrotic lung matrix were more resistant to TGF-β-induced apoptosis. Both of these responses were mediated by integrin α2β1, a major collagen receptor. AECs treated with an α2 integrin inhibitor or with deletion of α2 integrin had loss of collagen-mediated protection from apoptosis. We found that mice with fibroblast-specific deletion of α2 integrin were protected from fibrosis whereas mice with AEC-specific deletion of α2 integrin had more lung injury and a greater fibrotic response to bleomycin. Intrapulmonary delivery of an α2 integrin-activating collagen peptide inhibited AEC apoptosis in vitro and in vivo and attenuated the fibrotic response. These studies underscore the need for a thorough understanding of the divergent response to matrix signaling.
Collapse
Affiliation(s)
- Manisha Agarwal
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Mitchell Goheen
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Shijing Jia
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Song Ling
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Eric S White
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Kevin K Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
33
|
Di Mauro S, Scamporrino A, Fruciano M, Filippello A, Fagone E, Gili E, Scionti F, Purrazzo G, Di Pino A, Scicali R, Di Martino MT, Malaguarnera R, Malatino L, Purrello F, Vancheri C, Piro S. Circulating Coding and Long Non-Coding RNAs as Potential Biomarkers of Idiopathic Pulmonary Fibrosis. Int J Mol Sci 2020; 21:ijms21228812. [PMID: 33233868 PMCID: PMC7709007 DOI: 10.3390/ijms21228812] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Idiopathic Pulmonary Fibrosis (IPF) is a chronic degenerative disease with a median survival of 2-5 years after diagnosis. Therefore, IPF patient identification represents an important and challenging clinical issue. Current research is still searching for novel reliable non-invasive biomarkers. Therefore, we explored the potential use of long non-coding RNAs (lncRNAs) and mRNAs as biomarkers for IPF. METHODS We first performed a whole transcriptome analysis using microarray (n = 14: 7 Control, 7 IPF), followed by the validation of selected transcripts through qPCRs in an independent cohort of 95 subjects (n = 95: 45 Control, 50 IPF). Diagnostic performance and transcript correlation with functional/clinical data were also analyzed. RESULTS 1059 differentially expressed transcripts were identified. We confirmed the downregulation of FOXF1 adjacent non-coding developmental regulatory RNA (FENDRR) lncRNA, hsa_circ_0001924 circularRNA, utrophin (UTRN) and Y-box binding protein 3 (YBX3) mRNAs. The two analyzed non-coding RNAs correlated with Forced Vital Capacity (FVC)% and Diffusing Capacity of the Lung for carbon monoxide (DLCO)% functional data, while coding RNAs correlated with smock exposure. All analyzed transcripts showed excellent performance in IPF identification with Area Under the Curve values above 0.87; the most outstanding one was YBX3: AUROC 0.944, CI 95% = 0.895-0.992, sensitivity = 90%, specificity = 88.9%, p-value = 1.02 × 10-13. CONCLUSIONS This study has identified specific transcript signatures in IPF suggesting that validated transcripts and microarray data could be useful for the potential future identification of RNA molecules as non-invasive biomarkers for IPF.
Collapse
Affiliation(s)
- Stefania Di Mauro
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (G.P.); (A.D.P.); (R.S.); (F.P.); (S.P.)
| | - Alessandra Scamporrino
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (G.P.); (A.D.P.); (R.S.); (F.P.); (S.P.)
| | - Mary Fruciano
- Department of Clinical and Experimental Medicine, Respiratory Medicine Unit, A.O.U. “Policlinico-Vittorio Emanuele”, University of Catania, 95123 Catania, Italy; (M.F.); (E.F.); (E.G.)
| | - Agnese Filippello
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (G.P.); (A.D.P.); (R.S.); (F.P.); (S.P.)
| | - Evelina Fagone
- Department of Clinical and Experimental Medicine, Respiratory Medicine Unit, A.O.U. “Policlinico-Vittorio Emanuele”, University of Catania, 95123 Catania, Italy; (M.F.); (E.F.); (E.G.)
| | - Elisa Gili
- Department of Clinical and Experimental Medicine, Respiratory Medicine Unit, A.O.U. “Policlinico-Vittorio Emanuele”, University of Catania, 95123 Catania, Italy; (M.F.); (E.F.); (E.G.)
| | - Francesca Scionti
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (F.S.); (M.T.D.M.)
| | - Giacomo Purrazzo
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (G.P.); (A.D.P.); (R.S.); (F.P.); (S.P.)
| | - Antonino Di Pino
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (G.P.); (A.D.P.); (R.S.); (F.P.); (S.P.)
| | - Roberto Scicali
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (G.P.); (A.D.P.); (R.S.); (F.P.); (S.P.)
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (F.S.); (M.T.D.M.)
| | - Roberta Malaguarnera
- School of Human and Social Sciences, “Kore” University of Enna, 94100 Enna, Italy;
| | - Lorenzo Malatino
- Department of Clinical and Experimental Medicine, Unit of Internal Medicine, Azienda Ospedaliera Cannizzaro, University of Catania, 95100 Catania, Italy;
| | - Francesco Purrello
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (G.P.); (A.D.P.); (R.S.); (F.P.); (S.P.)
| | - Carlo Vancheri
- Department of Clinical and Experimental Medicine, Respiratory Medicine Unit, A.O.U. “Policlinico-Vittorio Emanuele”, University of Catania, 95123 Catania, Italy; (M.F.); (E.F.); (E.G.)
- Correspondence: ; Tel.: +390-9-5378-1774 (ext. 1424)
| | - Salvatore Piro
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (G.P.); (A.D.P.); (R.S.); (F.P.); (S.P.)
| |
Collapse
|
34
|
Lei X, Qing A, Yuan X, Qiu D, Li H. A Landscape of lncRNA Expression Profile and the Predictive Value of a Candidate lncRNA for Silica-Induced Pulmonary Fibrosis. DNA Cell Biol 2020; 39:2272-2280. [PMID: 33202189 DOI: 10.1089/dna.2020.5531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Silicosis is the most common type of pneumoconiosis with the fastest progress and the most serious harm. At present, there is still a lack of effective treatment for silicosis, and the molecular mechanism of silicosis is very complex, which is not completely clear. This study aimed to identify crucial long noncoding RNA (lncRNA)-mRNA networks for silica-induced pulmonary fibrosis using microarray data from Gene Expression Omnibus database, including human lung epithelial cells Beas-2B and continuously exposed to 5 μg/mL amorphous silica nanoparticles for 40 passages. Differently expressed genes were calculated by "DESeq2" R package. Then we selected the differently expressed mRNAs (DEmRNAs) and differently expressed long noncoding RNAs (DElncRNAs) data construct lncRNA-mRNA coexpression network using weighted gene coexpression network analysis (WCGNA). A total of 1140 DEmRNA and 1406 DElncRNAs were identified, including 20 upregulated DEmRNAs, 1120 downregulated DEmRNAs as well as 213 upregulated DElncRNAs and 1193 downregulated DElncRNAs. Furthermore, we demonstrate that lncRNA AK131029 was specifically overexpressed in silicosis. Loss-of-function assay indicated that silencing AK131029 of inhibited cell proliferation in human lung fibroblast cells. In conclusion, this study preliminarily indicates that lncRNA AK131029 may play a role in pulmonary fibrosis.
Collapse
Affiliation(s)
- Xiaohong Lei
- Department of Anesthesiology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Ailing Qing
- Department of Anesthesiology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xuemei Yuan
- Department of Anesthesiology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Delu Qiu
- Department of Anesthesiology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Haiyu Li
- Department of Infectious Disease, Chongqing Public Health Medical Center, Chongqing, China
| |
Collapse
|
35
|
The NRF2-LOC344887 signaling axis suppresses pulmonary fibrosis. Redox Biol 2020; 38:101766. [PMID: 33126057 PMCID: PMC7573654 DOI: 10.1016/j.redox.2020.101766] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and irreversible disease characterized by an increase in differentiation of fibroblasts to myofibroblasts and excessive accumulation of extracellular matrix in lung tissue. Pharmacological activation of NRF2 has proved to be a valuable antifibrotic approach, however the detailed mechanisms of how NRF2 mediates antifibrotic function remain unclear. In this study, we found that the antifibrotic function of sulforaphane (SFN), an NRF2 activator, was largely dependent on LOC344887, a long noncoding RNA. Two functional AREs were identified in both the promoter and intron 1 of LOC344887, which defines LOC344887 as a novel anti-fibrotic NRF2 target gene. RNA-seq analysis revealed that LOC344887 controls genes and signaling pathways associated with fibrogenesis. Deletion or downregulation of LOC344887 enhanced expression of CDH2/N-cadherin, as well as a number of other fibrotic genes and blunted the antifibrotic effects of SFN. Furthermore, LOC344887-mediated downregulation of fibrotic genes may involve the PI3K-AKT signaling pathway, as pharmacologic inhibition of PI3K activity blocked the effects of LOC344887 knockdown. Our findings demonstrate that NRF2-mediated LOC344887 upregulation contributes to the antifibrotic potential of SFN by repressing the expression of CDH2 and other fibrotic genes, providing novel insight into how NRF2 controls the regulatory networks of IPF. This study provides a better understanding of the molecular mechanisms of NRF2 activators against pulmonary fibrosis and presents a novel therapeutic axis for prevention and intervention of fibrosis-related diseases.
Collapse
|
36
|
Long non-coding RNA FENDRR regulates IFNγ-induced M1 phenotype in macrophages. Sci Rep 2020; 10:13672. [PMID: 32792604 PMCID: PMC7426844 DOI: 10.1038/s41598-020-70633-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/29/2020] [Indexed: 01/27/2023] Open
Abstract
Macrophages play an essential role in host defense and display remarkable plasticity in switching between classically (pro-inflammatory-M1) and alternatively activated (anti-inflammatory-M2) phenotypes. The molecular mechanisms of macrophage polarization are not fully understood. Long non-coding RNAs (lncRNAs) with a length of > 200 nucleotides have been shown to play diverse roles in biological processes. Aberrant expression of lncRNAs is associated with a variety of pathophysiological conditions such as cancer, diabetes, cardiovascular, pulmonary diseases, and tissue fibrosis. In this study, we investigated the role of lncRNA FENDRR in human and mouse macrophage polarization. Human THP-1 monocytes were activated with phorbol-12-myristate-13-acetate (PMA) and differentiated into M1 macrophages with IFNγ or M2 macrophages with IL4. Real-time PCR analysis revealed that FENDRR was expressed 80-fold higher in M1 macrophages than that in M2 macrophages. Overexpression of FENDRR in PMA-activated THP-1 cells increased the IFNγ-induced expression of M1 markers, including IL1β and TNFα at both mRNA and protein levels. Knockdown of FENDRR had an opposite effect. Similarly, FENDRR overexpression in primary mouse bone marrow-derived macrophages increased mRNA expression of M1 markers. FENDRR overexpression increased, while FENDRR knock-down decreased, the IFNγ-induced phosphorylation of STAT1 in PMA-activated THP-1 cells. Our studies suggest that FENDRR enhances IFNγ-induced M1 macrophage polarization via the STAT1 pathway.
Collapse
|
37
|
Poulet C, Njock MS, Moermans C, Louis E, Louis R, Malaise M, Guiot J. Exosomal Long Non-Coding RNAs in Lung Diseases. Int J Mol Sci 2020; 21:E3580. [PMID: 32438606 PMCID: PMC7279016 DOI: 10.3390/ijms21103580] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Within the non-coding genome landscape, long non-coding RNAs (lncRNAs) and their secretion within exosomes are a window that could further explain the regulation, the sustaining, and the spread of lung diseases. We present here a compilation of the current knowledge on lncRNAs commonly found in Chronic Obstructive Pulmonary Disease (COPD), asthma, Idiopathic Pulmonary Fibrosis (IPF), or lung cancers. We built interaction networks describing the mechanisms of action for COPD, asthma, and IPF, as well as private networks for H19, MALAT1, MEG3, FENDRR, CDKN2B-AS1, TUG1, HOTAIR, and GAS5 lncRNAs in lung cancers. We identified five signaling pathways targeted by these eight lncRNAs over the lung diseases mentioned above. These lncRNAs were involved in ten treatment resistances in lung cancers, with HOTAIR being itself described in seven resistances. Besides, five of them were previously described as promising biomarkers for the diagnosis and prognosis of asthma, COPD, and lung cancers. Additionally, we describe the exosomal-based studies on H19, MALAT1, HOTAIR, GAS5, UCA1, lnc-MMP2-2, GAPLINC, TBILA, AGAP2-AS1, and SOX2-OT. This review concludes on the need for additional studies describing the lncRNA mechanisms of action and confirming their potential as biomarkers, as well as their involvement in resistance to treatment, especially in non-cancerous lung diseases.
Collapse
Affiliation(s)
- Christophe Poulet
- Department of Rheumatology, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (M.-S.N.); (M.M.)
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
| | - Makon-Sébastien Njock
- Department of Rheumatology, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (M.-S.N.); (M.M.)
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Respiratory Diseases, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
| | - Catherine Moermans
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Respiratory Diseases, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
| | - Edouard Louis
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Gastroenterology, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
| | - Renaud Louis
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Respiratory Diseases, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
| | - Michel Malaise
- Department of Rheumatology, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (M.-S.N.); (M.M.)
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
| | - Julien Guiot
- Fibropôle Research Group, University Hospital of Liège (CHULiege), 4000 Liège, Belgium; (E.L.); (R.L.)
- GIGA-I3 Research Group, GIGA Institute, University of Liège (ULiege) and University Hospital of Liège (CHULiege), 4000 Liège, Belgium;
- Department of Respiratory Diseases, University Hospital of Liège (CHULiege), 4000 Liège, Belgium
| |
Collapse
|
38
|
Chen L, Yang Y, Peng X, Yan H, Zhang X, Yin L, Yu H. Transcription factor YY1 inhibits the expression of THY1 to promote interstitial pulmonary fibrosis by activating the HSF1/miR-214 axis. Aging (Albany NY) 2020; 12:8339-8351. [PMID: 32396525 PMCID: PMC7244040 DOI: 10.18632/aging.103142] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/31/2020] [Indexed: 04/07/2023]
Abstract
Interstitial pulmonary fibrosis (IPF) is a progressive disease of diverse etiology manifesting with proliferation of lung fibroblasts and accumulation of extracellular matrix deposition in pulmonary interstitium. Recent studies show aberrant expression of mRNAs and microRNAs (miRNAs) in human embryonic pulmonary fibroblasts (HEPFs). In this study, we investigated effects of the YY1/HSF1/miR-214/THY1 axis on the functions of HEPFs and IPF. Loss- and gain-of-function tests were conducted to identify roles of YY1, HSF1, miR-214, and THY1 in IPF. As determined by RT-qPCR or western blot assay, silencing YY1 down-regulated HSF1 expression and attenuated the expression of pro-proliferative and fibrosis markers in HEPFs. Meanwhile, viability of HEPFs was impeded by YY1 knockdown. The binding relationship between miR-214 and THY1 was verified using dual-luciferase reporter assay. In HEPFs, down-regulation of HSF1 reduced miR-214 expression to repress proliferation and fibrogenic transformation of HEPFs, while inhibition of miR-214 expression could restrain the fibrogenic transformation property of HEPFs by up-regulating THY1. Subsequently, IPF model in mice was induced by bleomycin treatment. These animal experiments validated the protective effects of YY1 knockdown against IPF-induced lung pathological manifestations, which could be reversed by THY1 knockdown. Our study demonstrates the important involvement of YY1/HSF1/miR-214/THY1 axis in the development of IPF.
Collapse
Affiliation(s)
- Lin Chen
- Department of Respiratory and Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, P.R. China
| | - Yang Yang
- Department of Respiratory and Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, P.R. China
| | - Xiaying Peng
- Department of Respiratory and Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, P.R. China
| | - Haiying Yan
- Department of Respiratory and Critical Care Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, P.R. China
| | - Xin Zhang
- Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, P.R. China
| | - Lin Yin
- Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, P.R. China
| | - Hua Yu
- Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, P.R. China
| |
Collapse
|
39
|
Affiliation(s)
- Collynn F Woeller
- Department of OphthalmologySchool of Medicine and DentistryUniversity of Rochester Medical CenterRochester, New Yorkand
| | - Michael A O'Reilly
- Department of PediatricsSchool of Medicine and DentistryUniversity of Rochester Medical CenterRochester, New York
| |
Collapse
|
40
|
Gong L, Zhu L, Yang T. Fendrr involves in the pathogenesis of cardiac fibrosis via regulating miR-106b/SMAD3 axis. Biochem Biophys Res Commun 2020; 524:169-177. [PMID: 31982134 DOI: 10.1016/j.bbrc.2020.01.062] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 01/11/2020] [Indexed: 01/15/2023]
Abstract
Cardiovascular diseases (CVDs) is the first cause of death worldwide, generally exhibiting a high morbidity, high disability rate and high mortality especially in the elderly persons (>50 years old). Previously, extensive studies have demonstrated that cardiac fibrosis plays cardinal roles in the pathogenesis of CVDs. However, due to the unclear underlying mechanisms of cardiac fibrosis, its clinical intervention remains very lacking. Long non-coding RNAs (lncRNAs), a class of non-coding RNA but differing from microRNAs, are generally considered as transcripts with a length ranging 200 to 100 nucleotides. Recently, accumulating evidence showed that lncRNAs involve in the pathogenesis of cardiac fibrosis. Fendrr (FOXF1 adjacent non-coding developmental regulatory RNA), is a spliced long non-coding RNA transcribed bi-directionally with FOXF1 on the opposite strand. Fendrr has been demonstrated to be essential for normal development of the heart and body wall in mouse, and shows a good anti-fibrotic activity in pulmonary fibrosis. In this study, we aimed to explore the effects of Fendrr on cardiac fibrosis. Intriguingly, we first observed that lncRNA Fendrr was up-regulated in the heart tissues of transverse aortic constriction (TAC) induced cardiac fibrosis mouse models, determined by RT-QPCR. Loss-function of Fendrr significantly alleviated the cardiac fibrosis phenotypes induced by TAC, indicating that Fendrr is required for the pathogenesis of cardiac fibrosis. In mechanism, we demonstrated experimentally that Fendrr directly targeting miR-106b, by which the lncRNA promotes cardiac fibrosis (indicated by the elevation of Col1a1, Col3a1, CTGF and ACTA2 expression) in a miR-106b mediated manner. Collectively, our findings highlight the axis of Fendrr/miR-106b/Samd3 in the pathogenesis of cardiac fibrosis, which may be a promising target for clinical intervention target of cardiac fibrosis.
Collapse
Affiliation(s)
- Li Gong
- Department of Cardiology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, PR China
| | - Lingyan Zhu
- Department of Cardiology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, PR China; Department of Endocrinology, The First Affiliated Hospital of Nanchang University, Nanchang, PR China
| | - Tianlun Yang
- Department of Cardiology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, PR China.
| |
Collapse
|